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Northrup V, Perez LJ, Edgett BA, Karakach T, Simpson JA, Brunt KR. Intron retention is a mechanism of erythropoietin regulation in brain cell models. Gene 2024; 898:148099. [PMID: 38128788 DOI: 10.1016/j.gene.2023.148099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Intron retention is a mechanism of post-transcriptional gene regulation, including genes involved in erythropoiesis. Erythropoietin (EPO) is a hormone without evidence of intracellular vesicle storage that regulates erythropoiesis. We hypothesize that EPO uses intron retention as a mechanism of post-transcriptional regulation in response to hypoxia and ischemia. Cell models of hypoxia and ischemia for kidney, liver, and brain cells were examined for intron retention by real time quantitative PCR. EPO expression increased in most cells except for blood brain barrier and liver cells. The intron retained transcript ratio decreased in brain cells, except for Astrocytes, but showed no change in kidney or liver after 24 h of ischemia. The shift in intron ratio was maintained when using poly (A) enriched cDNA, suggesting that intron retention is not due to immature transcripts. The expression of EPO was elevated at variable time points amongst cell models with the intron ratio also changing over a time course of 2 to 16 h after ischemia. We conclude that intron retention is a mechanism regulating EPO expression in response to ischemia in a tissue specific manner.
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Affiliation(s)
- Victoria Northrup
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada
| | - Lester J Perez
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada
| | - Brittany A Edgett
- Department of Kinesiology, University of Calgary, Calgary, Alberta, Canada; IMPART investigator team Canada
| | - Tobias Karakach
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; IMPART investigator team Canada
| | - Jeremy A Simpson
- Department of Human and Nutritional Science, University of Guelph, Guelph, Ontario, Canada; IMPART investigator team Canada
| | - Keith R Brunt
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada.
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2
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Zou C, Zan X, Jia Z, Zheng L, Gu Y, Liu F, Han Y, Xu C, Wu A, Zhi Q. Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives. Clin Transl Med 2023; 13:e1479. [PMID: 37983927 PMCID: PMC10659771 DOI: 10.1002/ctm2.1479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/07/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD). METHODS Our review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next-generation sequencing (NGS) for AS events in IBD have been also discussed. RESULTS Available evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis-associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro-fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third-generation sequencing (TGS), single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), will be desired with great expectations. CONCLUSIONS To our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.
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Affiliation(s)
- Chentao Zou
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xinquan Zan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhenyu Jia
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Lu Zheng
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yijie Gu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Fei Liu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Ye Han
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chunfang Xu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Airong Wu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qiaoming Zhi
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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3
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Zhou J, Zhang Q, Zhao Y, Song Y, Leng Y, Chen M, Zhou S, Wang Z. The regulatory role of alternative splicing in inflammatory bowel disease. Front Immunol 2023; 14:1095267. [PMID: 37153612 PMCID: PMC10160418 DOI: 10.3389/fimmu.2023.1095267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) mainly includes Crohn's disease and ulcerative colitis. These diseases have a progressive course of chronic relapse and remission and affect a large number of children and adults worldwide. The burden of IBD is rising worldwide, with levels and trends varying greatly in countries and regions. Like most chronic diseases, the costs associated with IBD are high, including hospitalizations, outpatient and emergency visits, surgeries, and pharmacotherapies. However, there is no radical cure for it yet, and its therapeutic targets still need further study. Currently, the pathogenesis of IBD remains unclear. It is generally assumed that the occurrence and development of IBD are related to the environmental factors, gut microbiota, immune imbalance, and genetic susceptibility. Alternative splicing contributes to a various diseases, such as spinal muscular atrophy, liver diseases, and cancers. In the past, it has been reported that alternative splicing events, splicing factors, and splicing mutations were associated with IBD, but there were no reports on the practical application for clinical diagnosis and treatment of IBD using splicing-related methods. Therefore, this article reviews research progress on alternative splicing events, splicing factors, and splicing mutations associated with IBD.
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Affiliation(s)
- Jianli Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Qiao Zhang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuzhen Zhao
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuchen Song
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yanan Leng
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Moxian Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Shaoming Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Zhaoxia Wang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
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4
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The Heterochromatin protein 1 is a regulator in RNA splicing precision deficient in ulcerative colitis. Nat Commun 2022; 13:6834. [PMID: 36400769 PMCID: PMC9674647 DOI: 10.1038/s41467-022-34556-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
Defects in RNA splicing have been linked to human disorders, but remain poorly explored in inflammatory bowel disease (IBD). Here, we report that expression of the chromatin and alternative splicing regulator HP1γ is reduced in ulcerative colitis (UC). Accordingly, HP1γ gene inactivation in the mouse gut epithelium triggers IBD-like traits, including inflammation and dysbiosis. In parallel, we find that its loss of function broadly increases splicing noise, favoring the usage of cryptic splice sites at numerous genes with functions in gut biology. This results in the production of progerin, a toxic splice variant of prelamin A mRNA, responsible for the Hutchinson-Gilford Progeria Syndrome of premature aging. Splicing noise is also extensively detected in UC patients in association with inflammation, with progerin transcripts accumulating in the colon mucosa. We propose that monitoring HP1γ activity and RNA splicing precision can help in the management of IBD and, more generally, of accelerated aging.
