產品資訊 > 小鼠表達譜晶片 Mouse OneArray® v2

 
  Mouse microarray for gene expression   小鼠表達譜晶片 v2 保留 v1 中專一性佳的 MEEBO 探針, 並依據 RefSeq 42Ensembl 59 資料庫進行探針的更新, 提供更高基因覆蓋率的表達譜晶片。探針設計採用 “一個基因,一個探針” 的設計原理, 以 IMPORT 專利技術針對蛋白質編碼基因設計高專一性探針, 並以自主的高速佈放技術進行晶片生產。
 
 
 
小鼠表達譜晶片 v2 探針內容
探針種類 探針數
  基因探針設計資料庫: 26,423
          - RefSeq release 42
          - Ensembl release 59
  控制探針數 884
  總探針數 27,307
  

基 因 探 針
 
小鼠表達譜晶片 v2 版次除了保留 v1 中專一性佳的 MEEBO 探針外, 更參考國際公認之RefSeq 42Ensembl 59 序列資料庫, 設計長鏈 60 個鹼基寡核酸 (sense-strand) 的基因探針, 內容以蛋白質編碼基因 (protein-coding gene) 為主, 提高整體的基因覆蓋率外與提供完整的生理途徑反應相關的基因, 並且每一個探針對其來源資料庫的目標基因皆具高度專一性,避免非目標基因的雜交影響。

此外,華聯專業團隊建構 ”華聯探針註解搜尋引擎”(PASS) 網站,方便使用者查詢各探針相對應於 NCBIEnsembl 資料庫的詳細註解。
 
   
    

控 制 探 針
 
 
為確保晶片數據品質,華聯技術團隊經過一連串的測試及驗證,設計一系列的品質控制探針, 以監控完整的晶片實驗步驟,包含樣本 RNA 完整性、樣本 RNA 放大流程、螢光標記效率、晶片雜交、晶片掃描等。
 
 
 

使用MOA文獻 ( 88 )

 International Journal of Molecular Sciences. doi:10.3390/ijms17010098.
 Optimizing a Male Reproductive Aging Mouse Model by d-Galactose Injection 
 
  Abstract
The d-galactose (d-gal)-injected animal model, which is typically established by administering consecutive subcutaneous d-gal injections to animals for approximately six or eight weeks, has been frequently used for aging research. In addition, this animal model has been demonstrated to accelerate aging in the brain, kidneys, liver and blood cells. However, studies on aging in male reproductive organs that have used this animal model remain few. Therefore, the current study aimed to optimize a model of male reproductive aging by administering d-gal injections to male mice and to determine the possible mechanism expediting senescence processes during spermatogenesis. In this study, C57Bl/6 mice were randomized into five groups (each containing 8–10 mice according to the daily intraperitoneal injection of vehicle control or 100 or 200 mg/kg dosages of d-gal for a period of six or eight weeks). First, mice subjected to d-gal injections for six or eight weeks demonstrated considerably decreased superoxide dismutase activity in the serum and testis lysates compared to those in the control group. The lipid peroxidation in testis also increased in the d-gal-injected groups. Furthermore, the d-gal-injected groups exhibited a decreased ratio of testis weight/body weight and sperm count compared to the control group. The percentages of both immotile sperm and abnormal sperm increased considerably in the d-gal-injected groups compared to those of the control group. To determine the genes influenced by the d-gal injection during murine spermatogenesis, a c-DNA microarray was conducted to compare testicular RNA samples between the treated groups and the control group. The d-gal-injected groups exhibited RNA transcripts of nine spermatogenesis-related genes (Cycl2, Hk1, Pltp, Utp3, Cabyr, Zpbp2, Speer2, Csnka2ip and Katnb1) that were up- or down-regulated by at least two-fold compared to the control group. Several of these genes are critical for forming sperm-head morphologies or maintaining nuclear integration (e.g., cylicin, basic protein of sperm head cytoskeleton 2 (Cylc2), casein kinase 2, alpha prime interacting protein (Csnka2ip) and katanin p80 (WD40-containing) subunit B1 (Katnb1)). These results indicate that d-gal-injected mice are suitable for investigating male reproductive aging.
   

 Histochemistry and Cell Biology. doi: 10.1007/s00418-015-1348-9..
 Impact of diethylhexyl phthalate on gene expression and development of mammary glands of pregnant mouse.
 
 
 
  Abstract
The widely used diethylhexyl phthalate (DEHP) is a known endocrine disruptor that causes persistent alterations in the structure and function of female reproductive system, including ovaries, uterus and oviducts. To explore the molecular mechanism of the effect of DEHP on the development of mammary glands, we investigated the cell cycle, growth, proliferation and gene expression of mammary gland cells of pregnant mice exposed to DEHP. It was demonstrated, for the first time, that the mammary gland cells of pregnant mice treated with DEHP for 0.5–3.5 days post-coitum had increased proliferation, growth rate and number of cells in the G2/S phase. The expression of cell proliferation-related genes was significantly altered after short time and low-dose DEHP treatment of mammary gland cells in vivo and in vitro. These findings showed adverse effects of DEHP on mammary gland cells in pregnant mice.
   

 Histochemistry and Cell Biology. 2015 Jul 14.
 Impact of diethylhexyl phthalate on gene expression and development of mammary glands of pregnant mouse
 
 
 Lan Li, Jing‑Cai Liu, Yong Zhao, Fang‑Nong Lai, Fan Yang, Wei Ge, Cheng‑Li Dou, Xi‑Feng Zhang, Hong Chen, Wei Shen
  Abstract
The widely used diethylhexyl phthalate (DEHP) is a known endocrine disruptor that causes persistent alterations in the structure and function of female reproductive system, including ovaries, uterus and oviducts. To explore the molecular mechanism of the effect of DEHP on the development of mammary glands, we investigated the cell cycle, growth, proliferation and gene expression of mammary gland cells of pregnant mice exposed to DEHP. It was demonstrated, for the first time, that the mammary gland cells of pregnant mice treated with DEHP for 0.5-3.5 days post-coitum had increased proliferation, growth rate and number of cells in the G2/S phase. The expression of cell proliferation-related genes was significantly altered after short time and low-dose DEHP treatment of mammary gland cells in vivo and in vitro. These findings showed adverse effects of DEHP on mammary gland cells in pregnant mice.
   

 Scientific Reports. 2015, ;5:12061. doi: 10.1038/srep12061.
 Nogo-B protects mice against lipopolysaccharide-induced acute lung injury
 
 
 Wujian Xu, Ying Zhu, Yunye Ning, Yuchao Dong, Haidong Huang, Wei Zhang, Qinying Sun, Qiang Li
  Abstract
Nogo-B, a member of the reticulon 4 protein family, plays a critical role in tissue repair and acute inflammation. Its role in acute lung injury (ALI) remains unclear. Here, we assessed the function of Nogo-B during tissue injury in a lipopolysaccharide (LPS)-induced ALI mouse model. We found that pulmonary Nogo-B was significantly repressed after LPS instillation in C57BL/6 mice. Over-expression of pulmonary Nogo-B using an adenovirus vector carrying the Nogo-B-RFP-3flag gene (Ad-Nogo-B) significantly prolonged the survival of mice challenged with a lethal dose of LPS. The Ad-Nogo-B-treated mice also had less severe lung injury, less alveolar protein exudation, and a higher number of macrophages but less neutrophil infiltration compared with Ad-RFP-treated mice. Interestingly, microarray analysis showed that the Ad-Nogo-B-treated mice had different gene expression profiles compared with the controls and the prominent expression of genes related to wound healing and the humoral immune response after LPS induction. Of the 49 differently expressed genes, we found that the expression of PTX3 was significantly up-regulated following Nogo-B over-expression as observed in lung tissues and RAW264.7 cells. In conclusion, Nogo-B plays a protective role against LPS-induced ALI, and this effect might be exerted through the modulation of alveolar macrophage recruitment and PTX3 production.
   

 Journal of Allergy and Clinical Immunology. 2015, 136(1):59-68.e14. doi: 10.1016/j.jaci.2014.11.037.
 Persistence of asthma requires multiple feedback circuits involving type 2 innate lymphoid cells and IL-33
 
 
 Christianson CA, Goplen NP, Zafar I, Irvin C, Good JT Jr, Rollins DR, Gorentla B, Liu W, Gorska MM, Chu H, Martin RJ, Rafeul Alam
  Abstract
BACKGROUND: Asthma in a mouse model spontaneously resolves after cessation of allergen exposure. We developed a mouse model in which asthma features persisted for 6 months after cessation of allergen exposure. OBJECTIVE: We sought to elucidate factors contributing to the persistence of asthma. METHODS: We used a combination of immunologic, genetic, microarray, and pharmacologic approaches to dissect the mechanism of asthma persistence. RESULTS: Elimination of T cells though antibody-mediated depletion or lethal irradiation and transplantation of recombination-activating gene (Rag1)(-/-) bone marrow in mice with chronic asthma resulted in resolution of airway inflammation but not airway hyperreactivity or remodeling. Elimination of T cells and type 2 innate lymphoid cells (ILC2s) through lethal irradiation and transplantation of Rag2(-/-)£^c(-/-) bone marrow or blockade of IL-33 resulted in resolution of airway inflammation and hyperreactivity. Persistence of asthma required multiple interconnected feedback and feed-forward circuits between ILC2s and epithelial cells. Epithelial IL-33 induced ILC2s, a rich source of IL-13. The latter directly induced epithelial IL-33, establishing a positive feedback circuit. IL-33 autoinduced, generating another feedback circuit. IL-13 upregulated IL-33 receptors and facilitated IL-33 autoinduction, thus establishing a feed-forward circuit. Elimination of any component of these circuits resulted in resolution of chronic asthma. In agreement with the foregoing, IL-33 and ILC2 levels were increased in the airways of asthmatic patients. IL-33 levels correlated with disease severity. CONCLUSIONS: We present a critical network of feedback and feed-forward interactions between epithelial cells and ILC2s involved in maintaining chronic asthma. Although T cells contributed to the severity of chronic asthma, they were redundant in maintaining airway hyperreactivity and remodeling.
   

 Science Signaling. 2015, 8(375):ra41. doi: 10.1126/scisignal.2005781.
 Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice
 
 
 Yuka Morikawa, Min Zhang, Todd Heallen, John Leach, Ge Tao, Yang Xiao, Yan Bai, Wei Li, James T. Willerson, James F. Martin
  Abstract
The mammalian heart regenerates poorly, and damage commonly leads to heart failure. Hippo signaling is an evolutionarily conserved kinase cascade that regulates organ size during development and prevents adult mammalian cardiomyocyte regeneration by inhibiting the transcriptional coactivator Yap, which also responds to mechanical signaling in cultured cells to promote cell proliferation. To identify Yap target genes that are activated during cardiomyocyte renewal and regeneration, we performed Yap chromatin immunoprecipitation sequencing (ChIP-Seq) and mRNA expression profiling in Hippo signaling¡Vdeficient mouse hearts. We found that Yap directly regulated genes encoding cell cycle progression proteins, as well as genes encoding proteins that promote F-actin polymerization and that link the actin cytoskeleton to the extracellular matrix. Included in the latter group were components of the dystrophin glycoprotein complex, a large molecular complex that, when defective, results in muscular dystrophy in humans. Cardiomyocytes near the scar tissue of injured Hippo signaling¡Vdeficient mouse hearts showed cellular protrusions suggestive of cytoskeletal remodeling. The hearts of mdx mutant mice, which lack functional dystrophin and are a model for muscular dystrophy, showed impaired regeneration and cytoskeleton remodeling, but normal cardiomyocyte proliferation, after injury. Our data showed that, in addition to genes encoding cell cycle progression proteins, Yap regulated genes that enhance cytoskeletal remodeling. Thus, blocking the Hippo pathway input to Yap may tip the balance so that Yap responds to mechanical changes associated with heart injury to promote repair.
   

 OncoImmunology. 2015 Apr 16. doi:10.1080/2162402X.2015.1040215.
 Blockade of TNF-£ signaling benefits cancer therapy by suppressing effector regulatory T cell expansion
 
 
 Li-Yuan Chang, Yung-Chang Lin, Jy-Ming Chiang, Jayashri Mahalingam, Shih-Huan Su, Ching-Tai Huang, Wei-Ting Chen, Chien-Hao Huang, Wen-Juei Jeng, Yi-Cheng Chen, Shi-Ming Lin, I-Shyan Sheen, Chun-Yen Lin
  Abstract
Effector but not naïve regulatory T cells (Treg cells) can accumulate in the peripheral blood as well as the tumor microenvironment, expand during tumor progression and be one of the main suppressors for anti-tumor immunity. However, the underlying mechanisms for effector Treg cell expansion in tumor are still unknown. We demonstrate that effector Treg cell-mediated suppression of anti-tumor CD8+ T cells is tumor non-specific. Furthermore, TNFR2 expression is increased in these Treg cells by Affymetrix chip analysis which was confirmed by monoclonal antibody staining in both hepatocellular carcinoma and colorectal cancer patients and murine models. Correspondingly, increased levels of TNF-£ in both tissue and serum were also demonstrated. Interestingly, TNF-£ could not only expand effector Treg cells through TNFR2 signaling, but also enhanced their suppressive activity against anti-tumor immunity of CD8+ T cells. Furthermore, targeting TNFR2 signaling with a TNF-£ inhibitor could selectively reduce rapid resurgence of effector Treg cells after cyclophosphamide-induced lymphodepletion and markedly inhibit the growth of established tumors. Herein, we propose a novel mechanism in which TNF-£ could promote tumor-associated effector Treg cell expansion and suggest a new cancer immunotherapy strategy using TNF-£ inhibitors to reduce effector Treg cells expansion after cyclophosphamide-induced lymphodepletion.
   

 PLoS One. 2015, 10(3):e0118832. doi: 10.1371/journal.pone.0118832. eCollection 2015.
 Behavior Training Reverses Asymmetry in Hippocampal Transcriptome of the Cav3.2 Knockout Mice
 
 
 Ni-Chun Chung, Ying-Hsueh Huang, Chuan-Hsiung Chang, James C. Liao, Chih-Hsien Yang, Chien-Chang Chen, Ingrid Y. Liu
  Abstract
.Homozygous Cav3.2 knockout mice, which are defective in the pore-forming subunit of a low voltage activated T-type calcium channel, have been documented to show impaired maintenance of late-phase long-term potentiation (L-LTP) and defective retrieval of context-associated fear memory. To investigate the role of Cav3.2 in global gene expression, we performed a microarray transcriptome study on the hippocampi of the Cav3.2-/- mice and their wild-type littermates, either naïve (untrained) or trace fear conditioned. We found a significant left-right asymmetric effect on the hippocampal transcriptome caused by the Cav3.2 knockout. Between the naive Cav3.2-/- and the naive wild-type mice, 3522 differentially expressed genes (DEGs) were found in the left hippocampus, but only 4 DEGs were found in the right hippocampus. Remarkably, the effect of Cav3.2 knockout was partially reversed by trace fear conditioning. The number of DEGs in the left hippocampus was reduced to 6 in the Cav3.2 knockout mice after trace fear conditioning, compared with the wild-type naïve mice. To our knowledge, these results demonstrate for the first time the asymmetric effects of the Cav3.2 and its partial reversal by behavior training on the hippocampal transcriptome.
   

 PLoS One. 2015, 10(3):e0121765. doi: 10.1371/journal.pone.0121765. eCollection 2015.
 Smyd1 Facilitates Heart Development by Antagonizing Oxidative and ER Stress Responses
 
 
 Tara L. Rasmussen, Yanlin Ma, Chong Yon Park, June Harriss, Stephanie A. Pierce, Joseph D. Dekker, Nicolas Valenzuela, Deepak Srivastava, Robert J. Schwartz, M. David Stewart, Haley O. Tucker
  Abstract
Smyd1/Bop is an evolutionary conserved histone methyltransferase previously shown by conventional knockout to be critical for embryonic heart development. To further explore the mechanism(s) in a cell autonomous context, we conditionally ablated Smyd1 in the first and second heart fields of mice using a knock-in (KI) Nkx2.5-cre driver. Robust deletion of floxed-Smyd1 in cardiomyocytes and the outflow tract (OFT) resulted in embryonic lethality at E9.5, truncation of the OFT and right ventricle, and additional defects consistent with impaired expansion and proliferation of the second heart field (SHF). Using a transgenic (Tg) Nkx2.5-cre driver previously shown to not delete in the SHF and OFT, early embryonic lethality was bypassed and both ventricular chambers were formed; however, reduced cardiomyocyte proliferation and other heart defects resulted in later embryonic death at E11.5-12.5. Proliferative impairment prior to both early and mid-gestational lethality was accompanied by dysregulation of transcripts critical for endoplasmic reticulum (ER) stress. Mid-gestational death was also associated with impairment of oxidative stress defense-a phenotype highly similar to the previously characterized knockout of the Smyd1-interacting transcription factor, skNAC. We describe a potential feedback mechanism in which the stress response factor Tribbles3/TRB3, when directly methylated by Smyd1, acts as a co-repressor of Smyd1-mediated transcription. Our findings suggest that Smyd1 is required for maintaining cardiomyocyte proliferation at minimally two different embryonic heart developmental stages, and its loss leads to linked stress responses that signal ensuing lethality.
   