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Gárate-Rascón M, Recalde M, Rojo C, Fernández-Barrena MG, Ávila MA, Arechederra M, Berasain C. SLU7: A New Hub of Gene Expression Regulation—From Epigenetics to Protein Stability in Health and Disease. Int J Mol Sci 2022; 23:ijms232113411. [PMID: 36362191 PMCID: PMC9658179 DOI: 10.3390/ijms232113411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
SLU7 (Splicing factor synergistic lethal with U5 snRNA 7) was first identified as a splicing factor necessary for the correct selection of 3′ splice sites, strongly impacting on the diversity of gene transcripts in a cell. More recent studies have uncovered new and non-redundant roles of SLU7 as an integrative hub of different levels of gene expression regulation, including epigenetic DNA remodeling, modulation of transcription and protein stability. Here we review those findings, the multiple factors and mechanisms implicated as well as the cellular functions affected. For instance, SLU7 is essential to secure liver differentiation, genome integrity acting at different levels and a correct cell cycle progression. Accordingly, the aberrant expression of SLU7 could be associated with human diseases including cancer, although strikingly, it is an essential survival factor for cancer cells. Finally, we discuss the implications of SLU7 in pathophysiology, with particular emphasis on the progression of liver disease and its possible role as a therapeutic target in human cancer.
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Affiliation(s)
- María Gárate-Rascón
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
| | - Miriam Recalde
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
| | - Carla Rojo
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
| | - Maite G. Fernández-Barrena
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Matías A. Ávila
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - María Arechederra
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Carmen Berasain
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-948-194700; Fax: +34-948-194717
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6
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Boby N, Cao X, Ransom A, Pace BT, Mabee C, Shroyer MN, Das A, Didier PJ, Srivastav SK, Porter E, Sha Q, Pahar B. Identification, Characterization, and Transcriptional Reprogramming of Epithelial Stem Cells and Intestinal Enteroids in Simian Immunodeficiency Virus Infected Rhesus Macaques. Front Immunol 2021; 12:769990. [PMID: 34887863 PMCID: PMC8650114 DOI: 10.3389/fimmu.2021.769990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/02/2021] [Indexed: 12/18/2022] Open
Abstract
Epithelial cell injury and impaired epithelial regeneration are considered key features in HIV pathogenesis and contribute to HIV-induced generalized immune activation. Understanding the molecular mechanisms underlying the disrupted epithelial regeneration might provide an alternative approach for the treatment of HIV-mediated enteropathy and immune activation. We have observed a significant increased presence of α defensin5+ (HD5) Paneth cells and proliferating Ki67+ epithelial cells as well as decreased expression of E-cadherin expression in epithelial cells during SIV infection. SIV infection did not significantly influence the frequency of LGR5+ stem cells, but the frequency of HD5+ cells was significantly higher compared to uninfected controls in jejunum. Our global transcriptomics analysis of enteroids provided novel information about highly significant changes in several important pathways like metabolic, TCA cycle, and oxidative phosphorylation, where the majority of the differentially expressed genes were downregulated in enteroids grown from chronically SIV-infected macaques compared to the SIV-uninfected controls. Despite the lack of significant reduction in LGR5+ stem cell population, the dysregulation of several intestinal stem cell niche factors including Notch, mTOR, AMPK and Wnt pathways as well as persistence of inflammatory cytokines and chemokines and loss of epithelial barrier function in enteroids further supports that SIV infection impacts on epithelial cell proliferation and intestinal homeostasis.
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Affiliation(s)
- Nongthombam Boby
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, United States
| | - Alyssa Ransom
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Barcley T Pace
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Christopher Mabee
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Monica N Shroyer
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, United States
| | - Arpita Das
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA, United States
| | - Peter J Didier
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Sudesh K Srivastav
- Department of Biostatistics, Tulane University, New Orleans, LA, United States
| | - Edith Porter
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA, United States
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, United States
| | - Bapi Pahar
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States.,Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States.,Department of Tropical Medicine, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, United States
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7
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Li D, Tan Y. Dysregulation of alternative splicing is associated with the pathogenesis of ulcerative colitis. Biomed Eng Online 2021; 20:121. [PMID: 34838026 PMCID: PMC8627048 DOI: 10.1186/s12938-021-00959-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
Background Although numerous risk loci for ulcerative colitis (UC) have been identified in the human genome, the pathogenesis of UC remains unclear. Recently, multiple transcriptomic analyses have shown that aberrant gene expression in the colon tissues of UC patients is associated with disease progression. A pioneering study also demonstrated that altered post-transcriptional regulation is involved in the progression of UC. Here, we provide a genome-wide analysis of alternative splicing (AS) signatures in UC patients. We analyzed three datasets containing 74 tissue samples from UC patients and identified over 2000 significant AS events. Results Skipped exon and alternative first exon were the two most significantly altered AS events in UC patients. The immune response-related pathways were remarkably enriched in the UC-related AS events. Genes with significant AS events were more likely to be dysregulated at the expression level. Conclusions We present a genomic landscape of AS events in UC patients based on a combined analysis of two cohorts. Our results indicate that dysregulation of AS may have a pivotal role in determining the pathogenesis of UC. In addition, our study uncovers genes with potential therapeutic implications for UC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12938-021-00959-4.
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Affiliation(s)
- Daowei Li
- Department of Radiology, The People's Hospital of China Medical University & The People's Hospital of Liaoning Province, No. 33, Wenyi Road, Shenhe District, Shenyang, 110016, China
| | - Yue Tan
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Tiexi District, 39 Huaxiang Road, Shenyang, 110022, China.
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8
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Li D, Liang Y, Lu J, Tan Y. An alternative splicing signature in human Crohn's disease. BMC Gastroenterol 2021; 21:420. [PMID: 34749666 PMCID: PMC8573860 DOI: 10.1186/s12876-021-02001-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/26/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Although hundreds of risk loci for Crohn's disease (CD) have been identified, the underlying pathogenesis of CD remains unclear. Recently, evidence has shown that aberrant gene expression in colon tissues of CD patients is associated with the progression of CD. We reasoned that post-transcriptional regulation, especially alternative splicing (AS), may also play important roles in the pathogenesis of CD. METHODS We re-analyzed public mRNA-seq data from the NCBI GEO dataset (GSE66207) and identified approximately 3000 unique AS events in CD patients compared to healthy controls. RESULTS "Lysine degradation" and "Sphingolipid metabolism" were the two most enriched AS events in CD patients. In a validation study, we also sequenced eight subjects and demonstrated that key genes that were previously linked to CD, such as IRF1 and STAT3, also had significant AS events in CD. CONCLUSION Our study provided a landscape of AS events in CD, especially as the first study focused on a Chinese cohort. Our data suggest that dysregulation of AS may be a new mechanism that contributes to the pathogenesis of CD.
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Affiliation(s)
- Daowei Li
- Department of Radiology, The People's Hospital of China Medical University and The People's Hospital of Liaoning Province, No. 33, Wenyi Road, Shenhe District, Shenyang, 110016, China
| | - Yuanzi Liang
- Department of Radiology, The People's Hospital of China Medical University and The People's Hospital of Liaoning Province, No. 33, Wenyi Road, Shenhe District, Shenyang, 110016, China
| | - Jia Lu
- Department of Radiology, The People's Hospital of China Medical University and The People's Hospital of Liaoning Province, No. 33, Wenyi Road, Shenhe District, Shenyang, 110016, China
| | - Yue Tan
- Department of Gastroenterology, Shengjing Hospital of China Medical University, 39 Huaxiang Road, Tiexi District, Shenyang, 110022, China.
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9
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Huang R, Wang S, Zhu R, Xian S, Huang Z, Cheng L, Zhang J. Identification of Key eRNAs for Spinal Cord Injury by Integrated Multinomial Bioinformatics Analysis. Front Cell Dev Biol 2021; 9:728242. [PMID: 34708039 PMCID: PMC8542800 DOI: 10.3389/fcell.2021.728242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Spinal cord injury (SCI) is a severe neurological deficit affecting both young and older people worldwide. The potential role of key enhancer RNAs (eRNAs) in SCI remains elusive, which is a prominent challenge in the trauma repair process. This study aims to investigate the roles of key eRNAs, transcription factors (TFs), signaling pathways, and small-molecule inhibitors in SCI using multi-omics bioinformatics analysis. Methods: Microarray data of peripheral blood mononuclear cell (PBMC) samples from 27 healthy volunteers and 25 chronic-phase SCI patients were retrieved from the Gene Expression Omnibus database. Differentially expressed transcription factors (DETFs), differentially expressed enhancer RNAs (DEeRNAs), and differentially expressed target genes (DETGs) were identified using the Linear Models for Microarray Data (limma) package. Fraction of immune cells was estimated using CIBERSORT algorithm. Gene Set Variation Analysis (GSVA) was applied to identify the downstream signaling pathways. The eRNA regulatory network was constructed based on the correlation results. Connectivity Map (CMap) database was used to find potential drugs for SCI patients. The cellular communication analysis was performed to explore the molecular regulation mechanism of SCI based on single-cell RNA sequencing (scRNA-seq) data. Chromatin immunoprecipitation sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data were used to validate the key regulatory mechanisms. scRNA-seq dataset was used to validate the cell subtype localization of the key eRNAs. Results: In total, 21 DETFs, 24 DEeRNAs, and 829 DETGs were identified. A regulatory network of 13 DETFs, six DEeRNAs, seven DETGs, two hallmark pathways, two immune cells, and six immune pathways was constructed. The link of Splicing factor proline and glutamine rich (SFPQ) (TF) and vesicular overexpressed in cancer prosurvival protein 1 (VOPP1) (eRNA) (R = 0.990, p < 0.001, positive), VOPP1 (eRNA) and epidermal growth factor receptor (EGFR) (target gene) (R = 0.974, p < 0.001, positive), VOPP1, and T helper (Th) cells (R = -0.987, p < 0.001, negative), and VOPP1 and hallmark coagulation (R = 0.937, p < 0.001, positive) was selected. Trichostatin A was considered the best compound target to SCI-related eRNAs (specificity = 0.471, p < 0.001). Conclusion: VOPP1, upregulated by SFPQ, strengthened the transient expression of EGFR. Th cells and coagulation were the potential downstream pathways of VOPP1. This regulatory network and potential inhibitors provide novel diagnostic biomarkers and therapeutic targets for SCI.