 International forum of allergy & rhinology. 2015 Jul 3. doi: 10.1002/alr.21586.
 Dexamethasone affects mouse olfactory mucosa gene expression and attenuates genes related to neurite outgrowth
 
 
 Jun Tian, Jayant M. Pinto, Yi Xin, Henghui Zhang, Li Li, Zhifu Sun, Yongxiang Wei
  Abstract
BACKGROUND: Olfaction is one of the important senses for humans. Systemic glucocorticoids are the most commonly used medications for olfactory loss because of their strong anti-inflammatory effects. However, their effect on olfactory function is still controversial and the precise mechanism is not clear. To gain a global view of the effect of systematic glucocorticoid treatment on gene expression in the olfactory mucosa (OM), we profiled these changes in a murine model of olfaction in order to identify underlying molecular mechanisms. METHODS: C57BL/6 mice were injected daily for 2 weeks (WK2) with dexamethasone (DEX, intraperitoneally, 1 mg/kg body weight) vs 1 day of DEX (D1) vs controls, which received saline (Ctrl) (n = 9/group). Total RNA from the OM was used to analyze global gene expression. Genes showing changes in expression were compared using the Database for Annotation, Visualization and Integrated Discovery (DAVID, v6.7) and the General Olfactory Sensitivity Database (GOSdb; http://genome.weizmann.ac.il/GOSdb). RESULTS: Between the WK2 and Ctrl groups, 3351 genes were differentially expressed, of which 236 genes were related to olfactory function. Genes involved in axon guidance, cell projection, and inflammation were enriched and overlapped significantly with those in the GOSdb. CONCLUSION: Systemic glucocorticoids exert effects on transcription of a notable number of genes in the OM and appear to orchestrate changes related to axon guidance, cell projection, and inflammation. Further examination may allow targeted therapies that lack the side effects of this category of medication.
   

 Molecular Medicine Reports. 2015, 11(2):887-95. doi: 10.3892/mmr.2014.2823.
 Biological effect of ketamine in urothelial cell lines and global gene expression analysis in the bladders of ketamine‑injected mice
 
 
 CHENG‑HUANG SHEN, SHOU‑TSUNG WANG, YING‑RAY LEE, SHIAU‑YUAN LIU, YI‑ZHEN LI, JIANN‑DER WU, YI‑JU CHEN, Yi‑Wen Liu
  Abstract
Ketamine is used clinically for anesthesia but is also abused as a recreational drug. Previously, it has been established that ketamine‑induced bladder interstitial cystitis is a common syndrome in ketamine‑abusing individuals. As the mechanisms underlying ketamine‑induced cystitis have yet to be revealed, the present study investigated the effect of ketamine on human urothelial cell lines and utilized a ketamine‑injected mouse model to identify ketamine‑induced changes in gene expression in mice bladders. In the in vitro bladder cell line assay, ketamine induced cytotoxicity in a dose‑ and time‑dependent manner. Ketamine arrested the cells in G1 phase and increased the sub‑G1 population, and also increased the barrier permeability of these cell lines. In the ketamine‑injected mouse model, ketamine did not change the body weight and bladder histology of the animals at the dose of 30 mg/kg/day for 60 days. Global gene expression analysis of the animals' bladders following data screening identified ten upregulated genes and 36 downregulated genes induced by ketamine. A total of 52% of keratin family genes were downregulated, particularly keratin 6a, 13 and 14, which was confirmed by polymerase chain reaction analysis. Keratin 14 protein, one of the 36 ketamine‑induced downregulated genes, was also reduced in the ketamine‑treated mouse bladder, as determined by immunohistochemical analysis. This suggested that cytotoxicity and keratin gene downregulation may have a critical role in ketamine‑induced cystitis.
   

 Biomaterials. 2015, 66:29-40. doi: 10.1016/j.biomaterials.2015.06.028.
 Chitosan facilitates structure formation of the salivary gland by regulating the basement membrane components
 
 
 Ya-Chuan Hsiao, Tsung-Lin Yang
  Abstract
Tissue structure is important for inherent physiological function and should be recapitulated during tissue engineering for regenerative purposes. The salivary gland is a branched organ that is responsible for saliva secretion and regulation. The salivary glands develop from epithelial-mesenchymal interactions, and depend on the support of the basement membrane (BM). Chitosan-based biomaterials have been demonstrated to be competent in facilitating the formation of salivary gland tissue structure. However, the underlying mechanisms have remained elusive. In the developing submandibular gland (SMG), the chitosan effect was found to diminish when collagen and laminin were removed from cultured SMG explants. Chitosan increased the expression of BM components including collagen, laminin, and heparan sulfate proteoglycan, and also facilitated BM components and the corresponding receptors to be expressed in tissue-specific patterns beneficial for SMG branching. The chitosan effect decreased when either laminin components or receptors were inhibited, as well when the downstream signaling was blocked. Our results revealed that chitosan promotes salivary glands branching through the BM. By regulating BM components and receptors, chitosan efficiently stimulated downstream signaling to facilitate salivary gland branching. The present study revealed the underlying mechanism of the chitosan effect in engineering SMG structure formation.
   

 PLoS One. 2015, 10(2):e112716. doi: 10.1371/journal.pone.0112716. eCollection 2015.
 Inhibited Wnt Signaling Causes Age-Dependent Abnormalities in the Bone Matrix Mineralization in the Apert Syndrome FGFR2S252W/+ Mice
 
 
 Li Zhang, Peng Chen, Lin Chen, Tujun Weng, Shichang Zhang, Xia Zhou, Luchuan Liu, Bo Zhang
  Abstract
Apert syndrome (AS) is a type of autosomal dominant disease characterized by premature fusion of the cranial sutures, severe syndactyly, and other abnormalities in internal organs. Approximately 70% of AS cases are caused by a single mutation, S252W, in fibroblast growth factor receptor 2 (FGFR2). Two groups have generated FGFR2 knock-in mice Fgfr2S252W/+ that exhibit features of AS. During the present study of AS using the Fgfr2S252W/+ mouse model, an age-related phenotype of bone homeostasis was discovered. The long bone mass was lower in 2 month old mutant mice than in age-matched controls but higher in 5 month old mutant mice. This unusual phenotype suggested that bone marrow-derived mesenchymal stem cells (BMSCs), which are vital to maintain bone homeostasis, might be involved. BMSCs were isolated from Fgfr2S252W/+ mice and found that S252W mutation could impair osteogenic differentiation BMSCs but enhance mineralization of more mature osteoblasts. A microarray analysis revealed that Wnt pathway inhibitors SRFP1/2/4 were up-regulated in mutant BMSCs. This work provides evidence to show that the Wnt/£]-catenin pathway is inhibited in both mutant BMSCs and osteoblasts, and differentiation defects of these cells can be ameliorated by Wnt3a treatment. The present study suggested that the bone abnormalities caused by deregulation of Wnt pathway may underlie the symptoms of AS.
   

 PLoS One. 2015, 10(4):e0124504. doi: 10.1371/journal.pone.0124504. eCollection 2015.
 Transcriptional Modulation of Intestinal Innate Defense/Inflammation Genes by Preterm Infant Microbiota in a Humanized Gnotobiotic Mouse Model
 
 
 Lei Lu, Yueyue Yu, Yuee Guo, Yunwei Wang, Eugene B. Chang, Erika C. Claud
  Abstract
Background and Aims: It is known that postnatal functional maturation of the small intestine is facilitated by microbial colonization of the gut. Preterm infants exhibit defects in gut maturation, weak innate immunity against intestinal infection and increased susceptibility to inflammatory disorders, all of which may be related to the inappropriate microbial colonization of their immature intestines. The earliest microbes to colonize the preterm infant gut encounter a naïve, immature intestine. Thus this earliest microbiota potentially has the greatest opportunity to fundamentally influence intestinal development and immune function. The aim of this study was to characterize the effect of early microbial colonization on global gene expression in the distal small intestine during postnatal gut development. Methods: Gnotobiotic mouse models with experimental colonization by early (prior to two weeks of life) intestinal microbiota from preterm human infants were utilized. Microarray analysis was used to assess global gene expression in the intestinal epithelium. Results and Conclusion: Multiple intestinal genes involved in metabolism, cell cycle regulation, cell-cell or cell-extracellular matrix communication, and immune function are developmental- and intestinal microbiota- regulated. Using a humanized gnotobiotic mouse model, we demonstrate that certain early preterm infant microbiota from prior to 2 weeks of life specifically induce increased NF-£eB activation and a phenotype of increased inflammation whereas other preterm microbiota specifically induce decreased NF-£eB activation. These fundamental differences correlate with altered clinical outcomes and suggest the existence of optimal early microbial communities to improve health outcomes.
   

 The International Journal of Biochemistry & Cell Biology. 2015, 60:99-111. doi: 10.1016/j.biocel.2014.12.024.
 Identification of stage-specific markers during differentiation of hair cells from mouse inner ear stem cells or progenitor cells in vitro
 
 
 Quanwen Liu, JiarongChen, XiangliGao, JieDing, ZihuaTang, CuiZhang, Jianling Chen, Liang Li, PingChen, JinfuWang
  Abstract
The induction of inner ear hair cells from stem cells or progenitor cells in the inner ear proceeds through a committed inner ear sensory progenitor cell stage prior to hair cell differentiation. To increase the efficacy of inducing inner ear hair cell differentiation from the stem cells or progenitor cells, it is essential to identify comprehensive markers for the stem cells/progenitor cells from the inner ear, the committed inner ear sensory progenitor cells and the differentiating hair cells to optimize induction conditions. Here, we report that we efficiently isolated and expanded the stem cells or progenitor cells from postnatal mouse cochleae, and induced the generation of inner ear progenitor cells and subsequent differentiation of hair cells. We profiled the gene expression of the stem cells or progenitor cells, the inner ear progenitor cells, and hair cells using aRNA microarray analysis. The pathway and gene ontology (GO) analysis of differentially expressed genes was performed. Analysis of genes exclusively detected in one particular cellular population revealed 30, 38, and 31 genes specific for inner ear stem cells, inner ear progenitor cells, and hair cells, respectively. We further examined the expression of these genes in vivo and determined that Gdf10+Ccdc121, Tmprss9+Orm1, and Chrna9+Espnl are marker genes specific for inner ear stem cells, inner ear progenitor cells, and differentiating hair cells, respectively. The identification of these marker genes will likely help the effort to increase the efficacy of hair cell induction from the stem cells or progenitor cells.
   

 PLoS One. 2014 Oct 14. doi: 10.1371/journal.pone.0109198.
 Cellular Intrinsic Mechanism Affecting the Outcome of AML Treated with Ara-C in a Syngeneic Mouse Model
 
 
 Bin Yin, Wenjun Zhao, Lirong Wei, Dongming Tan, Guangsong Su, Yanwen Zheng, Chao He, Zhengwei J. Mao, Timothy P. Singleton
  Abstract
The mechanisms underlying acute myeloid leukemia (AML) treatment failure are not clear. Here, we established a mouse model of AML by syngeneictransplantation of BXH-2 derived myeloid leukemic cells and developed an efficacious Ara-C-based regimen for treatment of these mice. We proved that leukemic cell load was correlated with survival. We also demonstrated that the susceptibility of leukemia cells to Ara-C could significantly affect the survival. To examine the molecular alterations in cells with different sensitivity, genome-wide expression of the leukemic cells was profiled, revealing that overall 366 and 212 genes became upregulated or downregulated, respectively, in the resistant cells. Many of these genes are involved in the regulation of cell cycle, cellular proliferation, and apoptosis. Some of them were further validated by quantitative PCR. Interestingly, the Ara-Cresistant cells retained the sensitivity to ABT-737, an inhibitor of anti-apoptosis proteins, and treatment with ABT-737 prolonged the life span of mice engrafted with resistant cells. These results suggest that leukemic load and intrinsic cellular resistance can affect the outcome of AML treated withAra-C. Incorporation of apoptosis inhibitors, such as ABT-737, into traditional cytotoxic regimens merits consideration for the treatment of AML in a subset of patients with resistance to Ara-C. This work provided direct in vivo evidence that leukemic load and intrinsic cellular resistance can affect theoutcome of AML treated with Ara-C, suggesting that incorporation of apoptosis inhibitors into traditional cytotoxic regimens merits consideration for the treatment of AML in a subset of patients with resistance to Ara-C.
   

 Molecular Medicine Reports. 2014 Oct 30. doi: 10.3892/mmr.2014.2823.
 Biological effect of ketamine in urothelial cell lines and global gene expression analysis in the bladders of ketamine‑injected mice
 
 
 YI‑WEN LIU, CHENG‑HUANG SHEN, SHOU‑TSUNG WANG, YING‑RAY LEE, SHIAU‑YUAN LIU, YI‑ZHEN LI, JIANN‑DER WU, YI‑JU CHEN
  Abstract
Ketamine is used clinically for anesthesia but is also abused as a recreational drug. Previously, it has been established that ketamine‑inducedbladder interstitial cystitis is a common syndrome in ketamine‑abusing individuals. As the mechanisms underlying ketamine‑induced cystitis have yet to be revealed, the present study investigated the effect of ketamine on human urothelial cell lines and utilized a ketamine‑injected mouse model to identify ketamine‑induced changes in gene expression in mice bladders. In the in vitro bladder cell line assay, ketamine induced cytotoxicity in a dose‑ and time‑dependent manner. Ketamine arrested the cells in G1 phase and increased the sub‑G1 population, and also increased the barrier permeability of these cell lines. In the ketamine‑injected mouse model, ketamine did not change the body weight and bladder histology of the animals at the dose of 30 mg/kg/day for 60 days. Global gene expression analysis of the animals' bladders following data screening identified ten upregulated genes and 36 downregulated genes induced by ketamine. A total of 52% of keratin family genes were downregulated, particularly keratin 6a, 13 and 14, which was confirmed by polymerase chain reaction analysis. Keratin 14 protein, one of the 36 ketamine‑induced downregulated genes, was also reduced in the ketamine‑treated mouse bladder, as determined by immunohistochemical analysis. This suggested that cytotoxicity and keratin genedownregulation may have a critical role in ketamine‑induced cystitis.
   

 Molecular and Cellular Endocrinology. 2014, 382(2):804-13. doi: 10.1016/j.mce.2013.10.031.
 Knockdown of TrkA in cumulus oocyte complexes (COCs) inhibits EGF-induced cumulus expansion by down-regulation of IL-6
 
 
 Sun F, Wang Y, Liang N, Yao G, Tian H, Zhai Y, Yin Y
  Abstract
Tyrosine kinase receptor A (TrkA), the high-affinity receptor of nerve growth factor (NGF), is known to play key roles in ovarian follicular development, such as assembly of early follicles and follicular ovulation. However, little is known about the roles of TrkA in cumulus oocyte complex (COC)expansion. In this study, we found that TrkA was abundant in large antral follicles and knockdown of TrkA in COCs attenuated epidermal growth factor (EGF)-induced COC expansion and further decreased the ovulation rate. The effect of TrkA on COC expansion was not mediated through downstream EGF effectors, phosphorylation of extracellular regulated protein kinases 1/2 (ERK1/2) or drosophila mothers against decapentaplegic protein (SMAD), or through up-regulation of COC expansion-related transcripts such as prostaglandin-endoperoxide synthase 2 (Ptgs2), hyaluronan synthase 2 (Has2), TNF-induced protein 6 (Tnfaip6) or pentraxin 3 (Ptx3). However, pharmacological blockade of TrkA transducing activity (K252£) in COCsdecreased the mRNA expression and protein secretion of interleukin-6 (IL-6), identified from mRNA microarray of K252£-treated COCs. Meanwhile,knockdown of IL-6 attenuated EGF-induced COC expansion. In addition, IL-6 rescued the inhibitory effect of K252£ on EGF-induced cumulusexpansion. Therefore, IL-6 may act as a new potential cumulus expansion-related transcript, which may be involved in the integration of TrkA and EGF signaling in affecting COC expansion. Here, we provide mechanistic insights into the roles of TrkA in EGF-induced cumulus expansion. Understanding potential cross-points between TrkA and EGF affecting cumulus expansion will help in the discovery of new therapeutic targets in ovulation-related diseases.
   

 Archives of Toxicology. 2014 Oct 2.
 Di-(2-ethylhexyl) phthalate accelerates atherosclerosis in apolipoprotein E-deficient mice
 
 
 Jin‑Feng Zhao, Sheng‑Huang Hsiao, Ming‑Hua Hsu, Kuan‑Chuan Pao, Yu Ru Kou, Song‑Kun Shyue, Tzong‑Shyuan Lee
  Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is associated with atherosclerosis-related cardiovascular disease complications, but we lack direct evidence of its unfavorable effect on atherogenesis. In this study, we aimed to clarify in vivo and in vitro the contribution of DEHP to the development ofatherosclerosis and its underlying mechanisms. Apolipoprotein E-deficient (apoE-/-) mice chronically treated with DEHP for 4 weeks showed exacerbated hyperlipidemia, systemic inflammation, and atherosclerosis. In addition, DEHP promoted low-density lipoprotein (LDL) oxidation, which led to inflammation in endothelial cells as evidenced by increased protein expression of pro-inflammatory mediators. Furthermore, chronic DEHP treatment increased hepatic cholesterol accumulation by downregulating the protein expression of key regulators in cholesterol clearance including LDL receptor, cholesterol 7£-hydrolase, ATP-binding cassette transporter G5 and G8, and liver X receptor £. Moreover, the adiposity and inflammation of white adipose tissues were promoted in DEHP-treated apoE-/- mice. In conclusion, DEHP may disturb cholesterol homeostasis and deregulate the inflammatory response, thus leading to accelerated atherosclerosis.
   

 Journal of Agricultural and Food Chemistry. 2014, 62(36):8952-61. doi: 10.1021/jf5002099.
 A Novel Insulin Receptor-Binding Protein from Momordica charantia Enhances Glucose Uptake and Glucose Clearance in Vitro and in Vivo through Triggering Insulin Receptor Signaling Pathway
 
 
 Chien-Yun Hsiang, Hsin-Yi Lo, Tin-Yun Ho, Chia-Cheng Li, Jaw-Chyun Chen, Jau-Jin Liu
  Abstract
Diabetes, a common metabolic disorder, is characterized by hyperglycemia. Insulin is the principal mediator of glucose homeostasis. In a previous study, we identified a trypsin inhibitor, named Momordica charantia insulin receptor (IR)-binding protein (mcIRBP) in this study, that might interact with IR. The physical and functional interactions between mcIRBP and IR were clearly analyzed in the present study. Photo-cross-linking coupled with mass spectrometry showed that three regions (17-21, 34-40, and 59-66 residues) located on mcIRBP physically interacted with leucine-rich repeat domain and cysteine-rich region of IR. IR-binding assay showed that the binding behavior of mcIRBP and insulin displayed a cooperative manner. After binding to IR, mcIRBP activated the kinase activity of IR by (5.87 ¡Ó 0.45)-fold, increased the amount of phospho-IR protein by (1.31 ¡Ó 0.03)-fold, affected phosphoinositide-3-kinase/Akt pathways, and consequently stimulated the uptake of glucose in 3T3-L1 cells by (1.36 ¡Ó 0.12)-fold. Intraperitoneal injection of 2.5 nmol/kg mcIRBP significantly decreased the blood glucose levels by 20.9 ¡Ó 3.2% and 10.8 ¡Ó 3.6% in normal and diabetic mice, respectively. Microarray analysis showed that mcIRBP affected genes involved in insulin signaling transduction pathway in mice. In conclusion, our findings suggest that mcIRBP is a novel IRBP that binds to sites different from the insulin-binding sites on IR and stimulates both theglucose uptake in cells and the glucose clearance in mice.
   