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Affiliation(s)
- Runzhi Huang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai, China
| | - Rui Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Shuyuan Xian
- Tongji University School of Medicine, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liming Cheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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10
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Xiu MX, Liu YM, Chen GY, Hu C, Kuang BH. Identifying Hub Genes, Key Pathways and Immune Cell Infiltration Characteristics in Pediatric and Adult Ulcerative Colitis by Integrated Bioinformatic Analysis. Dig Dis Sci 2021; 66:3002-3014. [PMID: 32974809 DOI: 10.1007/s10620-020-06611-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/10/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS In the present study, we investigated the differentially expressed genes (DEGs), pathways and immune cell infiltration characteristics of pediatric and adult ulcerative colitis (UC). METHODS We conducted DEG analysis using the microarray dataset GSE87473 containing 19 pediatric and 87 adult UC samples downloaded from the Gene Expression Omnibus. Gene ontology and pathway enrichment analyses were conducted using Metascape. We constructed the protein-protein interaction (PPI) network and the drug-target interaction network of DEGs and identified hub modules and genes using Cytoscape and analyzed immune cell infiltration in pediatric and adult UC using CIBERSORT. RESULTS In total, 1700 DEGs were screened from the dataset. These genes were enriched mainly in inter-cellular items relating to cell junctions, cell adhesion, actin cytoskeleton and transmembrane receptor signaling pathways and intra-cellular items relating to the splicing, metabolism and localization of RNA. CDC42, POLR2A, RAC1, PIK3R1, MAPK1 and SRC were identified as hub DEGs. Immune cell infiltration analysis revealed higher proportions of naive B cells, resting memory T helper cells, regulatory T cells, monocytes, M0 macrophages and activated mast cells in pediatric UC, along with lower proportions of memory B cells, follicular helper T cells, γδ T cells, M2 macrophages, and activated dendritic cells. CONCLUSIONS Our study suggested that hub genes CDC42, POLR2A, RAC1, PIK3R1, MAPK1 and SRC and immune cells including B cells, T cells, monocytes, macrophages and mast cells play vital roles in the pathological differences between pediatric and adult UC and may serve as potential biomarkers in the diagnosis and treatment of UC.
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Affiliation(s)
- Meng-Xi Xiu
- Medical School of Nanchang University, 603 Bayi Road, Nanchang, 330006, Jiangxi, China
| | - Yuan-Meng Liu
- Medical School of Nanchang University, 603 Bayi Road, Nanchang, 330006, Jiangxi, China
| | - Guang-Yuan Chen
- Medical School of Nanchang University, 603 Bayi Road, Nanchang, 330006, Jiangxi, China
| | - Cong Hu
- Medical School of Nanchang University, 603 Bayi Road, Nanchang, 330006, Jiangxi, China
| | - Bo-Hai Kuang
- Medical School of Nanchang University, 603 Bayi Road, Nanchang, 330006, Jiangxi, China.
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11
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Park CY, Zhou J, Wong AK, Chen KM, Theesfeld CL, Darnell RB, Troyanskaya OG. Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk. Nat Genet 2021; 53:166-173. [PMID: 33462483 PMCID: PMC7886016 DOI: 10.1038/s41588-020-00761-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023]
Abstract
Despite the strong genetic basis of psychiatric disorders, the underlying molecular mechanisms are largely unmapped. RNA-binding proteins (RBPs) are responsible for most post-transcriptional regulation, from splicing to translation to localization. RBPs thus act as key gatekeepers of cellular homeostasis, especially in the brain. However, quantifying the pathogenic contribution of noncoding variants impacting RBP target sites is challenging. Here, we leverage a deep learning approach that can accurately predict the RBP target site dysregulation effects of mutations and discover that RBP dysregulation is a principal contributor to psychiatric disorder risk. RBP dysregulation explains a substantial amount of heritability not captured by large-scale molecular quantitative trait loci studies and has a stronger impact than common coding region variants. We share the genome-wide profiles of RBP dysregulation, which we use to identify DDHD2 as a candidate schizophrenia risk gene. This resource provides a new analytical framework to connect the full range of RNA regulation to complex disease.
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Affiliation(s)
- Christopher Y. Park
- Flatiron Institute, Simons Foundation, New York, New York, United States of America,()Corresponding authors: Olga G. Troyanskaya, , Christopher Y. Park,
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Aaron K. Wong
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Kathleen M. Chen
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Chandra L. Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Robert B. Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.,Howard Hughes Medical Institute
| | - Olga G. Troyanskaya
- Flatiron Institute, Simons Foundation, New York, New York, United States of America,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America,Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America,()Corresponding authors: Olga G. Troyanskaya, , Christopher Y. Park,
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12
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Monteuuis G, Schmitz U, Petrova V, Kearney PS, Rasko JEJ. Holding on to Junk Bonds: Intron Retention in Cancer and Therapy. Cancer Res 2020; 81:779-789. [PMID: 33046441 DOI: 10.1158/0008-5472.can-20-1943] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
Intron retention (IR) in cancer was for a long time overlooked by the scientific community, as it was previously considered to be an artifact of a dysfunctional spliceosome. Technological advancements made in the last decade offer unique opportunities to explore the role of IR as a widespread phenomenon that contributes to the transcriptional diversity of many cancers. Numerous studies in cancer have shed light on dysregulation of cellular mechanisms that lead to aberrant and pathologic IR. IR is not merely a mechanism of gene regulation, but rather it can mediate cancer pathogenesis and therapeutic resistance in various human diseases. The burden of IR in cancer is governed by perturbations to mechanisms known to regulate this phenomenon and include epigenetic variation, mutations within the gene body, and splicing factor dysregulation. This review summarizes possible causes for aberrant IR and discusses the role of IR in therapy or as a consequence of disease treatment. As neoepitopes originating from retained introns can be presented on the cancer cell surface, the development of personalized cancer vaccines based on IR-derived neoepitopes should be considered. Ultimately, a deeper comprehension about the origins and consequences of aberrant IR may aid in the development of such personalized cancer vaccines.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Veronika Petrova
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia
| | - Padraic S Kearney
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia. .,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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13
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Yang G, Ma A, Qin ZS, Chen L. Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules. Bioinformatics 2020; 36:2352-2358. [PMID: 31899481 DOI: 10.1093/bioinformatics/btz975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/29/2019] [Accepted: 12/30/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The availability of thousands of genome-wide coupling chromatin immunoprecipitation (ChIP)-Seq datasets across hundreds of transcription factors (TFs) and cell lines provides an unprecedented opportunity to jointly analyze large-scale TF-binding in vivo, making possible the discovery of the potential interaction and cooperation among different TFs. The interacted and cooperated TFs can potentially form a transcriptional regulatory module (TRM) (e.g. co-binding TFs), which helps decipher the combinatorial regulatory mechanisms. RESULTS We develop a computational method tfLDA to apply state-of-the-art topic models to multiple ChIP-Seq datasets to decipher the combinatorial binding events of multiple TFs. tfLDA is able to learn high-order combinatorial binding patterns of TFs from multiple ChIP-Seq profiles, interpret and visualize the combinatorial patterns. We apply the tfLDA to two cell lines with a rich collection of TFs and identify combinatorial binding patterns that show well-known TRMs and related TF co-binding events. AVAILABILITY AND IMPLEMENTATION A software R package tfLDA is freely available at https://github.com/lichen-lab/tfLDA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Guodong Yang
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P. R. China
| | - Aiqun Ma
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P. R. China
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Li Chen
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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14
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Thoo L, Noti M, Krebs P. Keep calm: the intestinal barrier at the interface of peace and war. Cell Death Dis 2019; 10:849. [PMID: 31699962 PMCID: PMC6838056 DOI: 10.1038/s41419-019-2086-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/11/2019] [Accepted: 10/23/2019] [Indexed: 12/19/2022]
Abstract
Epithelial barriers have to constantly cope with both harmless and harmful stimuli. The epithelial barrier therefore serves as a dynamic and not static wall to safeguard its proper physiological function while ensuring protection. This is achieved through multiple defence mechanisms involving various cell types - epithelial and non-epithelial - that work in an integrated manner to build protective barriers at mucosal sites. Damage may nevertheless occur, due to pathogens, physical insults or dysregulated immune responses, which trigger a physiologic acute or a pathologic chronic inflammatory cascade. Inflammation is often viewed as a pathological condition, particularly due to the increasing prevalence of chronic inflammatory (intestinal) diseases. However, inflammation is also necessary for wound healing. The aetiology of chronic inflammatory diseases is incompletely understood and identification of the underlying mechanisms would reveal additional therapeutic approaches. Resolution is an active host response to end ongoing inflammation but its relevance is under-appreciated. Currently, most therapies aim at dampening inflammation at damaged mucosal sites, yet these approaches do not efficiently shut down the inflammation process nor repair the epithelial barrier. Therefore, future treatment strategies should also promote the resolution phase. Yet, the task of repairing the barrier can be an arduous endeavour considering its multiple integrated layers of defence - which is advantageous for damage prevention but becomes challenging to repair at multiple levels. In this review, using the intestines as a model epithelial organ and barrier paradigm, we describe the consequences of chronic inflammation and highlight the importance of the mucosae to engage resolving processes to restore epithelial barrier integrity and function. We further discuss the contribution of pre-mRNA alternative splicing to barrier integrity and intestinal homeostasis. Following discussions on current open questions and challenges, we propose a model in which resolution of inflammation represents a key mechanism for the restoration of epithelial integrity and function.