 PLoS One. 2014 Aug 18. doi: 10.1371/journal.pone.0104650.
 A Novel Glycated Hemoglobin A1c-Lowering Traditional Chinese Medicinal Formula, Identified by Translational Medicine Study
 
 
 Hsin-Yi Lo, Chien-Yun Hsiang, Tsai-Chung Li, Chia-Cheng Li, Hui-Chi Huang, Jaw-Chyun Chen, Tin-Yun Ho
  Abstract
Diabetes is a chronic metabolic disorder that has a significant impact on the health care system. The reduction of glycated hemoglobin A1c is highly associated with the improvements of glycemic control and diabetic complications. In this study, we identified a traditional Chinese medicinal formula with a HbA1c-lowering potential from clinical evidences. By surveying 9,973 diabetic patients enrolled in Taiwan Diabetic Care Management Program, we found that Chu-Yeh-Shih-Kao-Tang (CYSKT) significantly reduced HbA1c values in diabetic patients. CYSKT reduced the levels of HbA1c and fasting blood glucose, and stimulated the blood glucose clearance in type 2 diabetic mice. CYSKT affected the expressions of genes associated with insulin signaling pathway, increased the amount of phosphorylated insulin receptor in cells and tissues, and stimulated the translocation of glucose transporter 4. Moreover, CYSKT affected the expressions of genes related to diabetic complications, improved the levels of renal function indexes, and increased the survival rate of diabetic mice. In conclusion, this was a translational medicine study that applied a ¡§bedside-to-bench¡¨ approach to identify a novel HbA1c-lowering formula. Our findings suggested that oral administration of CYSKT affected insulin signaling pathway, decreased HbA1c and blood glucose levels, and consequently reduced mortality rate in type 2 diabetic mice.
   

 Evidence-Based Complementary and Alternative Medicine. 2014 June 9.
 Electroacupuncture Improves Trinitrobenzene Sulfonic Acid-Induced Colitis, Evaluated by Transcriptomic Study
 
 
 Tin-Yun Ho, Hsin-Yi Lo, De-Cheng Chao, Chia-Cheng Li, Jau-Jin Liu, Chingju Lin, Chien-Yun Hsiang
  Abstract
Inflammatory bowel disease is a chronic colonic inflammation that displays symptoms like diarrhea and weight loss. Acupuncture has been widely accepted by Western countries for the treatment of pain. Here, we analyzed efficacy and mechanism of electroacupuncture (EA) on trinitrobenzene sulfonic acid- (TNBS-) induced colitis in mice. Mice were intrarectally administered with 250 mg/kg TNBS and electroacupunctured at Quze (PC3) and Neiguan (PC6) acupoints, which have been applied for gastrointestinal disorders. Gene expression profiles in colons and spleens were analyzed by microarray for the elucidation of mechanism of EA. Our data showed that EA at PC3 and PC6 improved macroscopic and microscopic features of colitis and the improvement displayed a frequency-dependent manner. Administration of TNBS upregulated the expression of most cytokine genes in colons, while EA downregulated the expression of TNBS-induced cytokine genes. Pathway analysis showed that EA significantly affected inflammatory pathways in colons and immunity-associated pathway in spleens. Immunohistochemical staining further showed that EA decreased the expression of interleukin-1£] and nuclear factor-£eB. In conclusion, this is the first study reporting the global gene expression profiles of EA on TNBS-induced colitis. Our findings suggested that inflammatory and immunity pathways were involved in the anti-inflammatory mechanism of EA on colitis induced by TNBS.
   

 Evidence-Based Complementary and Alternative Medicine. 2014 February 20.
 Deer Antler Extract Improves Fatigue Effect through Altering the Expression of Genes Related to Muscle Strength in Skeletal Muscle of Mice
 
 
 Jaw-Chyun Chen, Chien-Yun Hsiang, Yung-Chang Lin, Tin-Yun Ho
  Abstract
Deer antler is a well-known traditional Chinese medicine used in Asian countries for the tonic and the improvement of aging symptoms. The present study was designed to investigate the antifatigue effect and mechanism of Formosan sambar deer tip antler extract (FSDTAE). The swimming times to exhaustion of mice administered FSDTAE (8.2 mg/day) for 28 days were apparently longer than those of the vehicle-treated mice in forced swim test. However, the indicators of fatigue, such as the reduction in glucose level and the increases in blood urea nitrogen and lactic acid levels, were not significantly inhibited by FSDTAE. Therefore, microarray analysis was further used to examine the anti-fatigue mechanism of FSDTAE. We selected genes with fold changes >2 or <−2 in skeletal muscle for pathway analysis. FSDTAE-affected genes were involved in 9 different signaling pathways, such as GnRH signaling pathway and insulin signaling pathway. All of the significantly expressed genes were classified into 8 different categories by their functions. The most enriched category was muscular system, and 6 upregulated genes, such as troponin I, troponin T1, cysteine and glycine-rich protein 2, myosin heavy polypeptide 7, tropomyosin 2, and myomesin family member 3, were responsible for the development and contraction of muscle. Real-time PCR analysis indicated that FSDTAE increased troponins mRNA expression in skeletal muscle. In conclusion, our findings suggested that FSDTAE might increase the muscle strength through the upregulation of genes responsible for muscle contraction and consequently exhibited the anti-fatigue effect in mice.
   

 Cancer Research. 2013 Dec 9.
 Immune chaperone gp96 drives the contributions of macrophages to inflammatory colon tumorigenesis
 
 
 Crystal Morales, Saleh Rachidi, Feng Hong, Shaoli Sun, Xinshou Ouyang, Caroline Wallace, Yongliang Zhang, Elizabeth Garret-Mayer, Jennifer Wu, Bei Liu, Zihai Li
  Abstract
Macrophages are important drivers in the development of inflammation-associated colon cancers, but the mechanistic underpinnings for their contributions are not fully understood. Further, Toll-like receptors (TLR) have been implicated in colon cancer, but their relevant cellular sites of action are obscure. In this study, we show that the endoplasmic reticulum chaperone gp96 is essential in tumor-associated macrophages (TAM) to license their contributions to inflammatory colon tumorigenesis. Mice where gp96 was genetically deleted in a macrophage-specific manner exhibited reduced colitis and inflammation-associated colon tumorigenesis. Attenuation of colon cancer in these mice correlated strikingly with reduced mutation rates of £]-catenin, increased efficiency of the DNA repair machinery and reduced expression of pro-inflammatory cytokines, including IL-17 and IL-23 in the tumor microenvironment. The genotoxic nature of TAM-associated inflammation was evident by increased expression of genes in the DNA repair pathway. Our work deepens understanding of how TAM promote oncogenesis by altering the molecular oncogenic program within epithelial cells, and it identifies gp96 as a lynchpin chaperone needed in TAM to license their function and impact on expression of critical inflammatory cytokines in colon tumorigenesis.
   

 Biochemical and Biophysical Research Communications. 2013 Dec 2. doi: 10.1016/j.bbrc.2013.11.108.
 Transgenic mice expressing mutant Pinin exhibit muscular dystrophy, nebulin deficiency and elevated expression of slow-type muscle fiber genes
 
 
 Hsu-Pin Wu, Shu-Yuan Hsu, Wen-Ai Wu, Ji-Wei Hu, Pin Ouyang
  Abstract
Pinin (Pnn) is a nuclear speckle-associated SR-like protein. The N-terminal region of the Pnn protein sequence is highly conserved from mammals to insects, but the C-terminal RS domain-containing region is absent in lower species. The N-terminal coiled-coil domain (CCD) is, therefore, of interest not only from a functional point of view, but also from an evolutionarily standpoint. To explore the biological role of the Pnn CCD in a physiological context, we generated transgenic mice overexpressing Pnn mutant in skeletal muscle. We found that overexpression of the CCD reduces endogenous Pnn expression in cultured cell lines as well as in transgenic skeletal muscle fibers. Pnn mutant mice exhibited reduced body mass and impaired muscle function during development. Mutant skeletal muscles show dystrophic histological features with muscle fibers heavily loaded with centrally located myonuclei. Expression profiling and pathway analysis identified over-representation of genes in gene categories associated with muscle contraction, specifically those related to slow type fiber. In addition nebulin (NEB) expression level is repressed in Pnn mutant skeletal muscle. We conclude that Pnn downregulation in skeletal muscle causes a muscular dystrophic phenotype associated with NEB deficiency and the CCD domain is incapable of replacing full length Pnn in terms of functional capacity.
   

 Journal of Biological Chemistry. 2013 Nov 29..
 The A2A adenosine receptor is a dual-coding gene: a novel mechanism of gene usage and signal transduction.
 
 
 Chien-fei Lee, Hsin-Lin Lai, Yi-Chao Lee, Chen-Li Chien, Yijuang Chern
  Abstract
The A2A adenosine receptor (A2AR) is a G protein-coupled receptor and a major target of caffeine. The A2AR gene encodes alternative transcripts that are initiated from at least two independent promoters. The different transcripts of the A2AR gene contain the same coding region and 3'-untranslated region and different 5'-untranslated regions that are highly conserved among species. We report here that in addition to the production of the A2AR protein, translation from an upstream, out-of-frame AUG of the rat A2AR gene produces a 134-amino acid protein (designated uORF5). An anti-uORF5 antibody recognized a protein of the predicted size of uORF5 in PC12 cells and rat brains. Upregulation of A2AR transcripts by hypoxia led to increased levels of both the A2AR and uORF5 proteins. Moreover, stimulation of A2AR increased the level of the uORF5 protein via post-transcriptional regulation. Expression of the uORF5 protein suppressed the AP1-mediated transcription promoted by nerve growth factor, and modulated the expression of several proteins that were implicated in the mitogen-activated protein (MAP) kinase pathway. Taken together, our results show that the rat A2AR gene encodes two distinct proteins (A2AR and uORF5) in an A2AR-dependent manner. Our study reveals a new example of the complexity of the mammalian genome and provides novel insights into the function of A2AR.
   

 Experimental Eye Research. 2013 Nov 1. doi: 10.1016/j.exer.2013.10.018.
 Lens specific RLIP76 transgenic mice show a phenotype similar to microphthalmia
 
 
 Sahu M, Sharma R, Yadav S, Wakamiya M, Chaudhary P, Awasthi S, Yogesh C. Awasthi
  Abstract
RALBP1/RLIP76 is a ubiquitously expressed protein, involved in promotion and regulation of functions initiated by Ral and R-Ras small GTPases. Presence of multiple domains in its structure enables RLIP76 to be involved in a number of physiological processes such as endocytosis, exocytosis, mitochondrial fission, actin cytoskeleton remodeling, and transport of exogenous and endogenous toxicants. Previously, we have established that RLIP76 provides protection to ocular tissues against oxidative stress by transporting the glutathione-conjugates of the toxic, electrophilic products of lipid peroxidation generated during oxidative stress. Therefore, we developed lens specific RLIP76 transgenic mice (lensRLIP76 Tg) to elucidate the role of RLIP76 in protection against oxidative stress, but these transgenic mice showed impaired lens development and a phenotype with small eyes similar to that observed in microphthalmia. These findings prompted us to investigate the mechanisms via which RLIP76 affects lens and eye development. In the present study, we report engineering of lensRLIP76 Tg mice, characterization of the associated phenotype, and the possible molecular mechanisms that lead to the impaired development of eye and lens in these mice. The results of microarray array analysis indicate that the genes involved in pathways for G-Protein signaling, actin cytoskeleton reorganization, endocytosis, and apoptosis are affected in these transgenic mice. The expression of transcription factors, Pax6, Hsf1, and Hsf4b known to be involved in lens development is down regulated in the lens of these Tg mice. However, the expression of heat shock proteins (Hsps), the downstream targets of Hsfs, is differentially affected in the lens showing down regulation of Hsp27, Hsp40, up regulation of Hsp60, and no effect on Hsp70 and Hsp90 expression. The disruption in the organization of actin cytoskeleton of these Tg mice was associated with the inhibition of the activation of Cdc42 and down regulation of cofilin phosphorylation. These mice may provide useful animal model for elucidating the mechanisms of lens development, and etiology of microphthalmia.
   

 PLOS ONE. 2013, 8(10): e76265. doi:10.1371/journal.pone.0076265.
 Modeling the Neurovascular Niche: Unbiased Transcriptome Analysis of the Murine Subventricular Zone in Response to Hypoxic Insult
 
 
 Qi Li, Sandra Canosa, Kelly Flynn, Michael Michaud, Michael Krauthammer, Joseph A. Madri
  Abstract
Premature infants often experience chronic hypoxia, resulting in cognitive & motor neurodevelopmental handicaps. These sometimes devastating handicaps are thought to be caused by compromised neural precursor cell (NPC) repair/recovery resulting in variable central nervous system (CNS) repair/recovery. We have identified differential responses of two mouse strains (C57BL/6 & CD1) to chronic hypoxia that span the range of responsiveness noted in the premature human population. We previously correlated several CNS tissue and cellular behaviors with the different behavioral parameters manifested by these two strains. In this report, we use unbiased array technology to interrogate the transcriptome of the subventricular zone (SVZ) in these strains. Our results illustrate differences in mRNA expression in the SVZ of both C57BL/6 and CD1 mice following hypoxia as well as differences between C57BL/6 and CD1 SVZ under both normoxic and hypoxic conditions. Differences in expression were found in gene sets associated with Sox10-mediated neural functions that explain, in part, the differential cognitive and motor responsiveness to hypoxic insult. This may shed additional light on our understanding of the variable responses noted in the human premature infant population and facilitate early intervention approaches. Further interrogation of the differentially expressed gene sets will provide a more complete understanding of the differential responses to, and recovery from, hypoxic insult allowing for more informed modeling of the ranges of disease severity observed in the very premature human population.
   

 Infection, Genetics and Evolution. 2013, 20C:257-269. doi: 10.1016/j.meegid.2013.09.016.
 Global gene expression changes in BV2 microglial cell line during rabies virus infection
 
 
 Zhao P, Yang Y, Feng H, Zhao L, Qin J, Zhang T, Wang H, Yang S, Xia X
  Abstract
Microglia plays a crucial role during virus pathogenesis in the central nervous system (CNS). Infection by rabies virus (RABV) causes a fatal infectionin the CNS of all warm-blooded animals. However, the microglial responses to RABV infection have been scarcely reported. To better understand microglia-RABV interactions at the transcriptional level, a genome wide gene expression profile in mouse microglial cells line BV2 was performed using microarray analysis. The global messenger RNA changes in murine microglial cell line BV2 after 12, 24 and 48h of infection with rabies virusCVS-11 strain were investigated using DNA Microarray and quantitative real-time PCR. Infection of CVS-11 at different time points induced differentgene expression signatures in BV2 cells. The expression patterns of differentially expressed genes are shown by K-means clustering in four clusters in RABV- or mock-infected microglia at 12, 24 and 48h post infection (hpi). Gene ontology and network analysis of the differentially expressed genes in responses to RABV were performed by the Ingenuity Pathway Analysis system (IPA, Ingenuity® Systems, http://www.ingenuity.com). The results revealed that 28 genes were significantly up-regulated (P<0.01) and 1 gene was significantly down-regulated (P<0.01) in microglial cells at 12hpi, 72 genes were significantly up-regulated (P<0.01) and 24 genes were significantly down-regulated (P<0.01) at 24hpi, and 671 genes were significantly up-regulated (P<0.01) and 190 genes were significantly down-regulated (P<0.01) at 48hpi. Genes in BV2 were significantly regulated (P<0.01) in response to RABV infection and they were found to be interferon stimulated genes (Isg15, Isg20, Oasl1, Oasl2, Ifit2, Irf7 and Ifi203), chemokine genes (Ccl5, Cxcl10 and Ccrl2) and the proinflammatory factor gene (Interleukin 6). The results indicated that the differentially expressed genes frommicroglial cells after RABV infection were mainly involved in innate immune responses, inflammatory responses and host antiviral responses.
   

 Cellular Microbiology. 2013 Sep 17. doi: 10.1111/cmi.12216.
 Streptococcal co-infection augments Candida pathogenicity by amplifying the mucosal inflammatory response
 
 
 Xu H, Sobue T, Thompson A, Xie Z, Poon K, Ricker A, Cervantes J, Diaz PI, Dongari-Bagtzoglou A
  Abstract
Mitis-group streptococci are ubiquitous oral commensals that can promote polybacterial biofilm virulence. Using a novel murine oral mucosal co-infection model we sought to determine for the first time whether these organisms promote the virulence of C. albicans mucosal biofilms in oropharyngeal infection and explored mechanisms of pathogenic synergy. We found that Streptococcus oralis colonization of the oral and gastrointestinal tract was augmented in the presence of C. albicans. S. oralis and C. albicans co-infection significantly augmented the frequency and size of oral thrush lesions. Importantly, S. oralis promoted deep organ dissemination of C. albicans. Whole mouse genome tongue microarray analysis showed that when compared with animals infected with one organism, the doubly infected animals had genes in the major categories of neutrophilic response/chemotaxis/inflammation significantly upregulated, indicative of an exaggerated inflammatory response. This response was dependent on TLR2 signalling since oral lesions, transcription of pro-inflammatory genes and neutrophil infiltration, were attenuated in TLR2-/- animals. Furthermore, S. oralis activated neutrophils in a TLR2-dependent manner in vitro. In summary, this study identifies a previously unrecognized pathogenic synergy between oral commensal bacteriaand C. albicans. This is the first report of the ability of mucosal commensal bacteria to modify the virulence of an opportunistic fungal pathogen.
   

 Science. 2013, 341(6146): 651-654. doi: 10.1126/science.1239278.
 Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small-Molecule Compounds
 
 
 Pingping Hou, Yanqin Li, Xu Zhang, Chun Liu, Jingyang Guan, Honggang Li, Ting Zhao, Junqing Ye, Weifeng Yang, Kang Liu, Jian Ge, Jun Xu, Qiang Zhang, Yang Zhao, Hongkui Deng
  Abstract
Pluripotent stem cells can be induced from somatic cells, providing an unlimited cell resource, with potential for studying disease and use in regenerative medicine. However, genetic manipulation and technically challenging strategies such as nuclear transfer used in reprogramming limit their clinical applications. Here, we show that pluripotent stem cells can be generated from mouse somatic cells at a frequency up to 0.2% using a combination of seven small-molecule compounds. The chemically induced pluripotent stem cells (CiPSCs) resemble embryonic stem cells (ESCs) in terms of their gene expression profiles, epigenetic status, and potential for differentiation and germline transmission. By using small molecules, exogenous ¡§master genes¡¨ are dispensable for cell fate reprogramming. This chemical reprogramming strategy has potential use in generating functional desirable cell types for clinical applications.
   

 The American Journal of Human Genetics. 2013 Jun 26. doi: 10.1016/j.ajhg.2013.05.025.
 miR-196a Ameliorates Phenotypes of Huntington Disease in Cell, Transgenic Mouse, and Induced Pluripotent Stem Cell Models
 
 
 Pei-Hsun Cheng, Chia-Ling Li, Yu-Fan Chang, Shaw-Jeng Tsai, Yen-Yu Lai, Anthony W.S. Chan, Chuan-Mu Chen, Shang-Hsun Yang
  Abstract
Huntington disease (HD) is a dominantly inherited neurodegenerative disorder characterized by dysregulation of various genes. Recently, microRNAs (miRNAs) have been reported to be involved in this dysregulation, suggesting that manipulation of appropriate miRNA regulation may have a therapeutic benefit. Here, we report the beneficial effects of miR-196a (miR196a) on HD in cell, transgenic mouse models, and human induced pluripotent stem cells derived from one individual with HD (HD-iPSCs). In the in vitro results, a reduction of mutant HTT and pathological aggregates, accompanying the overexpression of miR-196a, was observed in HD models of human embryonic kidney cells and mouse neuroblastoma cells. In the in vivo model, HD transgenic mice overexpressing miR-196a revealed the suppression of mutant HTT in the brain and also showed improvements in neuropathological progression, such as decreases of nuclear, intranuclear, and neuropil aggregates and late-stage behavioral phenotypes. Most importantly, miR-196a also decreased HTT expression and pathological aggregates when HD-iPSCs were differentiated into the neuronal stage. Mechanisms of miR-196a in HD might be through the alteration of ubiquitin-proteasome systems, gliosis, cAMP response element-binding protein pathway, and several neuronal regulatory pathways in vivo. Taken together, these results show that manipulating miR-196a provides beneficial effects in HD, suggesting the potential therapeutical role of miR-196a in HD.
   

 European Journal of Oral Sciences. 2013, 1¡V10. doi: 10.1111/eos.12056.
 Expression of Clu and Tgfb1 during murine tooth development: effects of in-vivo transfection with anti-miR-214
 
 
 Amer Sehic, Cuong Khuu, Steinar Risnes, Harald Osmundsen, Qalb-E-Saleem Khan
  Abstract
Expression of clusterin (Clu) in the murine first molar tooth germ was markedly increased at postnatal developmental stages. The time-course of expression of this gene paralleled those of other genes encoding proteins involved during the secretory phase of odontogenesis, as described previously. Immunohistochemical studies of clusterin in murine molar tooth germs suggested this protein to be located in outer enamel epithelium, regressing enamel organ, secretory ameloblasts, and the dental epithelium connecting the tooth to the oral epithelium at an early eruptive stage. Immunolabelling of transforming growth factor beta-1 (TGF-b1) revealed it to be located close to clusterin. The levels of expression of Clu and Tgfb1 were markedly decreased following in-vivo transfection with anti-miR-214. In contrast, the expression of several genes associated with regulation of growth and development were increased by this treatment. We suggest that clusterin has functions during secretory odontogenesis and the early eruptive phase. Bioinformatic analysis after treatment with anti-miR-214 suggested that, whilst cellular activities associated with tooth mineralization and eruption were inhibited, activities associated with an alternative developmental activity (i.e. biosynthesis of contractile proteins) appeared to be stimulated. These changes probably occur through regulation mediated by a common cluster of transcription factors and support suggestions that microRNAs (miRNAs) are highly significant as regulators of differentiation during odontogenesis.
   

 Evidence-Based Complementary and Alternative Medicine. 2013 May 8. doi:10.1155/2013/262796.
 The Phytochemical Shikonin Stimulates Epithelial-Mesenchymal Transition (EMT) in Skin Wound Healing
 
 
 Shu-Yi Yin, An-Ping Peng, Li-Ting Huang, Ya-TingWang, Chun-Wen Lan, Ning-Sun Yang
  Abstract
Although various pharmacological activities of the shikonins have been documented, understanding the hierarchical regulation of these diverse bioactivities at the genome level is unsubstantiated. In this study, through cross examination between transcriptome and microRNA array analyses, we predicted that topical treatment of shikonin in vivo affects epithelial-mesenchymal transition (EMT) and the expression of related microRNAs, including 200a, 200b, 200c, 141, 205, and 429 microRNAs, in mouse skin tissues. In situ immunohistological analyses further demonstrated that specificEMTregulatorymolecules are enhanced in shikonin-treated epidermal tissues. RT-PCR analyses subsequently confirmed that shikonin treatment downregulated expression of microRNA-205 and other members of the 200 family microRNAs. Further, expression of two RNA targets of the 200 family microRNAs in EMT regulation, Sip1 (Zeb2) and Tcf8 (Zeb1), was consistently upregulated by shikonin treatment. Enhancement of these EMT activities was also detected in shikonin-treated wounds, which repaired faster than controls. These results suggest that topical treatment with shikonin can confer a potent stimulatory effect on EMT and suppress the expression of the associated microRNAs in skin wound healing. Collectively, these cellular and molecular data provide further evidence in support of our previous findings on the specific pharmacological effects of shikonin in wound healing and immune modulation.
   

 Cell. 2013, 153(5): 963-975. doi: 10.1016/j.cell.2013.05.001.
 Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers
 
 
 Jian Shu, Chen Wu, Yetao Wu, Zhiyuan Li, Sida Shao, Wenhui Zhao, Xing Tang, Huan Yang, Lijun Shen, Xiaohan Zuo, Weifeng Yang, Yan Shi, Xiaochun Chi, Hongquan Zhang, Ge Gao, Youmin Shu, Kehu Yuan, Weiwu He, Yang Zhao, Chao Tang, Hongkui Deng
  Abstract
The reprogramming factors that induce pluripotency have been identified primarily from embryonic stem cell (ESC)-enriched, pluripotency-associated factors. Here, we report that, during mouse somatic cell reprogramming, pluripotency can be induced with lineage specifiers that are pluripotency rivals to suppress ESC identity, most of which are not enriched in ESCs. We found that OCT4 and SOX2, the core regulators of pluripotency, can be replaced by lineage specifiers that are involved in mesendodermal (ME) specification and in ectodermal (ECT) specification, respectively. OCT4 and its substitutes attenuated the elevated expression of a group of ECT genes, whereas SOX2 and its substitutes curtailed a group of ME genes during reprogramming. Surprisingly, the two counteracting lineage specifiers can synergistically induce pluripotency in the absence of both OCT4 and SOX2. Our study suggests a ¡¥¡¥seesaw model¡¦¡¦ in which a balance that is established using pluripotency factors and/or counteracting lineage specifiers can facilitate reprogramming.
   

 Evidence-Based Complementary and Alternative Medicine. 2013 May 8.
 Phytochemical shikonin stimulates epithelial¡Vmesenchymal transition (EMT) in skin wound-healing
 
 
 Shu-Yi Yin, An-Ping Peng, Li-Ting Huang, Ya-Ting Wang, Chun-Wen Lan, Ning-Sun Yang
  Abstract
Although various pharmacological activities of the shikonins have been documented, understanding of the hierarchical regulation of these diverse bio-activities at the genome level is unsubstantiated. In this study, through cross-examination between transcriptome and microRNA array analyses, we predicted that topical treatment of shikonin in vivo affects epithelial¡Vmesenchymal transition (EMT) and the expression of related microRNAs, including 200a, 200b, 200c, 141, 205 and 429 microRNAs, in mouse skin tissues. In situ immunohistological analyses further demonstrated that specific EMT regulatory molecules are enhanced in shikonin-treated epidermal tissues. RT-PCR analyses subsequently confirmed that shikonin treatment downregulated expression of microRNA-205 and other members of the 200 family microRNAs. Further, expression of two RNA targets of the 200 family microRNAs in EMT regulation, Sip1 (Zeb2) and Tcf8 (Zeb1), were consistently upregulated by shikonin treatment. Enhancement of these EMT activities was also detected in shikonin-treated wounds, which repaired faster than controls. These results suggest that topical treatment with shikonin can confer a potent stimulatory effect on EMT and suppress the expression of the associated microRNAs in skin wound-healing. These cellular and molecular evidences support our previous findings on the specific pharmacological effects of shikonin in wound-healing and immune-modulation.
   

 Current Molecular Medicine. 2013, 13(1): 205-219. doi: 10.2174/1566524011307010205.
 Rock1 & 2 Perform Overlapping and Unique Roles in Angiogenesis and Angiosarcoma Tumor Progression
 
 
 J Montalvo, C Spencer, A Hackathorn, K Masterjohn, A Perkins, C Doty, A Arumugam, PP Ongusaha, R Lakshmanaswamy, JK Liao, DC Mitchell, BA Bryan
  Abstract
The serine/threonine protein kinase paralogs ROCK1 & 2 have been implicated as essential modulators of angiogenesis; however their paralog-specific roles in endothelial function are unknown. shRNA knockdown of ROCK1 or 2 in endothelial cells resulted in a significant disruption of in vitro capillary network formation, cell polarization, and cell migration compared to cells harboring non-targeting control shRNA plasmids. Knockdowns led to alterations in cytoskeletal dynamics due to ROCK1 & 2-mediated reductions in actin isoform expression, and ROCK2-specific reduction in myosin phosphatase and cofilin phosphorylation. Knockdowns enhanced cell survival and led to ROCK1 & 2-mediated reduction in caspase 6 and 9 cleavage, and a ROCK2-specific reduction in caspase 3 cleavage. Microarray analysis of ROCK knockdown lines revealed overlapping and unique control of global transcription by the paralogs, and a reduction in the transcriptional regulation of just under 50% of VEGF responsive genes. Finally, paralog knockdown in xenograft angiosarcoma tumors resulted in a significant reduction in tumor formation. Our data reveals that ROCK1 & 2 exhibit overlapping and unique roles in normal and dysfunctional endothelial cells, that alterations in cytoskeletal dynamics are capable of overriding mitogen activated transcription, and that therapeutic targeting of ROCK signaling may have profound impacts for targeting angiogenesis.
   

 American journal of physiology-gastrointestinal and liver physiology. 2013, 304(1):G72-86. doi: 10.1152/ajpgi.00328.2012.
 Nordihydroguaiaretic acid improves metabolic dysregulation and aberrant hepatic lipid metabolism in mice by both PPAR£-dependent and -independent pathways
 
 
 Haiyan Zhang, Wen-Jun Shen, Yuan Cortez, Fredric B. Kraemer, Salman Azhar
  Abstract
Creosote bush-derived nordihydroguaiaretic acid (NDGA), a lipoxygenase inhibitor, possesses antioxidant properties and functions as a potent antihyperlipidemic agent in rodent models. Here, we examined the effect of chronic NDGA treatment of ob/ob mice on plasma dyslipidemia, hepatic steatosis, and changes in hepatic gene expression. Feeding ob/ob mice a chow diet supplemented with either low (0.83 g/kg diet) or high-dose (2.5 g/kg diet) NDGA for 16 wk significantly improved plasma triglyceride (TG), inflammatory chemokine levels, hyperinsulinemia, insulin sensitivity, and glucose intolerance. NDGA treatment caused a marked reduction in liver weight and TG content, while enhancing rates of fatty acid oxidation. Microarray analysis of hepatic gene expression demonstrated that NDGA treatment altered genes for lipid metabolism, with genes involved in fatty acid catabolism most significantly increased. NDGA upregulated the mRNA and nuclear protein levels of peroxisome proliferator-activated receptor (PPAR), and the activated (phosphorylated) form of AMPactivated kinase. NDGA increased PPAR promoter activity in AML12 hepatocytes and also prevented the fatty acid suppression of PPAR expression. In contrast, PPAR siRNA abrogated the stimulatory effect of NDGA on fatty acid catabolism. Likewise, no stimulatory effect of NDGA on hepatic fatty acid oxidation was observed in the livers of PPAR-deficient mice, but the ability of NDGA to reverse fatty liver conditions was unaffected. In conclusion, the beneficial actions of NDGA on dyslipidemia and hepatic steatosis in ob/ob mice are exerted primarily through enhanced fatty acid oxidation via PPAR-dependent pathways. However, PPAR-independent pathways also contribute to NDGA¡¦s action to ameliorate hepatic steatosis.
   

 Molecular vision. 2013, 19:775-88.
 Profiling of genes associated with the murine model of oxygen-induced retinopathy
 
 
 Xia Yang, Xiaoguang Dong, Changkai Jia, Yiqiang Wang
  Abstract
Purpose: To compare the clinical features and gene expression patterns of the physiologic development of retinal vessels and oxygen-induced retinopathy (OIR) in a mouse model, with the aim of identifying differential regulators of physiologic and pathological angiogenesis in the retina. Results: The sequential orders and patterns of vasculature development in normal mice and the OIR models were significantly different. In brief, in the early days (P1 to P7) for normal mice, retinal vessels grew from the optic disc into the non-vascularized retina in a radial fashion. In the hyperoxic stage of the OIR model, the main central retina became devoid of a vascular network, and when the mice returned to the normoxic room, the vessels grew from peripheral perfused areas toward the center of the retina, but the development of intermediate and deep layers of vasculature was significantly delayed. Gene profiling at three critical time points (P8, P12, and P13) showed that 162 probes were upregulated to ≥1.5-fold or downregulated to ≤0.67-fold at one or more time points in the OIR model compared to the controls. In the 45 upregulated genes for the P8-O/P8-N group, enriched genes were mainly related to cytoskeleton formation, whereas the 62 upregulated genes for P13-O/P13-N participated in various pathological processes. In the physiologic conditions on P9, however, 135 genes were upregulated compared with P30; the gap junction and Fc gamma R-mediated phagocytosis were the two main enriched pathways for these genes. Fifty-three probes, including vascular endothelium growth factor A, annexin A2, and endothelin 2, changed at P13-O but not at P9-N, and these changed genes might reflect the modulation of pathological neovascularization. Conclusions: Angiogenesis in physiologic and pathological conditions is characterized by the differential presentation of vasculature and gene expression patterns. Investigation of those genes unique to the OIR model may help develop new strategies and therapies for intervening in retinal neovascularization.
   

 Cellular Immunology. 2013 April 10. doi: 10.1016/j.cellimm.2013.04.001.
 MicroRNA-155 regulates T cell proliferation through targeting GSK3£] in cardiac allograft rejection in a murine transplantation model
 
 
 Zhiyu Feng, Yu Xia, Mingjie Zhang, Jinghao Zheng
  Abstract
Here we investigated the activity and regulation of miR-155 during cardiac allograft rejection (AR), and to examine the feasibility of using miR-155 as a biomarker of graft status. Expression of miR-155 in graft-infiltrating lymphocytes (GIL), T cells isolated from spleen (TFS), and lymphocytes separated from blood (LFB) was significantly increased during cardiac AR while GSK3£] was downregulated in GIL and TFS. Inhibition of miR-155 impaired lymphocyte proliferation and enhanced the expression of GSK3£]. Moreover, pharmacological inactivation of GSK3£] resulted in rescue of the proliferative capability of T cells pretreated with a miR-155 inhibitor. Luciferase reporter assay confirmed that miR-155 interacted with the 3¡¬-untranslated region (UTR) of GSK3£] directly. In particular, the miR-155 in LFB can distinguish recipients with AR from syngeneic controls from POD 3 and later. The present study provides a better understanding of the pathophysiological process underlying cardiac AR progression.
   

 Journal of Agricultural and Food Chemistry. 2013 Feb 15. doi: 10.1021/jf3042402.
 Momordica charantia and Its Novel Polypeptide Regulate the Glucose Homeostasis in Mice via Binding to Insulin Receptor
 
 
 Hsin-Yi Lo, Tin-Yun Ho, Chingju Lin, Chia-Cheng Li, Chien-Yun Hsiang
  Abstract
Momordica charantia (MC) has been used as an alternative therapy for diabetes mellitus. Herein we analyzed and elucidated therapeutic targets contributing to the hypoglycemic effect of aqueous extract of MC seeds (MCSE) by transcriptomic analysis. Protein ingredients aimed at the hypoglycemic target were further identified by proteomic, docking, and receptor-binding assays. Our data showed that MSCE (1 g/kg) significantly lowered the blood glucose level in normal and diabetic mice. Moreover, MCSE primarily regulated the insulin signaling pathway in muscles and adipose tissues, suggesting that MCSE might target to insulin receptor (IR), stimulate the IR-downstream pathway, and subsequently display the hypoglycemic activity in mice. We further identified that inhibitor against trypsin (TI) of MC directly docked into IR and activated the kinase activity of IR in a dose-dependent manner. In conclusion, our findings suggested that MCSE regulated glucose metabolism mainly via insulin signaling pathway. Moreover, we newly identified that TI was a novel IR-binding protein of MC that triggered the insulin signaling pathway via binding to IR.
   