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Affiliation(s)
- Lester Thoo
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Mario Noti
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland.,Department of Gastro-Intestinal Health, Immunology, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Philippe Krebs
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland.
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15
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Hewitt WM, Calabrese DR, Schneekloth JS. Evidence for ligandable sites in structured RNA throughout the Protein Data Bank. Bioorg Med Chem 2019; 27:2253-2260. [PMID: 30982658 PMCID: PMC8283815 DOI: 10.1016/j.bmc.2019.04.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
Abstract
RNA has attracted considerable attention as a target for small molecules. However, methods to identify, study, and characterize suitable RNA targets have lagged behind strategies for protein targets. One approach that has received considerable attention for protein targets has been to utilize computational analysis to investigate ligandable "pockets" on proteins that are amenable to small molecule binding. These studies have shown that selected physical properties of pockets are important parameters that govern the ability of a structure to bind to small molecules. This work describes a similar analysis to study pockets on all RNAs in the Protein Data Bank (PDB). Using parameters such as buriedness, hydrophobicity, volume, and other properties, the set of all RNAs is analyzed and compared to all proteins. Considerable overlap is observed between the properties of pockets on RNAs and proteins. Thus, many RNAs are capable of populating conformations with pockets that are likely suitable for small molecule binding. Further, principal moment of inertia (PMI) calculations reveal that liganded RNAs exist in diverse structural space, much of which overlaps with protein structural space. Taken together, these results suggest that complex folded RNAs adopt unique structures with pockets that may represent viable opportunities for small molecule targeting.
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Affiliation(s)
- William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States.
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16
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Wang X, Shi J, Zhu HJ. Functional Study of Carboxylesterase 1 Protein Isoforms. Proteomics 2019; 19:e1800288. [PMID: 30520264 DOI: 10.1002/pmic.201800288] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/29/2018] [Indexed: 12/16/2022]
Abstract
Carboxylesterase 1 (CES1) is a primary human hepatic hydrolase involved in hydrolytic biotransformation of numerous medications. Considerable interindividual variability in CES1 expression and activity has been consistently reported. Four isoforms of the CES1 protein are produced by alternative splicing (AS). In the current study, the activity and expression of each CES1 isoform are examined using transfected cell lines, and CES1 isoform composition and its impact on CES1 activity in human livers are determined. In transfected cells, isoforms 3 and 4 show mRNA and protein expressions comparable to isoforms 1 and 2, but have significantly impaired activity when hydrolyzing enalapril and clopidogrel. In individual human liver samples, isoforms 1 and 2 are the major forms, contributing 73-90% of the total CES1 protein expression. In addition, the protein expression ratios of isoforms 1 and 2 to isoforms 3 and 4 are positively associated with CES1 activity in the liver, suggesting that CES1 isoform composition is a factor contributing to the variability in hepatic CES1 function. Further investigations of the regulation of CES1 AS would improve the understanding of CES1 variability and help develop a strategy to optimize the pharmacotherapy of many CES1 substrate medications.