 Molecular Pharmacology. 2012, 82(6):1115-28. doi: 10.1124/mol.112.078485.
 Betulinic Acid Decreases Specificity Protein 1 (Sp1) Level via Increasing the Sumoylation of Sp1 to Inhibit Lung Cancer Growth
 
 
 Tsung-I. Hsu, Mei-Chun Wang, Szu-Yu Chen, Shih-Ting Huang, Yu-Min Yeh, Wu-Chou Su, Wen-Chang Chang, Jan-Jong Hung
  Abstract
Previous studies have shown that the inhibitory effect of betulinic acid (BA) on specificity protein 1 (Sp1) expression is involved in the prevention of cancer progression, but the mechanism of this effect remains to be delineated. In this study, we determined that BA treatment in HeLa cells increased the sumoylation of Sp1 by inhibiting sentrin-specific protease 1 expression. The subsequent recruitment of E3 ubiquitin-protein ligase RING finger protein 4 resulted in ubiquitin-mediated degradation in a 26S-proteosome-dependent pathway. In addition, both BA treatment and mithramycin A (MMA) treatment inhibited lung tumor growth and down-regulated Sp1 protein expression in KrasG12D-induced lung cancers of bitransgenic mice. In gene expression profiles of KrasG12D-induced lung cancers in bitransgenic mice with and without Sp1 inhibition, 542 genes were affected by MMA treatment. One of the gene products, cyclin A2, which was involved in the S and G2/M phase transition during cell cycle progression, was investigated in detail because its expression was regulated by Sp1. The down-regulation of cyclin A2 by BA treatment resulted in decreased retinoblastoma protein phosphorylation and cell cycle G2/M arrest. The BA-mediated cellular Sp1 degradation and antitumor effect were also confirmed in a xenograft mouse model by using H1299 cells. The knockdown of Sp1 in lung cancer cells attenuated the tumor-suppressive effect of BA. Taken together, the results of this study clarify the mechanism of BA-mediated Sp1 degradation and identify a pivotal role for Sp1 in the BA-induced repression of lung cancer growth.
   

 BioMedicine. 2012, 2(1):10-16. doi: 10.1016/j.biomed.2012.02.002.
 DNA microarray analysis as a tool to investigate the therapeutic mechanisms and drug development of Chinese medicinal herbs
 
 
 Chia-Cheng Li, Hsin-Yi Lo, Chien-Yun Hsiang, Tin-Yun Ho
  Abstract
Chinese herbal medicines have been used for the treatment of various diseases for centuries. Although several herbal formulas and herbal components have shown therapeutic potential, the active components and the molecular mechanisms mediating the effects of said formulas remain to be discovered. Microarray analysis has become a widely used tool for the generation of gene expression data on a genome-wide scale. This paper discusses the application of whole genome expression profiling as a tool to investigate the molecular mechanisms governing the therapeutic effects of traditional Chinese medicine. This review also highlights how data derived from DNA microarray analysis can be used to screen for drug targets of various herbal drugs, to predict the therapeutic potential of herbal drugs, to analyze the safety of drugs in the preclinical stage of drug development, and to establish a modern definition of traditional Chinese medicine.
   

 Methods in Molecular Biology. 2012, 887:95-110. doi: 10.1007/978-1-61779-860-3_10.
 Deoxyoligonucleotide Microarrays for Gene Expression Profiling in Murine Tooth Germs
 
 
 Anne-Marthe Jevnaker, Maria A. Landin, Harald Osmundsen
  Abstract
The use of deoxyoligonucleotide microarrays facilitates rapid expression profiling of gene expression using samples of about 1 £gg of total RNA. Here are described practical aspects of the procedures involved, including essential reagents. Analysis of results is discussed from a practical, experimental, point of view together with software required to carry out the required statistical analysis to isolate populations of differentially expressed genes.
   

 Journal of Molecular Neuroscience. 2012, 47(3):604-618. doi: 10.1007/s12031-011-9690-4.
 The Effects of Unilateral Naris Occlusion on Gene Expression Profiles in Mouse Olfactory Mucosa
 
 
 Christopher T. Waggener, David M. Coppola
  Abstract
Unilateral naris occlusion has been the method of choice for effecting stimulus deprivation in studies of olfactory plasticity. Early experiments emphasized the deleterious effects of this technique on the developing olfactory system while more recent studies have pointed to several apparently ¡§compensatory¡¨ responses. However, the evidence for deprivation-induced compensatory processes in olfaction remains fragmentary. High-throughput methods such as microarray analysis can help fill the deficits in our understanding of naris occlusion as a mode of stimulus deprivation. Here we report for young adult mice the effects of early postnatal naris occlusion on the olfactory mucosal transcriptome using microarray analysis with RT¡VPCR confirmation. The transcripts of key genes involved in olfactory reception, transduction, and transmission were up-regulated in deprived-side olfactory mucosa, with opposite effects in non-deprived-side mucosa, compared to controls. Results support the hypothesis that odor environment triggers a previously unknown homeostatic control mechanism in olfactory receptor neurons designed to maximize information transfer.
   

 Journal of Natural Products. 2012, 75(10):1706-11. doi: 10.1021/np300250m.
 Dual Inhibition of £^-Oryzanol on Cellular Melanogenesis: Inhibition of Tyrosinase Activity and Reduction of Melanogenic Gene Expression by a Protein Kinase A-Dependent Mechanism
 
 
 Hee-jin Jun, Ji Hae Lee, Bo-Ram Cho, Woo-Duck Seo, Hang-Won Kang, Dong-Woo Kim, Kang-Jin Cho, Sung-Joon Lee
  Abstract
The in vitro effects on melanogenesis of £^-oryzanol (1), a rice bran-derived phytosterol, were investigated. The melanin content in B16F1 cells was significantly and dose-dependently reduced (?13% and ?28% at 3 and 30 £gM, respectively). Tyrosinase enzyme activity was inhibited by 1 both in a cell-free assay and when analyzed based on the measurement of cellular tyrosinase activity. Transcriptome analysis was performed to investigate the biological pathways altered by 1, and it was found that gene expression involving protein kinase A (PKA) signaling was markedly altered. Subsequent analyses revealed that 1 stimulation in B16 cells reduced cytosolic cAMP concentrations, PKA activity (?13% for cAMP levels and ?40% for PKA activity), and phosphorylation of the cAMP-response element binding protein (?57%), which, in turn, downregulated the expression of microphthalmia-associated transcription factor (MITF; ?59% for mRNA and ?64% for protein), a key melanogenic gene transcription factor. Accordingly, tyrosinase-related protein 1 (TRP-1; ?69% for mRNA and ?82% for protein) and dopachrome tautomerase (?51% for mRNA and ?92% for protein) in 1-stimulated B16F1 cells were also downregulated. These results suggest that 1 has dual inhibitory activities for cellular melanogenesis by inhibiting tyrosinase enzyme activity and reducing MITF and target genes in the PKA-dependent pathway.
   

 Inflammation Research. 2012, 61(12):1395-404. doi: 10.1007/s00011-012-0542-7.
 Mammalian target of rapamycin complex 2 regulates inflammatory response to stress
 
 
 Desmond Mascarenhas, Sheri Routt, Baljit K. Singh
  Abstract
To explore the role of mammalian target of rapamycin 2 (mTORC2) in the activation of inflammatory and oxidative responses in rodent models of acute injury and metabolic stress. The impact of nephrilin, an inhibitor of mTORC2 complex, was assessed in three CD-1 mouse models of acute xenobiotic stress and in a hypertensive Dahl rat model of metabolic stress. Animals received daily subcutaneous bolus injections of saline or 4 mg/kg nephrilin. Tissues were assayed by ELISA, gene arrays and immunohistochemical staining.Nephrilin significantly inhibited elevations in plasma tumor necrosis factor-alpha, kidney substance P, and CX3CR1, and urinary lipocalin-2 [urinary neutrophil gelatinase-associated lipocalin (uNGAL)] in models of acute xenobiotic stress. UCHL1 gene expression levels dropped and plasma HMGB1 levels rose in the rhabdomyolysis model. Both effects were reversed by nephrilin. The inhibitor also blocked diet-induced elevations of uNGAL and albumin-creatinine ratio (UACR) as well as kidney tissue phosphorylation of PKC-beta-2-T641 and p66shc-S36, and reduced dark ring-like staining of nuclei by anti-phos-p66shc-S36 antibody in frozen sections of diseased kidneys from hypertensive Dahl rats fed an 8 % NaCl diet for 4 weeks. Taken together, our results suggest a role for mTORC2 in the inflammatory-oxidative responses to stress.
   

 Food Chemistry. 2013, 136(2):426-34. doi: 10.1016/j.foodchem.2012.08.009.
 Toona sinensis and its major bioactive compound gallic acid inhibit LPS-induced inflammation in nuclear factor-£eB transgenic mice as evaluated by in vivo bioluminescence imaging
 
 
 Chien-Yun Hsiang, You-Cheng Hseu, Yi-Chih Chang, K.J. Senthil Kumar, Tin-Yun Ho, Hsin-Ling Yang
  Abstract
In the present study, we investigated the anti-inflammatory effects of a nutritious vegetable Toona sinensis (leaf extracts, TS) and its major bioactive compound gallic acid (GA) by analysing LPS-induced NF-£eB activation in transgenic mice, using bioluminescence imaging. Mice were challenged intraperitoneally with LPS (1 mg/kg) and treated orally with TS or GA (100 or 5 mg/kg, respectively). In vivo and ex vivo imaging showed that LPS increased NF-£eB luminescence in the abdominal region, which was significantly inhibited by TS or GA. Immunohistochemical and ELISA analyses confirmed that TS and GA inhibited LPS-induced NF-£eB, interleukin-1£], and tumour necrosis factor-£ expression. Microarray analysis revealed that biological pathways associated with metabolism and the immune responses were affected by TS or GA. Particularly, LPS-induced thioredoxin-like 4B (TXNL4B) 2 expression in the small intestine, and TXNL4B, iNOS, and COX-2 expression in RAW 264.7 cells were significantly inhibited by TS or GA. Thus, the anti-inflammatory potential of TS was mediated by the downregulation of NF-£eB pathway.
   

 Food Chemistry. 2013, 136(1):170-7. doi: 10.1016/j.foodchem.2012.07.124.
 Ginger extract and zingerone ameliorated trinitrobenzene sulfonic acid-induced colitis in mice via modulation of nuclear factor-£eB activity and interleukin-1£] signaling pathway
 
 
 Chien-Yun Hsiang, Hsin-Yi Lo, Hui-Chi Huang, Chia-Cheng Li, Shih-Lu Wu, Tin-Yun Ho
  Abstract
Ginger is a commonly used spice with anti-inflammatory potential. Colitis is the common pathological lesion of inflammatory bowel diseases. In this study, we investigated the therapeutic effects of ginger and its component zingerone in mice with 2,4,6-trinitrobenzene sulphonic acid (TNBS)-induced colitis. Ginger and zingerone ameliorated TNBS-induced colonic injury in a dose-dependent manner. Pathway analysis of ginger- and zingerone-regulated gene expression profiles showed that ginger and zingerone significantly regulated cytokine-related pathways. Network analysis showed that nuclear factor-£eB (NF-£eB) and interleukin-1£] (IL-1£]) were key molecules involved in the expression of ginger- and zingerone-affected genes. Ex vivo imaging and immunohistochemical staining further verified that ginger and zingerone suppressed TNBS-induced NF-£eB activation and IL-1£] protein level in the colon. In conclusion, ginger improved TNBS-induced colitis via modulation of NF-£eB activity and IL-1£] signalling pathway. Moreover, zingerone might be the active component of ginger responsible for the amelioration of colitis induced by TNBS.
   

 Virology Journal. 2012, 9:159. doi: 10.1186/1743-422X-9-159.
 Infection with street strain rabies virus induces modulation of the microRNA profile of the mouse brain
 
 
 Pingsen Zhao, Lili Zhao, Kun Zhang, Hao Feng, Hualei Wang, Tiecheng Wang, Tao Xu, Na Feng, Chengyu Wang, Yuwei Gao, Geng Huang, Chuan Qin, Songtao Yang, Xianzhu Xia
  Abstract
Rabies virus (RABV) causes a fatal infection of the central nervous systems (CNS) of warm-blooded animals. Once the clinical symptoms develop, rabies is almost invariably fatal. The mechanism of RABV pathogenesis remains poorly understood. Recent studies have shown that microRNA (miRNA) plays an important role in the pathogenesis of viral infections. Our recent findings have revealed that infection with laboratory-fixed rabies virus strain can induce modulation of the microRNA profile of mouse brains. However, no previous report has evaluated the miRNA expression profile of mouse brains infected with RABV street strain. The results of microarray analysis show that miRNA expression becomes modulated in the brains of mice infected with street RABV. Quantitative real-time PCR assay of the differentially expressed miRNAs confirmed the results of microarray assay. Functional analysis showed the differentially expressed miRNAs to be involved in many immune-related signaling pathways, such as the Jak-STAT signaling pathway, the MAPK signaling pathway, cytokine-cytokine receptor interactions, and Fc gamma R-mediated phagocytosis. The predicted expression levels of the target genes of these modulated miRNAs were found to be correlated with gene expression as measured by DNA microarray and qRT-PCR. RABV causes significant changes in the miRNA expression profiles of infected mouse brains. Predicted target genes of the differentially expression miRNAs are associated with host immune response, which may provide important information for investigation of RABV pathogenesis and therapeutic method.
   

 Food and Chemical Toxicology. 2012, 50(9):2978-86. doi: 10.1016/j.fct.2012.05.054.
 Genipin inhibits lipopolysaccharide-induced acute systemic inflammation in mice as evidenced by nuclear factor-£eB bioluminescent imaging-guided transcriptomic analysis
 
 
 Chia-Cheng Li, Chien-Yun Hsiang, Hsin-Yi Lo, Fu-Tzu Pai, Shih-Lu Wu, Tin-Yun Ho
  Abstract
Genipin is a natural blue colorant in food industry. Inflammation is correlated with human disorders, and nuclear factor-£eB (NF-£eB) is the critical molecule involved in inflammation. In this study, the anti-inflammatory effect of genipin on the lipopolysaccharide (LPS)-induced acute systemic inflammation in mice was evaluated by NF-£eB bioluminescence-guided transcriptomic analysis. Transgenic mice carrying the NF-£eB-driven luciferase genes were administered intraperitoneally with LPS and various amounts of genipin. Bioluminescent imaging showed that genipin significantly suppressed LPS-induced NF-£eB-dependent luminescence in vivo. The suppression of LPS-induced acute inflammation by genipin was further evidenced by the reductions of cytokine levels in sera and organs. Microarray analysis of these organs showed that the transcripts of 79 genes were differentially expressed in both LPS and LPS/genipin groups, and one third of these genes belonged to chemokine ligand, chemokine receptor, and interferon (IFN)-induced protein genes. Moreover, network analysis showed that NF-£eB played a critical role in the regulation of genipin-affected gene expression. In conclusion, we newly identified that genipin exhibited anti-inflammatory effects in a model of LPS-induced acute systemic inflammation via downregulation of chemokine ligand, chemokine receptor, and IFN-induced protein productions.
   

 PLoS ONE. 2012, 7(4):e34969. doi: 10.1371/journal.pone.0034969.
 Assessment of Chitosan-Affected Metabolic Response by Peroxisome Proliferator-Activated Receptor Bioluminescent Imaging-Guided Transcriptomic Analysis
 
 
 Chia-Hung Kao, Chien-Yun Hsiang, Tin-Yun Ho
  Abstract
Chitosan has been widely used in food industry as a weight-loss aid and a cholesterol-lowering agent. Previous studies have shown that chitosan affects metabolic responses and contributes to anti-diabetic, hypocholesteremic, and blood glucose-lowering effects; however, the in vivo targeting sites and mechanisms of chitosan remain to be clarified. In this study, we constructed transgenic mice, which carried the luciferase genes driven by peroxisome proliferator-activated receptor (PPAR), a key regulator of fatty acid and glucose metabolism. Bioluminescent imaging of PPAR transgenic mice was applied to report the organs that chitosan acted on, and gene expression profiles of chitosan-targeted organs were further analyzed to elucidate the mechanisms of chitosan. Bioluminescent imaging showed that constitutive PPAR activities were detected in brain and gastrointestinal tract. Administration of chitosan significantly activated the PPAR activities in brain and stomach. Microarray analysis of brain and stomach showed that several pathways involved in lipid and glucose metabolism were regulated by chitosan. Moreover, the expression levels of metabolism-associated genes like apolipoprotein B (apoB) and ghrelin genes were down-regulated by chitosan. In conclusion, these findings suggested the feasibility of PPAR bioluminescent imaging-guided transcriptomic analysis on the evaluation of chitosan-affected metabolic responses in vivo. Moreover, we newly identified that downregulated expression of apoB and ghrelin genes were novel mechanisms for chitosan-affected metabolic responses in vivo.
   

 PLoS ONE. 2012, 7(3):e31808. doi: 10.1371/journal.pone.0031808.
 5-Fluorouracil Induced Intestinal Mucositis via Nuclear Factor-£eB Activation by Transcriptomic Analysis and In Vivo Bioluminescence Imaging
 
 
 Chung-Ta Chang, Tin-Yun Ho, Ho Lin, Ji-An Liang, Hui-Chi Huang, Chia-Cheng Li, Hsin-Yi Lo, Shih-Lu Wu, Yi-Fang Huang, Chien-Yun Hsiang
  Abstract
5-Fluorouracil (5-FU) is a commonly used drug for the treatment of malignant cancers. However, approximately 80% of patients undergoing 5-FU treatment suffer from gastrointestinal mucositis. The aim of this report was to identify the drug target for the 5-FU-induced intestinal mucositis. 5-FU-induced intestinal mucositis was established by intraperitoneally administering mice with 100 mg/kg 5-FU. Network analysis of gene expression profile and bioluminescent imaging were applied to identify the critical molecule associated with 5-FU-induced mucositis. Our data showed that 5-FU induced inflammation in the small intestine, characterized by the increased intestinal wall thickness and crypt length, the decreased villus height, and the increased myeloperoxidase activity in tissues and proinflammatory cytokine production in sera. Network analysis of 5-FU-affected genes by transcriptomic tool showed that the expression of genes was regulated by nuclear factor-£eB (NF-£eB), and NF-£eB was the central molecule in the 5-FU-regulated biological network. NF-£eB activity was activated by 5-FU in the intestine, which was judged by in vivo bioluminescence imaging and immunohistochemical staining. However, 5-aminosalicylic acid (5-ASA) inhibited 5-FU-induced NF-£eB activation and proinflammatory cytokine production. Moreover, 5-FU-induced histological changes were improved by 5-ASA. In conclusion, our findings suggested that NF-£eB was the critical molecule associated with the pathogenesis of 5-FU-induced mucositis, and inhibition of NF-£eB activity ameliorated the mucosal damage caused by 5-FU.
   

 Neuron. 2012, 73(4):774-88. doi: 10.1016/j.neuron.2012.02.003.
 EPAC Null Mutation Impairs Learning and Social Interactions via Aberrant Regulation of miR-124 and Zif268 Translation
 
 
 Ying Yang, Xiaogang Shu, Dan Liu, You Shang, Yan Wu, Lei Pei, Xin Xu, Qing Tian, Jian Zhang, Kun Qian, Ya-Xian Wang, Ronald S. Petralia, Weihong Tu, Ling-Qiang Zhu, Jian-Zhi Wang, Youming Lu
  Abstract
EPAC proteins are the guanine nucleotide exchange factors that act as the intracellular receptors for cyclic AMP. Two variants of EPAC genes including EPAC1 and EPAC2 are cloned and are widely expressed throughout the brain. But, their functions in the brain remain unknown. Here, we genetically delete EPAC1 (EPAC1(-/-)), EPAC2 (EPAC2(-/-)), or both EPAC1 and EPAC2 genes (EPAC(-/-)) in the forebrain of mice. We show that EPAC null mutation impairs long-term potentiation (LTP) and that this impairment is paralleled with the severe deficits in spatial learning and social interactions and is mediated in a direct manner by miR-124 transcription and Zif268 translation. Knockdown of miR-124 restores Zif268 and hence reverses all aspects of the EPAC(-/-) phenotypes, whereas expression of miR-124 or knockdown of Zif268 reproduces the effects of EPAC null mutation. Thus, EPAC proteins control miR-124 transcription in the brain for processing spatial learning and social interactions.
   

 PLoS ONE. 2012, 7(2):e31005. doi: 10.1371/journal.pone.0031005.
 Conditional Ablation of Ezh2 in Murine Hearts Reveals Its Essential Roles in Endocardial Cushion Formation, Cardiomyocyte Proliferation and Survival
 
 
 Li Chen, Yanlin Ma, Eun Young Kim, Wei Yu, Robert J. Schwartz, Ling Qian, Jun Wang
  Abstract
Ezh2 is a histone trimethyltransferase that silences genes mainly via catalyzing trimethylation of histone 3 lysine 27 (H3K27Me3). The role of Ezh2 as a regulator of gene silencing and cell proliferation in cancer development has been extensively investigated; however, its function in heart development during embryonic cardiogenesis has not been well studied. In the present study, we used a genetically modified mouse system in which Ezh2 was specifically ablated in the mouse heart. We identified a wide spectrum of cardiovascular malformations in the Ezh2 mutant mice, which collectively led to perinatal death. In the Ezh2 mutant heart, the endocardial cushions (ECs) were hypoplastic and the endothelial-to-mesenchymal transition (EMT) process was impaired. The hearts of Ezh2 mutant mice also exhibited decreased cardiomyocyte proliferation and increased apoptosis. We further identified that the Hey2 gene, which is important for cardiomyocyte proliferation and cardiac morphogenesis, is a downstream target of Ezh2. The regulation of Hey2 expression by Ezh2 may be independent of Notch signaling activity. Our work defines an indispensible role of the chromatin remodeling factor Ezh2 in normal cardiovascular development.
   

 Development. 2012, 139(4):709-19. doi: 10.1242/dev.073197.
 Bmp signaling regulates a dose-dependent transcriptional program to control facial skeletal development
 
 
 Margarita Bonilla-Claudio, Jun Wang, Yan Bai, Elzbieta Klysik, Jennifer Selever, James F. Martin
  Abstract
We performed an in depth analysis of Bmp4, a critical regulator of development, disease, and evolution, in cranial neural crest (CNC). Conditional Bmp4 overexpression, using a tetracycline-regulated Bmp4 gain-of-function allele, resulted in facial skeletal changes that were most dramatic after an E10.5 Bmp4 induction. Expression profiling uncovered a signature of Bmp4-induced genes (BIG) composed predominantly of transcriptional regulators that control self-renewal, osteoblast differentiation and negative Bmp autoregulation. The complimentary experiment, CNC inactivation of Bmp2, Bmp4 and Bmp7, resulted in complete or partial loss of multiple CNC-derived skeletal elements, revealing a crucial requirement for Bmp signaling in membranous bone and cartilage development. Importantly, the BIG signature was reduced in Bmp loss-of-function mutants, indicating Bmp-regulated target genes are modulated by Bmp dose. Chromatin immunoprecipitation (ChIP) revealed a subset of the BIG signature, including Satb2, Smad6, Hand1, Gadd45£^ and Gata3, that was bound by Smad1/5 in the developing mandible, revealing direct Smad-mediated regulation. These data support the hypothesis that Bmp signaling regulates craniofacial skeletal development by balancing self-renewal and differentiation pathways in CNC progenitors.
   

 Biotechnol Lett. 2012, 34(5):805-12. doi: 10.1007/s10529-011-0838-7.
 Momilactione B inhibits protein kinase A signaling and reduces tyrosinase-related proteins 1 and 2 expression in melanocytes
 
 
 Ji Hae Lee, Boram Cho, Hee-jin Jun, Woo-Duck Seo, Dong-Woo Kim, Kang-Jin Cho, Sung-Joon Lee
  Abstract
Momilactone B (MB) is a terpenoid phytoalexin present in rice bran that exhibits several biological activities. MB reduced the melanin content in B16 melanocytes melanin content and inhibited tyrosinase activities. Using transcriptome analysis, the genes involved in protein kinase A (PKA) signaling were found to be markedly altered. B16 cells stimulated with MB had decreased concentrations of cAMP protein kinase A activity, and cAMP-response element-binding protein which is a key transcription factor for microphthalmia-associated transcription factor (MITF) expression. Accordingly, the expression of MITF and its target genes, which are essential for melanogenesis, were reduced. MB thus exhibits anti-melanogenic effects by repressing tyrosinase enzyme activity and inhibiting the PKA signaling pathway which, in turn, decreases melanogenic gene expression.
   

 Journal of Molecular and Cellular Cardiology. 2012, 52(3):638-49. doi: 10.1016/j.yjmcc.2011.11.011.
 Enhanced desumoylation in murine hearts by overexpressed SENP2 leads to congenital heart defects and cardiac dysfunction
 
 
 EunYoungKim, LiChen, YanlinMa, WeiYu, JiangChang, Ivan P.Moskowitz, JunWang
  Abstract
Sumoylation is a posttranslational modification implicated in a variety of cellular activities, and its role in a number of human pathogeneses such as cleft lip/palate has been well documented. However, the importance of the SUMO conjugation pathway in cardiac development and functional disorders is newly emerging. We previously reported that knockout of SUMO-1 in mice led to congenital heart diseases (CHDs). To further investigate the effects of imbalanced SUMO conjugation on heart development and function and its underlying mechanisms, we generated transgenic (Tg) mice with cardiac-specific expression of SENP2, a SUMO-specific protease that deconjugates sumoylated proteins, to evaluate the impact of desumoylation on heart development and function. Overexpression of SENP2 resulted in premature death of mice with CHDs-atrial septal defects (ASDs) and/or ventricular septal defects (VSDs). Immunobiochemistry revealed diminished cardiomyocyte proliferation in SENP2-Tg mouse hearts compared with that in wild type (WT) hearts. Surviving SENP2-Tg mice showed growth retardation, and developed cardiomyopathy with impaired cardiac function with aging. Cardiac-specific overexpression of the SUMO-1 transgene reduced the incidence of cardiac structural phenotypes in the sumoylation defective mice. Moreover, cardiac overexpression of SENP2 in the mice with Nkx2.5 haploinsufficiency promoted embryonic lethality and severity of CHDs, indicating the functional interaction between SENP2 and Nkx2.5 in vivo. Our findings indicate the indispensability of a balanced SUMO pathway for proper cardiac development and function. This article is part of a Special Issue entitled 'Post-translational Modification SI'.
   

 Transgenic Res. 2011, 20(5):1073-86. doi: 10.1007/s11248-010-9478-2.
 Epithelial cell-targeted transgene expression enables isolation of cyan fluorescent protein (CFP)-expressing prostate stem/progenitor cells
 
 
 Weidan Peng, Yunhua Bao, Janet A. Sawicki
  Abstract
To establish a method for efficient and relatively easy isolation of a cell population containing epithelial prostate stem cells, we developed two transgenic mouse models, K5/CFP and K18/RFP. In these models, promoters of the cytokeratin 5 (Krt5) and the cytokeratin 18 (Krt18) genes regulate cyan and red fluorescent proteins (CFP and RFP), respectively. CFP and RFP reporter protein fluorescence allows for visualization of K5(+) and K18(+) epithelial cells within the cellular spatial context of the prostate gland and for their direct isolation by FACS. Using these models, it is possible to test directly the stem cell properties of prostate epithelial cell populations that are positively selected based on expression of cytoplasmic proteins, K5 and K18. After validating appropriate expression of the K5/CFP and K18/RFP transgenes in the developing and adult prostate, we demonstrate that a subset of CFP-expressing prostate cells exhibits stem cell proliferation potential and differentiation capabilities. Then, using prostate cells sorted from double transgenic mice (K5/CFP + K18/RFP), we compare RNA microarrays of sorted K5(+)K18(+) basal and K5(-)K18(+) luminal epithelial cells, and identify genes that are differentially expressed. Several genes that are over-expressed in K5(+) cells have previously been identified as potential stem cell markers. These results suggest that FACS isolation of prostate cells from these mice based on combining reporter gene fluorescence with expression of potential stem cell surface marker proteins will yield populations of cells enriched for stem cells to a degree that has not been attained by using cell surface markers alone.
   

 Comparative Immunology, Microbiology and Infectious Diseases. 2011, 34(6):503-12. doi: 10.1016/j.cimid.2011.09.003.
 Innate immune response gene expression profiles in central nervous system of mice infected with rabies virus
 
 
 Pingsen Zhao, Lili Zhao, Tao Zhang, Yinglin Qi, Tiecheng Wang, Kejian Liu, Hualei Wang, Hao Feng, Hongli Jin, Chuan Qin, Songtao Yang, Xianzhu Xia
  Abstract
The present study was focused on the modulation of innate immune response genes in CNS of mouse in response to rabies virus (RABV) infection. The global gene expression changes in brains of RABV- or mock-infected mice were investigated using DNA microarray analysis and quantitative real-time PCR. Then functional enrichment of the differentially expressed mRNAs was performed. Microarray analysis showed that 390 genes in brain were significantly (P<0.01) regulated in response to RABV infection, with obviously up-regulated genes like interferon (IFN) stimulated genes (ISGs), IFN inducible transcription factors, cytokines and complement, etc. The significant pathways of differentially expressed genes are mainly involved in JAK-STAT signaling pathway, antigen processing and presentation, ubiquitin mediated proteolysis and complement cascades. The results suggest that the modulated genes in infected CNS were possibly involved in pathogenesis of rabies. Conversely, they may have protective effects.
   

 Microbial Pathogenesis. 2012, 52(1):47-54. doi: 10.1016/j.micpath.2011.10.001.
 Changes in microRNA expression induced by rabies virus infection in mouse brains
 
 
 Pingsen Zhao, Lili Zhao, Tao Zhang, Hualei Wang, Chuan Qin, Songtao Yang, Xianzhu Xia
  Abstract
MicroRNAs (miRNAs) are small RNA (? 22 nt) molecules expressed endogenously in cells. They are involved in the regulation of gene expression. Recently, evidence has shown that cellular miRNAs have key regulatory roles in virus-host interactions. The rabies virus (RABV) causes a fatal infection of the central nervous systems (CNS) of warm-blooded animals, yet its pathogenesis remains poorly understood. To gain more insight into the pathogenesis of RABV, a miRNA microarray was performed as part of an investigation of changes in host miRNA expression in the brains of mice infected with RABV. The results showed that RABV infection induced modulation of the expression of sixteen miRNA molecules. These data were verified by real-time PCR. Functional analysis showed the differentially expressed miRNAs to be involved in many immune-related signaling pathways, such as the RIG-I-like receptor signaling pathway, JAK-STAT signaling pathway, chemokine signaling pathway, T-cell receptor signaling pathway, MAPK signaling pathway, leukocyte transendothelial migration, and natural killer cell mediated cytotoxicity. The predicted expression levels of the target genes of these modulated miRNAs correlated with measurements of gene expression measured by DNA microarray and qRT-PCR.
   

 BMC Research Notes. 2011 Oct 5;4:381.
 Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cells
 
 
 Yana G Kamberov , Jihoon Kim , Ralph Mazitschek , Winston P Kuo, Malcolm Whitman
  Abstract
The small molecule Halofuginone (HF) is a potent regulator of extracellular matrix (ECM ) gene expression and is unique in its therapeutic potential. While the basis for HF effects is unknown, inhibition of TGF£] signaling and activation of the amino acid restriction response (AAR) have been linked to HF transcriptional control of a number of ECM components and amelioration of fibrosis and alleviation of autoimmune disease by regulation of Th17 cell differentiation, respectively. The aim of this study was to generate a global expression profile of HF targets in epithelial cells to identify potential mediators of HF function in this cell type. We report that HF modulation of the expression of the ECM remodeling protein Mmp13 in epithelial cells is separable from previously reported effects of HF on TGF£] signal inhibition, and use microarray expression analysis to correlate this with transcriptional responses characteristic of the Integrated Stress Response (ISR). Our findings suggest activation of the ISR may be a common mechanism underlying HF biological effects.
   

 The Journal of Immunology. 2011, 187(9):4426-30. doi: 10.4049/jimmunol.1101034.
 Cutting edge: IRF8 regulates Bax transcription in vivo in primary myeloid cells
 
 
 Jine Yang, Xiaolin Hu, Mary Zimmerman, Christina M. Torres, Dafeng Yang, Sylvia B. Smith, Kebin Liu
  Abstract
A prominent phenotype of IRF8 knockout (KO) mice is the uncontrolled expansion of immature myeloid cells. The molecular mechanism underlying this myeloproliferative syndrome is still elusive. In this study, we observed that Bax expression level is low in bone marrow preginitor cells and increases dramatically in primary myeloid cells in wt mice. In contrast, Bax expression level remained at a low level in primarymyeloid cells in IRF8 KO mice. However, in vitro IRF8 KO bone marrow-differentiated myeloid cells expressed Bax at a level as high as that in wild type myeloid cells. Furthermore, we demonstrated that IRF8 specifically binds to the Bax promoter region in primary myeloid cells. Functional analysis indicated that IRF8 deficiency results in increased resistance of the primary myeloid cells to Fas-mediated apoptosis. Our findings show that IRF8 directly regulates Bax transcription in vivo, but not in vitro during myeloid cell lineage differentiation.
   

 PLoS One. 2011, 6(8):e23682. doi: 10.1371/journal.pone.0023682.
 Comprehensive Assessment of Host Responses to Ionizing Radiation by Nuclear Factor-£eB Bioluminescence Imaging-Guided Transcriptomic Analysis
 
 
 Q Chang CT, Lin H, Ho TY, Li CC, Lo HY, Wu SL, Huang YF, Liang JA, Hsiang CY.
  Abstract
The aim of this study was to analyze the host responses to ionizing radiation by nuclear factor-£eB (NF-£eB) bioluminescence imaging-guided transcriptomic tool. Transgenic mice carrying the NF-£eB-driven luciferase gene were exposed to a single dose of 8.5 Gy total-body irradiation. In vivo imaging showed that a maximal NF-£eB-dependent bioluminescent intensity was observed at 3 h after irradiation and ex vivo imaging showed that liver, intestine, and brain displayed strong NF-£eB activations. Microarray analysis of these organs showed that irradiation altered gene expression signatures in an organ-specific manner and several pathways associated with metabolism and immune system were significantly altered. Additionally, the upregulation of fatty acid binding protein 4, serum amyloid A2, and serum amyloid A3 genes, which participate in both inflammation and lipid metabolism, suggested that irradiation might affect the cross pathways of metabolism and inflammation. Moreover, the alteration of chemokine (CC-motif) ligand 5, chemokine (CC-motif) ligand 20, and Jagged 1 genes, which are involved in the inflammation and enterocyte proliferation, suggested that these genes might be involved in the radiation enteropathy. In conclusion, this report describes the comprehensive evaluation of host responses to ionizing radiation. Our findings provide the fundamental information about the in vivo NF-£eB activity and transcriptomic pattern after irradiation. Moreover, novel targets involved in radiation injury are also suggested.
   

 Acta Histochem. 2012, 114(4):379-85. doi: 10.1016/j.acthis.2011.07.008.
 Expression of insulin-like growth factor binding protein-4 (IGFBP-4) in acute pancreatitis induced by l-arginine in mice
 
 
 Jia Qing Shen, Jie Shen, Xing Peng Wang.
  Abstract
The mechanisms of injury and regeneration after acute pancreatitis are still incompletely understood. Insulin-like growth factor binding proteins (IGFBPs) have been reported to play roles in various pancreatic diseases, but the involvement of insulin-like growth factor binding protein-4 (IGFBP-4) in acute pancreatitis is unknown. The aim of the study was to examine the expression of IGFBP-4 in mice with acute pancreatitis induced by two doses of L-arginine. IGFBP-4 expression was assayed by microarray test, real-time RT-PCR, Western blotting, ELISA and by an immunohistochemical assay. Microarray test of pancreatic mRNA showed that IGFBP-4 mRNA increased significantly after L-arginine treatment and the increase was confirmed by real-time RT-PCR. Western blotting and ELISA assay showed similar patterns of increase of IGFBP-4 in pancreatic tissues and serum. In the control pancreas, IGFBP-4 was mainly immunolocalized in the pancreatic islets. In the pancreatic tissues of mice with pancreatitis induced by L-arginine, the immunolocalization of IGFBP-4 was detected in both acinar cells and pancreatic islets. In conclusion, our results suggest that IGFBP-4 may play a potential role in pancreatic injury and regeneration in a murine model of acute pancreatitis induced by L-arginine.
   