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Affiliation(s)
- Xinwen Wang
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - Jian Shi
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109-1065, USA
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17
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Chu WK, Hung LM, Hou CW, Chen JK. Heterogeneous ribonucleoprotein F regulates YAP expression via a G-tract in 3'UTR. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:12-24. [PMID: 30312683 DOI: 10.1016/j.bbagrm.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 10/05/2018] [Accepted: 10/06/2018] [Indexed: 10/28/2022]
Abstract
The Yes-associated protein (YAP) is a transcription coactivator that plays crucial roles in organ size control and tumorigenesis, and was demonstrated to be inhibited by the Hippo signaling pathway. To date, the molecular mechanisms regulating the expression of YAP in human cells remain unknown. In the present study, we found that hnRNP F and hnRNP U negatively regulate YAP expression. We also showed that downregulation of YAP expression by hnRNP F and hnRNP U was not at the transcriptional level. Knockdown of hnRNP F or hnRNP U increased YAP mRNA stability, suggesting the downregulation of YAP expression was by a post-transcriptional mechanism. A putative hnRNP F binding site was identified in the YAP 3'UTR at 685 to 698, and deletion of this putative hnRNP F element abolished the down-regulation effect of YAP mRNA stability by hnRNP F. Binding of the hnRNP F to the YAP 3'UTR was demonstrated by Cross-linked RNA Immunoprecipitation. mRNA stability is a possible secondary effect of alternative splicing or other nuclear process. Understanding the regulation of YAP expression would provide insights into the mechanisms underlying the maintenance of tissue size homeostasis and tumorigenesis.
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Affiliation(s)
- Wing-Keung Chu
- Department of Physiology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; Healthy and Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Li-Man Hung
- Healthy and Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan; Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Chun-Wei Hou
- Healthy and Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Jan-Kan Chen
- Department of Physiology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; Healthy and Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan.
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18
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Kalva S, Bindusree G, Alexander V, Madasamy P. Interactome based biomarker discovery for irritable bowel syndrome—A systems biology approach. Comput Biol Chem 2018; 76:218-224. [DOI: 10.1016/j.compbiolchem.2018.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/12/2017] [Accepted: 07/04/2018] [Indexed: 02/07/2023]
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19
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Shainer R, Almogi-Hazan O, Berger A, Hinden L, Mueller M, Brodie C, Simillion C, Paidas M, Barnea ER, Or R. PreImplantation factor (PIF) therapy provides comprehensive protection against radiation induced pathologies. Oncotarget 2018; 7:58975-58994. [PMID: 27449294 PMCID: PMC5312289 DOI: 10.18632/oncotarget.10635] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/30/2016] [Indexed: 12/22/2022] Open
Abstract
Acute Radiation Syndrome (ARS) may lead to cancer and death and has few effective countermeasures. Efficacy of synthetic PIF treatment was demonstrated in preclinical autoimmune and transplantation models. PIF protected against inflammation and mortality following lethal irradiation in allogeneic bone marrow transplant (BMT) model. Herein, we demonstrate that PIF imparts comprehensive local and systemic protection against lethal and sub-lethal ARS in murine models. PIF treatment 2 h after lethal irradiation led to 100% survival and global hematopoietic recovery at 2 weeks after therapy. At 24 h after irradiation PIF restored hematopoiesis in a semi-allogeneic BMT model. PIF-preconditioning provided improved long-term engraftment. The direct effect of PIF on bone marrow cells was also demonstrated in vitro: PIF promoted pre-B cell differentiation and increased immunoregulatory properties of BM-derived mesenchymal stromal cells. PIF treatment also improved hematopoietic recovery and reduced systemic inflammatory cytokine production after sub-lethal radiation exposure. Here, PIF also prevented colonic crypt and basal membrane damage coupled with reduced nitric oxide synthetase (iNOS) and increased (B7h1) expression. Global upper GI gene pathway analysis revealed PIF's involvement in protein-RNA interactions, mitochondrial oxidative pathways, and responses to cellular stress. Some effects may be attributed to PIF's influence on macrophage differentiation and function. PIF demonstrated a regulatory effect on irradiated macrophages and on classically activated M1 macrophages, reducing inflammatory gene expression (iNOS, Cox2), promoting protective (Arg1) gene expression and inducing pro-tolerance cytokine secretion. Notably, synthetic PIF is stable for long-term field use. Overall, clinical investigation of PIF for comprehensive ARS protection is warranted.