 Cancer Genomics Proteomics. 2011 Mar-Apr; 8(2):77-85..
 Small Molecule Inhibition of Cytoskeletal Dynamics in Melanoma Tumors Results in Altered Transcriptional Expression Patterns of Key Genes Involved in Tumor Initiation and Progression
 
 
 Spencer C, Montalvo J, McLaughlin SR, Bryan BA.
  Abstract
Rho kinase signaling plays an important role in the oncogenic process largely through its regulation of F-actin dynamics, and inhibition of this pathway results in reduction in tumor volume and metastasis across a number of tumor types. While the cytoskeletal-regulatory role of Rho kinase has been a topic of in-depth study, the mechanisms linking Rho kinase to altered geneexpression are largely unknown. Global gene expression analysis was performed on melanoma tumors treated with sham or the small molecule inhibitor Y27632. Inhibition of Rho kinase activity in melanoma tumors results in a statistically significant change in gene transcription of 94 genes, many of which are critically involved in tumor initiation and progression. In addition to regulating tumorigenesis through modulation of the phosphoproteome, Rho kinase signaling also contributes to the regulation of the tumor transcriptome.
   

 Biomed Pharmacother.. 2011, 65(8):547-54. doi: 10.1016/j.biopha.2011.03.008.
 CXCL9 attenuated chemotherapy-induced intestinal mucositis by inhibiting proliferation and reducing apoptosis.
 
 
 Han X, Wu Z, Di J, Pan Y, Zhang H, Du Y, Cheng Z, Jin Z, Wang Z, Zheng Q, Zhang P, Wang Y.
  Abstract
Mucositis arising from cancer chemotherapy is a common problem for which there is no definitive treatment. 5-fluorouracil (5-FU) is a common cytotoxic agent used to treat solid tumors. A global gene expression array was performed to identify genetic signals involved in the pathogenesis of mucositis. The chemokine (C-X-C motif) ligand 9 (CXCL9) was one of the candidates identified that presented a characteristic gene expression profile; its temporal expression pattern was correlated with the damage and regeneration phases of the small intestine upon 5-FU chemotherapy. We found that prophylactic CXCL9 administration was able to attenuate the severity of mucositis, weight loss and diarrhea caused by chemotherapy. CXCL9 also increased the tolerance of the mice to lethal-dose chemotherapy. Moreover, we demonstrated that CXCL9 was able to promote the proliferation and regeneration of intestinal cells by inhibiting the proliferation of normal intestinal mucosal cells prior to chemotherapy and by reducing the 5-FU-induced apoptosis in intestinal crypts. Thus, pretreatment with CXCL9 is a new and promising strategy for the alleviation of chemotherapy-induced intestinal mucositis in clinical settings.
   

 Birth Defects Res A Clin Mol Teratol. 2011, 91(6):468-76. doi: 10.1002/bdra.20816.
 Defective sumoylation pathway directs congenital heart disease
 
 
 Wang J, Chen L, Wen S, Zhu H, Yu W, Moskowitz IP, Shaw GM, Finnell RH, Schwartz RJ.
  Abstract
Congenital heart defects (CHDs) are the most common of all birth defects, yet molecular mechanism(s) underlying highly prevalent atrial septal defects (ASDs) and ventricular septal defects (VSDs) have remained elusive. We demonstrate the indispensability of "balanced" posttranslational small ubiquitin-like modifier (SUMO) conjugation-deconjugation pathway for normal cardiac development. Both hetero- and homozygous SUMO-1 knockout mice exhibited ASDs and VSDs with high mortality rates, which were rescued by cardiac reexpression of the SUMO-1 transgene. Because SUMO-1 was also involved in cleft lip/palate in human patients, the previous findings provided a powerful rationale to question whether SUMO-1 was mutated in infants born with cleft palates and ASDs. Sequence analysis of DNA from newborn screening blood spots revealed a single 16 bp substitution in the SUMO-1 regulatory promoter of a patient displaying both oral-facial clefts and ASDs. Diminished sumoylation activity whether by genetics, environmental toxins, and/or pharmaceuticals may significantly contribute to susceptibility to the induction of congenital heart disease worldwide.
   

 Physiol Genomics. 2011, 43(9):488-98. doi: 10.1152/physiolgenomics.00248.2010.
 Effects of in vivo transfection with anti-miR-214 on gene expression in murine molar tooth germ
 
 
 Sehic A, Risnes S, Khuu C, Khan QE, Osmundsen H.
  Abstract
MicroRNAs (miRNAs) are an abundant class of noncoding RNAs that are believed to be important in many biological processes through regulation of gene expression. Little is known of their function in tooth morphogenesis and differentiation. MicroRNA-214 (miR-214), encoded by the polycistronic Dnm30os gene, is highly expressed during development of molar tooth germ and was selected as a target for silencing with anti-miR-214. Mandibular injection of 1-100 pmol of anti-miR-214 close to the developing first molar in newborn mice resulted in significant decrease in expression of miR-214, miR-466h, and miR-574-5p in the tooth germ. Furthermore, levels of miR-199a-3p, miR-199a-5p, miR-690, miR-720, and miR-1224 were significantly increased. Additionally, the expression of 863 genes was significantly increased and the expression of 305 genes was significantly decreased. Among the genes with increased expression was Twist-1 and Ezh2, suggested to regulate expression of miR-214. Microarray results were validated using real-time RT-PCR and Western blotting. Among genes with decreased expression were Amelx, Calb1, Enam, and Prnp; these changes also being reflected in levels of corresponding encoded proteins in the tooth germ. In the anti-miR-214-treated molars the enamel exhibited evidence of hypomineralization with remnants of organic material and reduced surface roughness after acid etching, possibly due to the transiently decreased expression of Amelx and Enam. In contrast, several genes encoding contractile proteins exhibited significantly increased expression. mRNAs involved in amelogenesis (Ambn, Amelx, Enam) were not found among targets of miRNAs that were differentially expressed following treatment with anti-miR-214. It is therefore suggested that effects of miR-214 on amelogenesis are indirect, perhaps mediated by the observed miR-214-dependent changes in levels of expression of numerous transcription factors.
   

 Methods Mol Biol. 2009;590:165-76.
 Methylated DNA Immunoprecipitation and Microarray-Based Analysis: Detection of DNA Methylation in Breast Cancer Cell Lines
 
 
 Tim H. M. Huang, and Pearlly S. Yan, Yu-I Weng
  Abstract
The methylated DNA immunoprecipitation microarray (MeDIP-chip) is a genome-wide, high-resolution approach to detect DNA methylation in whole genome or CpG (cytosine base followed by a guanine base) islands. The method utilizes anti-methylcytosine antibody to immunoprecipitate DNA that contains highly methylated CpG sites. Enriched methylated DNA can be interrogated using DNA microarrays or by massive parallel sequencing techniques. This combined approach allows researchers to rapidly identify methylated regions in a genome-wide manner, and compare DNA methylation patterns between two samples with diversely different DNA methylation status. MeDIP-chip has been applied successfully for analyses of methylated DNA in the different targets including animal and plant tissues. Here we present a MeDIP-chip protocol that is routinely used in our laboratory, illustrated with specific examples from MeDIP-chip analysis of breast cancer cell lines. Potential technical pitfalls and solutions are also provided to serve as workflow guidelines.
   

 Cell Research. 2011, 21(1):196-204. doi: 10.1038/cr.2010.142.
 Generation of iPSCs from mouse fibroblasts with a single gene, Oct4, and small molecules.
 
 
 Yanqin Li , Qiang Zhang , Xiaolei Yin , Weifeng Yang , Yuanyuan Du , Pingping Hou , Jian Ge , Chun Liu, Weiqi Zhang, Xu Zhang1,, Yetao Wu1,, Honggang Li, Kang Liu, Chen Wu1,, Zhihua Song, Yang Zhao, Yan Shi, Hongkui Deng.
  Abstract
The introduction of four transcription factors Oct4, Klf4, Sox2 and c-Myc by viral transduction can induce reprogramming of somatic cells into induced pluripotent stem cells (iPSCs), but the use of iPSCs is hindered by the use of viral delivery systems. Chemical-induced reprogramming offers a novel approach to generating iPSCs without any viral vector-based genetic modification. Previous reports showed that several small molecules could replace some of the reprogramming factors although at least two transcription factors, Oct4 and Klf4, are still required to generate iPSCs from mouse embryonic fibroblasts. Here, we identify a specific chemical combination, which is sufficient to permit reprogramming from mouse embryonic and adult fibroblasts in the presence of a single transcription factor, Oct4, within 20 days, replacing Sox2, Klf4 and c-Myc. The iPSCs generated using this treatment resembled mouse embryonic stem cells in terms of global gene expression profile, epigenetic status and pluripotency both in vitro and in vivo. We also found that 8 days of Oct4 induction was sufficient to enable Oct4-induced reprogramming in the presence of the small molecules, which suggests that reprogramming was initiated within the first 8 days and was independent of continuous exogenous Oct4 expression. These discoveries will aid in the future generation of iPSCs without genetic modification, as well as elucidating the molecular mechanisms that underlie the reprogramming process.
   

 Invest Ophthalmol Vis Sci. 2011, 25;52(1):527-40. doi: 10.1167/iovs.10-5731.
 Sigma receptor 1 modulates ER stress in retinal neurons.
 
 
 Yonju Ha, Ying Dun, Muthusamy Thangaraju, Jennifer N Duplantier, Zheng Dong, Kebin Liu, Vadivel Ganapathy, Sylvia B Smith
  Abstract
To investigate the mechanism of £m receptor 1 (£mR1) neuroprotection in retinal neurons. Oxidative stress, which is implicated in diabetic retinopathy, was induced in mouse primary ganglion cells (GCs) and RGC-5 cells, and the effect of the £mR1 ligand (+)-pentazocine on pro- and anti-apoptotic and endoplasmic reticulum (ER) stress gene expression was examined. Binding of £mR1 to BiP, an ER chaperone protein, and £mR1 phosphorylation status were examined by immunoprecipitation. Retinas were harvested from Ins2Akita/+ diabetic mice treated with (+)-pentazocine, and the expression of ER stress genes and of the retinal transcriptome was evaluated. Oxidative stress induced the death of primary GCs and RGC-5 cells. The effect was decreased by the application of (+)-pentazocine. Stress increased £mR1 binding to BiP and enhanced £mR1 phosphorylation in RGC-5 cells. BiP binding was prevented, and £mR1 phosphorylation decreased in the presence of (+)-pentazocine. The ER stress proteins PERK, ATF4, ATF6, IRE1£, and CHOP were upregulated in RGC-5 cells during oxidative stress, but decreased in the presence of (+)-pentazocine. A similar phenomenon was observed in retinas of Ins2Akita/+ diabetic mice. Retinal transcriptome analysis of Ins2Akita/+ mice compared with wild-type revealed differential expression of the genes critically involved in oxidative stress, differentiation, and cell death. The expression profile of those genes was reversed when the Ins2Akita/+ mice were treated with (+)-pentazocine. In retinal neurons, the molecular chaperone £mR1 binds BiP under stressful conditions; (+)-pentazocine may exert its effects by dissociating £mR1 from BiP. As stress in retinal cells increases, phosphorylation of £mR1 is increased, which is attenuated when agonists bind to the receptor.
   

 Journal of Environmental Science and Health. 2010, 28(1):60-87. doi: 10.1080/10590500903585416.
 Gene Expression Profiling as an Initial Approach for Mechanistic Studies of Toxicity and Tumorigenicity of Herbal Plants and Herbal Dietary Supplements.
 
 
 Nan Mei, Qingsu Xia, Tao Chen, Po-Chuen Chan, Peter P. Fu, Lei Guo
  Abstract
Dietary supplements are consumed by more than 300 million people worldwide, and herbal dietary supplements represent the most rapidly growing portion of this industry. Even though adverse health effects of many herbal dietary supplements have been reported, safety assurances are not being addressed adequately. Toxicological data on the identification of genotoxic and tumorigenic ingredients in many raw herbs are also lacking. Currently, more than 30 herbal dietary supplements and active ingredients have been selected by the National Toxicology Program (NTP) for toxicity and tumorigenicity studies. Due to the complexity of the chemical components present in plant extracts, there are no established methodologies for determining the mechanisms of toxicity (particularly tumorigenicity) induced by herbs, such as Gingko biloba leaf extract (GBE) and other herbal plant extracts. Consequently, the understanding of toxicity of herbal dietary supplements remains limited. We have proposed that application of DNA microarrays could be a highly practical initial approach for revealing biological pathways and networks associated with toxicity induced by herbal dietary supplements and the generation of hypotheses to address likely mechanisms. The changes in expression of subsets of genes of interest, such as the modulation of drug metabolizing genes, can be analyzed after treatment with an herbal dietary supplement. Although levels of gene expression do not represent fully the levels of protein activities, we propose that subsequent biochemical and genomic experiments based on these initial observations will enable elucidation of the mechanisms leading to toxicity, including tumorigenicity. This review summarizes the current practices of microarray analysis of gene expressions in animals treated with herbal dietary supplements and discusses perspectives for the proposed strategy.
   

 Biomedicine & Pharmacotherapy. 2011, 65(5):339-44. doi: 10.1016/j.biopha.2011.04.013.
 Interleukin 1 receptor antagonist reduces lethality and intestinal toxicity of 5-?uorouracil in a mouse mucositis model.
 
 
 Zhenqian Wu, Xiaodong Han, Shenyin Qin, Qi Zheng, Zhigang Wang, Di Xiang, Jing Zhang, Huili Lu, Mingyuan Wu, Shunying Zhu, Yan Yu, Yu Wang and Wei Han.
  Abstract
Chemotherapy-induced intestinal mucositis is still an unmet medical problem. 5-Fluorouracil (5-Fu), a chemotherapy drug, was used to create the animal model of mucositis. Global gene expression array was applied to identify genetic signals involved in the pathogenesis of mucositis. Interleukin 1 receptor antagonist (IL-1Ra) was one of the candidates with the characteristic gene expression profile. Its temporal expression pattern correlated to the damage and regeneration phase of the small intestine after a single injection of 5-Fu to mice. Administration of recombinant IL-1Ra to the mouse model of intestinal mucositis induced by 5-Fu demonstrated its therapeutic effects to the symptoms and pathology of the disease. The IL-1Ra treatment reduced the acute lethality, accelerated their body weight recovery, and eliminated severe diarrhea. The symptomatic benefits were supported by the pathological benefits, in which the mice treated with IL-1Ra had less damage and faster recovery of the structure integrity of their small intestine than that of the mice treated with vehicle control. To deliver the therapeutics to the unmet medical condition, further mechanism and translational studies of IL-1Ra in the settings of chemotherapy-induced intestinal mucositis are warranted.
   

 Journal of Ethnopharmacology. 2010, 132(2):429-37. doi: 10.1016/j.jep.2010.08.022.
 Application of bioactivity database of Chinese herbal medicine on the therapeutic prediction, drug development, and safety evaluation.
 
 
 Cheng HM, Li CC, Chen CY, Lo HY, Cheng WY, Lee CH, Yang SZ, Wu SL, Hsiang CY, Ho TY.
  Abstract
Chinese herbal medicine has been used for the treatments of various diseases for years. However, it is often difficult to analyze their biological activities and molecule mechanisms because of their complex nature. In this study, we applied DNA microarray to analyze the biological events induced by herbal formulae, predict the therapeutic potentials of formulae, and evaluate the safety of formulae. Mice were administrated orally with 15 formulae for 7 consecutive days, and the gene expression profiles in liver or kidney were further analyzed by transcriptomic tools. Our data showed that most formulae altered the metabolic pathways, such as glutathione metabolism and oxidative phosphorylation, and regulatory pathways, such as antigen processing and presentation and insulin-like growth factor signaling pathway. By comparing the gene expression signatures of formulae with those of disease states or drugs, we found that mice responsive to formula treatments might be related to disease states, especially metabolic and cardiovascular diseases, and drugs, which exhibit anti-cancer, anti-inflammatory, and anti-oxidative effects. Moreover, most formulae altered the expression levels of cytochrome p450, glutathione S-transferase, and UDP glycosyltransferase genes, suggesting that caution should be paid to possible drug interaction of these formulae. Furthermore, the similarities of gene expression profiles between formulae and toxic chemicals were low in kidney, suggesting that these formulae might not induce nephrotoxicities in mice. This report applied transcriptomic tools as a novel platform of translational medicine for Chinese herbal medicine. This platform will not only for understanding the therapeutic mechanisms involving herbal formulae and gene interactions, but also for the new theories in drug discovery.
   

 PNAS. 2010, 107(21):9753-8. doi: 10.1073/pnas.0912585107.
 Pitx2 prevents susceptibility to atrial arrhythmias by inhibiting left-sided pacemaker specification.
 
 
 Wang J, Klysik E, Sood S, Johnson RL, Wehrens XH, Martin JF
  Abstract
Atrial fibrillation (AF), the most prevalent sustained cardiac arrhythmia, often coexists with the related arrhythmia atrial flutter (AFL). Limitations in effectiveness and safety of current therapies make an understanding of the molecular mechanism underlying AF more urgent. Genome-wide association studies implicated a region of human chromosome 4q25 in familial AF and AFL, approximately 150 kb distal to the Pitx2 homeobox gene, a developmental left-right asymmetry (LRA) gene. To investigate the significance of the 4q25 variants, we used mouse models to investigate Pitx2 in atrial arrhythmogenesis directly. When challenged by programmed stimulation, Pitx2(null+/-) adult mice had atrial arrhythmias, including AFL and atrial tachycardia, indicating that Pitx2 haploinsufficiency predisposes to atrial arrhythmias. Microarray and in situ studies indicated that Pitx2 suppresses sinoatrial node (SAN)-specific gene expression, including Shox2, in the left atrium of embryos and young adults. In vivo ChIP and transfection experiments indicated that Pitx2 directly bound Shox2 in vivo, supporting the notion that Pitx2 directly inhibits the SAN-specific genetic program in left atrium. Our findings implicate Pitx2 and Pitx2-mediated LRA-signaling pathways in prevention of atrial arrhythmias.
   

 Eur J Oral Sci. 2010, 118(2):118-30. doi: 10.1111/j.1600-0722.2010.00722.x.
 Gene expression and dental enamel structure in developing mouse incisor.
 
 
 Risnes S, Khan QE, Khuu C, Osmundsen H, Amer Sehic
  Abstract
At the mouse incisor tip the initially differentiated ameloblasts produce a thin, prism-free enamel, while further apically, in the immediate adjacent segment, the enamel thickness increases and the four-layered enamel of mouse incisor is formed. Comparative gene-expression profiling was carried out on RNA isolated from these two segments of incisor tooth germs at embryonic day (E)17.5 and at postnatal days (P)0, 1, 2, and 10 using microarrays to measure messenger RNA (mRNA) and microRNA (miRNA) species present in the segments. Validation of expression data was achieved using real-time reverse transcription-polymerase chain reaction (RT-PCR) and western blotting. Bioinformatic data suggested enhanced cellular apoptosis in the incisal tip segment, which, together with diminished expression of the Amelx and Enam genes, may contribute to the production of the thin enamel seen in this tooth segment. For genes exhibiting higher levels of expression in the adjacent segment where complex enamel is being formed, bioinformatic analysis suggested significant associations with cellular functions involving the actin cytoskeleton, cellular development, morphology, and movement. This is suggested to reflect that ameloblasts with Tomes' process are being organized in transverse rows, facilitating the transverse movement that results in prism decussation in the inner enamel of the adjacent segment. Bioinformatic analysis of miRNA expression data lends support to these suggestions.
   

 Nanotechnology. 2010, 21(17):175101. doi: 10.1088/0957-4484/21/17/175101.
 Long-term hepatotoxicity of polyethylene-glycol functionalized multi-walled carbon nanotubes in mice.
 
 
 Zhang D, Deng X, Ji Z, Shen X, Gu T, Liu Y, Dong L, Wu M
  Abstract
The toxicity of polyethylene-glycol functionalized (PEGylated) multi-walled carbon nanotubes (MWCNTs) and non-PEGylated MWCNTs in vivo was evaluated and compared. Mice were exposed to MWCNTs by intravenous injection. The activity level of glutathione, superoxide dismutase and gene expression in liver, as well as some biochemical parameters and the tumor necrosis factor alpha level in blood were measured over 2 months. The pathological and electron micrographic observations of liver evidently indicate that the damage caused by non-PEGylated MWCNTs is slightly more severe than that of PEGylated MWCNTs, which means that PEGylation can partly, but not substantially, improve the in vivo biocompatibility of MWCNTs.
   

 OMICS: A Journal of Integrative Biology. 2010, 14(1):75-90. doi: 10.1089/omi.2009.0115.
 Ginkgo Biloba Extract Induces Gene Expression Changes in Xenobiotics Metabolism and the Myc-Centered Network.
 
 
 Nan Mei, Wayne Liao, Po-Chuen Chan, Peter P. Fu, Lei Guo
  Abstract
The use of herbal dietary supplements in the United States is rapidly growing, and it is crucial that the quality and safety of these preparations be ensured. To date, it is still a challenge to determine the mechanisms of toxicity induced by mixtures containing many chemical components, such as herbal dietary supplements. We previously proposed that analyses of the gene expression profiles using microarrays in the livers of rodents treated with herbal dietary supplements is a potentially practical approach for understanding the mechanism of toxicity. In this study, we utilized microarrays to analyze gene expression changes in the livers of male B6C3F1 mice administered Ginkgo biloba leaf extract (GBE) by gavage for 2 years, and to determine pathways and mechanisms associated with GBE treatments. Analysis of 31,802 genes revealed that there were 129, 289, and 2,011 genes significantly changed in the 200, 600, and 2,000 mg/kg treatment groups, respectively, when compared with control animals. Drug metabolizing genes were significantly altered in response to GBE treatments. Pathway and network analyses were applied to investigate the gene relationships, functional clustering, and mechanisms involved in GBE exposure. These analyses indicate alteration in the expression of genes coding for drug metabolizing enzymes, the NRF2-mediated oxidative stress response pathway, and the Myc gene-centered network named "cell cycle, cellular movement, and cancer" were found. These results indicate that Ginkgo biloba-related drug metabolizing enzymes may cause herb-drug interactions and contribute to hepatotoxicity. In addition, the outcomes of pathway and network analysis may be used to elucidate the toxic mechanisms of Ginkgo biloba.
   

 FOOD CHEM TOXICOL. 2010, 48(2):686-96. doi: 10.1016/j.fct.2009.11.050.
 Gene expression profiling in male B6C3F1 mouse livers exposed to kava identifies ¡V Changes in drug metabolizing genes and potential mechanisms linked to kava toxicity.
 
 
 Qiang Shi, Stacey Dial, Qingsu Xia, Nan Mei, Quan-Zhen Li, Po-Chuen Chan, Peter P. Fu, Lei Guo
  Abstract
The association of kava products with liver-related health risks has prompted regulatory action in many countries. We used a genome-wide gene expression approach to generate global gene expression profiles from the livers of male B6C3F1 mice administered kava extract by gavage for 14 weeks, and identified the differentially expressed drug metabolizing genes in response to kava treatments. Analyses of gene functions and pathways reveal that the levels of significant numbers of genes involving drug metabolism were changed and that the pathways involving xenobiotics metabolism, Nrf2-mediated oxidative stress response, mitochondrial functions and others, were altered. Our results indicate that kava extract can significantly modulate drug metabolizing enzymes, potentially leading to herb-drug interactions and hepatotoxicity.
   

 Biomaterials. 2009, 30(17):3042-3049. doi: 10.1016/j.biomaterials.2009.02.016.
 Nuclear factor-£eB bioluminescence imaging-guided transcriptomic analysis for the assessment of host¡Vbiomaterial interaction in vivo
 
 
 Chien-Yun Hsiang, Yueh-Sheng Chen, Tin-Yun Ho
  Abstract
Establishment of a comprehensive platform for the assessment of host¡Vbiomaterial interaction in vivo is an important issue. Nuclear factor-kB (NF-kB) is an inducible transcription factor that is activated by numerous stimuli. Therefore, NF-kB-dependent luminescent signal in transgenic mice carrying the luciferase genes was used as the guide to monitor the biomaterials-affected organs, and transcriptomic analysis was further applied to evaluate the complex host responses in affected organs in this study. In vivo imaging showed that genipin-cross-linked gelatin conduit (GGC) implantation evoked the strong NF-kB activity at 6 h in the implanted region, and transcriptomic analysis showed that the expressions of interleukin-6 (IL-6), IL-24, and IL-1 family were up-regulated. A strong luminescent signal was observed in spleen on 14 d, suggesting that GGC implantation might elicit the biological events in spleen. Transcriptomic analysis of spleen showed that 13 Kyoto Encyclopedia of Genes and Genomes pathways belonging to cell cycles, immune responses, and metabolism were significantly altered by GGC implants. Connectivity Map analysis suggested that the gene signatures of GGC were similar to those of compounds that affect lipid or glucose metabolism. GeneSetTest analysis further showed that host responses to GGC implants might be related to diseases states, especially the metabolic and cardiovascular diseases. In conclusion, our data provided a concept of molecular imaging-guided transcriptomic platform for the evaluation and the prediction of host¡Vbiomaterial interaction in vivo.
   

 Nanotechnology. 2009, 20(44):445101. doi: 10.1088/0957-4484/20/44/445101.
 The hepatotoxicity of multi-walled carbon nanotubes in mice
 
 
 Zongfei Ji, Danying Zhang, Ling Li, Xizhong Shen, Minhong Wu, Yuanfang Liu, Xiaoyong Deng, Ling Dong
  Abstract
The hepatotoxicity of two types of multi-walled carbon nanotubes (MWCNTs), acid-oxidized MWCNTs (O-MWCNTs) and Tween-80-dispersed MWCNTs (T-MWCNTs), were investigated with Kunming mice exposed to 10 and 60 mg kg(-1) by intravenous injection for 15 and 60 d. Compared with the PBS group, the body-weight gain of the mice decreased and the level of total bilirubin and aspartate aminotransferase increased in the MWCNT-exposed group with a significant dose-effect relationship, while tumor necrosis factor alpha level did not show significant statistical change within 60 d. Spotty necrosis, inflammatory cell infiltration in portal region, hepatocyte mitochondria swelling and lysis were observed with a significant dose-effect relationship in the MWCNT groups. Liver damage of the T-MWCNT group was more severe than that of the O-MWCNT group according to the Roenigk classification system. Furthermore, T-MWCNTs induce slight liver oxidative damage in mice at 15 d, which was recovered at 60 d. Part of the gene expressions of mouse liver in the MWCNT groups changed compared to the PBS group, including GPCRs (G protein-coupled receptors), cholesterol biosynthesis, metabolism by cytochrome P450, natural-killer-cell-mediated cytotoxicity, TNF- alpha, NF-kappaB signaling pathway, etc. In the P450 pathway, the gene expressions of Gsta2 (down-regulated), Cyp2B19 (up-regulated) and Cyp2C50 (down-regulated) had significant changes in the MWCNT groups. These results show that a high dose of T-MWCNTs can induce hepatic toxicity in mice while O-MWCNTs seem to have less toxicity.
   

 BLOOD. 2009, 114(15):3181-90. doi: 10.1182/blood-2009-02-205708.
 Characterization of Gaucher disease bone marrow mesenchymal stromal cells reveals an altered in?ammatory secretome.
 
 
 Philippe M. Campeau, Moutih Rafei, Marie-No ?le Boivin, Ying Sun, Gregory A. Grabowski, Jacques Galipeau
  Abstract
Gaucher disease causes pathologic skeletal changes that are not fully explained. Considering the important role of mesenchymal stromal cells (MSCs) in bone structural development and maintenance, we analyzed the cellular biochemistry of MSCs from an adult patient with Gaucher disease type 1 (N370S/L444P mutations). Gaucher MSCs possessed a low glucocerebrosidase activity and consequently had a 3-fold increase in cellular glucosylceramide. Gaucher MSCs have a typical MSC marker phenotype, normal osteocytic and adipocytic differentiation, growth, exogenous lactosylceramide trafficking, cholesterol content, lysosomal morphology, and total lysosomal content, and a marked increase in COX-2, prostaglandin E2, interleukin-8, and CCL2 production compared with normal controls. Transcriptome analysis on normal MSCs treated with the glucocerebrosidase inhibitor conduritol B epoxide showed an up-regulation of an array of inflammatory mediators, including CCL2, and other differentially regulated pathways. These cells also showed a decrease in sphingosine-1-phosphate. In conclusion, Gaucher disease MSCs display an altered secretome that could contribute to skeletal disease and immune disease manifestations in a manner distinct and additive to Gaucher macrophages themselves.
   

 Biochemical and Biophysical Research Communications. 2009, 387(3):611-6. doi: 10.1016/j.bbrc.2009.07.093.
 An essential role for DNA methyltransferase 3a in melanoma tumorigenesis.
 
 
 Tao Deng, Ying Kuang, Long Wang, Jiang Li, Zhugang Wang, Jian Fei
  Abstract
Abnormal DNA methylation and associated silencing of tumor suppressor genes are common to many types of cancers. Among the three coordinate DNA methyltransferases (Dnmts), Dnmt1 and Dnmt3b were both shown to be important for cancer cell survival and tumorigenesis. However, the relationship between Dnmt3a and tumorigenesis is still largely unknown. Here, we show that inhibition of Dnmt3a expression, by stable transfection of a Dnmt3a-RNA interference (RNAi) construct dramatically inhibited melanoma growth and metastasis in mouse melanoma models. Microarray analysis revealed that genes critical for the tumor immune response, were implicated in the inhibition of melanoma growth. Expression of a cluster of class I and class II MHC genes, class II transactivator (Ciita), as well as a subset of 5 chemokines (Cxcl9, Cxcl16, Ccl12, Ccl4, and Ccl2) were up-regulated. Furthermore, we determined that the promoter IV of Ciita was significantly demethylated in Dnmt3a-depleted tumors. In addition, several known tumor-related genes, which are critical for developmental processes and cell cycle, were confirmed to be misregulated, including TgfB1, Socs1, Socs2, E2F6, Ccne1, and Cyr61. The results presented in this report strongly suggest that Dnmt3a plays an essential role in melanoma tumorigenesis, and that the underlying mechanisms include the modulation of the tumor immune response, as well as other processes.
   

 Biomaterials. 2009, 30(17):3042-9. doi: 10.1016/j.biomaterials.2009.02.016.
 Nuclear factor-kB bioluminescence imaging-guided transcriptomic analysis for the assessment of host¡Vbiomaterial interaction in vivo.
 
 
 Hsiang CY, Chen YS, Ho TY.
  Abstract
Establishment of a comprehensive platform for the assessment of host-biomaterial interaction in vivo is an important issue. Nuclear factor-kappaB (NF-kappaB) is an inducible transcription factor that is activated by numerous stimuli. Therefore, NF-kappaB-dependent luminescent signal in transgenic mice carrying the luciferase genes was used as the guide to monitor the biomaterials-affected organs, and transcriptomic analysis was further applied to evaluate the complex host responses in affected organs in this study. In vivo imaging showed that genipin-cross-linked gelatin conduit (GGC) implantation evoked the strong NF-kappaB activity at 6h in the implanted region, and transcriptomic analysis showed that the expressions of interleukin-6 (IL-6), IL-24, and IL-1 family were up-regulated. A strong luminescent signal was observed in spleen on 14 d, suggesting that GGC implantation might elicit the biological events in spleen. Transcriptomic analysis of spleen showed that 13 Kyoto Encyclopedia of Genes and Genomes pathways belonging to cell cycles, immune responses, and metabolism were significantly altered by GGC implants. Connectivity Map analysis suggested that the gene signatures of GGC were similar to those of compounds that affect lipid or glucose metabolism. GeneSetTest analysis further showed that host responses to GGC implants might be related to diseases states, especially the metabolic and cardiovascular diseases. In conclusion, our data provided a concept of molecular imaging-guided transcriptomic platform for the evaluation and the prediction of host-biomaterial interaction in vivo.
   

 Journal of Ethnopharmacology. 2009, 123(1):68-73. doi: 10.1016/j.jep.2009.02.027.
 Transcriptomic analysis of EGb 761-regulated neuroactive receptor pathway in vivo.
 
 
 Su SY, Hsieh CL, Wu SL, Cheng WY, Li CC, Lo HY, Ho TY, Hsiang CY.
  Abstract
Although EGb 761 exhibits neuroprotective effects and exerts beneficial effects on many neurological disorders, its mechanism on the neuronal functions is unclear so far. In this study, we used oligonucleotide microarray technique to investigate the effect of EGb 761 on the transcriptional profile of mouse genes. RNA samples were obtained from frontal cortex, straitum, and kidneys after the oral administration of EGb 761 for seven consecutive days. Our data showed that EGb 761 significantly altered the neuroactive ligand-receptor interaction pathway in frontal cortex but not in straitum and kidney. Then we analyzed 26 receptor genes that were significantly altered by EGb 761 in this pathway and found that EGb 761 treatment highly up-regulated the subgroup of dopamine receptors, especially dopamine receptor 1a (Drd1a), in frontal cortex. Quantitative real-time reverse transcription-polymerase chain reaction and immunohistochemical staining confirmed the increased level of Drd1a expression after EGb 761 treatment. In summary, we investigated for the first time the overall effects of EGb 761 on the gene expression in brain using a powerful systemic biological technique. Our results suggested that EGb 761 altered unique pathways and regulated the expressions of some specific neuronal receptor genes exclusively in frontal cortex.
   

 Environmental and Molecular Mutagenesis. 2008, 49(9):741-5. doi: 10.1002/em.20429.
 Gene Expression Changes Associated with Xenobiotic Metabolism Pathways in Mice Exposed to Acrylamide.
 
 
 Guo L, Tseng J, Dial SL, Liao W, Manjanatha MG, Mei N
  Abstract
The discovery of acrylamide (AA) in a variety of fried foods has raised public health concerns. In this study, groups of male mice were administered 500 mg/L AA in drinking water for 3 weeks, and gene expression changes were evaluated in the livers of AA-treated mice within 24 hr of the last treatment. When a two-fold cutoff value and a P-value less than 0.05 were selected, 696 genes (233 up-regulated and 463 down-regulated) were identified as differentially expressed genes in AA-treated mice when compared with the controls. Gene ontology analysis revealed that the principle pathways affected by AA were xenobiotic metabolism by cytochrome P450 (CYPs) and glutathione metabolism, suggesting that drug and/or xenobiotic metabolism is most affected by exposure. The results provide more information about AA metabolism and further insight into the molecular mechanisms involved in AA-induced toxicity.
   

 Cell Stem Cell. 2008, 3(5):475-9. doi: 10.1016/j.stem.2008.10.002.
 Two Supporting Factors Greatly Improve the Efficiency of Human iPSC Generation.
 
 
 hao Y, Yin X, Qin H, Zhu F, Liu H, Yang W, Zhang Q, Xiang C, Hou P, Song Z, Liu Y, Yong J, Zhang P, Cai J, Liu M, Li H, Li Y, Qu X, Cui K, Zhang W, Xiang T, Wu Y, Zhao Y, Liu C, Yu C, Yuan K, Lou J, Ding M, Deng H.
  Abstract
Human ?broblasts can be induced into pluripotent stem cells (iPSCs), but the reprogramming ef?ciency is quite low. Here, we screened a panel of candidate factors in the presence of OCT4, SOX2, KLF4, and c-MYC in an effort to improve the reprogramming ef?ciency from human adult ?broblasts. We found that p53 siRNA and UTF1 enhanced the ef?ciency of iPSC generation up to 100-fold, even when the oncogene c-MYC was removed from the combinations.