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Affiliation(s)
- Reut Shainer
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah-Hebrew University Medical Center, Jerusalem, 91120, Israel
| | - Osnat Almogi-Hazan
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah-Hebrew University Medical Center, Jerusalem, 91120, Israel
| | - Arye Berger
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah-Hebrew University Medical Center, Jerusalem, 91120, Israel
| | - Liad Hinden
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah-Hebrew University Medical Center, Jerusalem, 91120, Israel
| | - Martin Mueller
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA.,Department of Obstetrics and Gynecology, University Hospital Bern, Bern, 3003, Switzerland
| | | | - Cedric Simillion
- Department of Clinical Research, University of Bern, Bern, 3003, Switzerland
| | - Michael Paidas
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Eytan R Barnea
- The Society for The Investigation of Early Pregnancy (SIEP), Cherry Hill, NJ 08003, USA.,BioIncept, LLC (PreImplantation Factor* Proprietary), Cherry Hill, NJ 08003, USA
| | - Reuven Or
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah-Hebrew University Medical Center, Jerusalem, 91120, Israel
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20
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Mager LF, Koelzer VH, Stuber R, Thoo L, Keller I, Koeck I, Langenegger M, Simillion C, Pfister SP, Faderl M, Genitsch V, Tcymbarevich I, Juillerat P, Li X, Xia Y, Karamitopoulou E, Lyck R, Zlobec I, Hapfelmeier S, Bruggmann R, McCoy KD, Macpherson AJ, Müller C, Beutler B, Krebs P. The ESRP1-GPR137 axis contributes to intestinal pathogenesis. eLife 2017; 6:28366. [PMID: 28975893 PMCID: PMC5665647 DOI: 10.7554/elife.28366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Aberrant alternative pre-mRNA splicing (AS) events have been associated with several disorders. However, it is unclear whether deregulated AS directly contributes to disease. Here, we reveal a critical role of the AS regulator epithelial splicing regulator protein 1 (ESRP1) for intestinal homeostasis and pathogenesis. In mice, reduced ESRP1 function leads to impaired intestinal barrier integrity, increased susceptibility to colitis and altered colorectal cancer (CRC) development. Mechanistically, these defects are produced in part by modified expression of ESRP1-specific Gpr137 isoforms differently activating the Wnt pathway. In humans, ESRP1 is downregulated in inflamed biopsies from inflammatory bowel disease patients. ESRP1 loss is an adverse prognostic factor in CRC. Furthermore, generation of ESRP1-dependent GPR137 isoforms is altered in CRC and expression of a specific GPR137 isoform predicts CRC patient survival. These findings indicate a central role of ESRP1-regulated AS for intestinal barrier integrity. Alterations in ESRP1 function or expression contribute to intestinal pathology.
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Affiliation(s)
- Lukas Franz Mager
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Regula Stuber
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Lester Thoo
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Irene Keller
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Ivonne Koeck
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Cedric Simillion
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Simona P Pfister
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Martin Faderl
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Vera Genitsch
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Irina Tcymbarevich
- Division of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Pascal Juillerat
- Department of Gastroenterology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Xiaohong Li
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yu Xia
- Department of Genetics, The Scripps Research Institute, La Jolla, United States
| | | | - Ruth Lyck
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Kathy D McCoy
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Andrew J Macpherson
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Department of Gastroenterology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Bruce Beutler
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
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21
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Thurman M, van Doorn J, Danzer B, Webb TR, Stamm S. Changes in Alternative Splicing as Pharmacodynamic Markers for Sudemycin D6. Biomark Insights 2017; 12:1177271917730557. [PMID: 28932105 PMCID: PMC5598794 DOI: 10.1177/1177271917730557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/08/2017] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE The aim of the study was to define pharmacodynamic markers for sudemycin D6, an experimental cancer drug that changes alternative splicing in human blood. METHODS Blood samples from 12 donors were incubated with sudemycin D6 for up to 24 hours, and at several time points total RNA from lymphocytes was prepared and the pre-messenger RNA (mRNA) splicing patterns were analyzed with reverse transcription-polymerase chain reaction. RESULTS Similar to immortalized cells, blood lymphocytes change alternative splicing due to sudemycin D6 treatment. However, lymphocytes in blood respond slower than immortalized cultured cells. CONCLUSIONS Exon skipping in the DUSP11 and SRRM1 pre-mRNAs are pharmacodynamic markers for sudemycin D6 treatment and show effects beginning at 9 hours after treatment.
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22
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Abernathy J, Brezas A, Snekvik KR, Hardy RW, Overturf K. Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis. PLoS One 2017; 12:e0180972. [PMID: 28723948 PMCID: PMC5517010 DOI: 10.1371/journal.pone.0180972] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/24/2017] [Indexed: 12/13/2022] Open
Abstract
Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.
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Affiliation(s)
- Jason Abernathy
- Hagerman Fish Culture Experiment Station, USDA-ARS, Hagerman, Idaho, United States of America
| | - Andreas Brezas
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, United States of America
| | - Kevin R. Snekvik
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Ronald W. Hardy
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, United States of America
| | - Ken Overturf
- Hagerman Fish Culture Experiment Station, USDA-ARS, Hagerman, Idaho, United States of America
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23
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Wang F, Xue R, Li X, Hu C, Xia Q. Characterization of a protein tyrosine phosphatase as a host factor promoting baculovirus replication in silkworm, Bombyx mori. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 57:31-7. [PMID: 26684065 PMCID: PMC7124732 DOI: 10.1016/j.dci.2015.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 05/09/2023]
Abstract
The relevance of protein tyrosine phosphatase (PTP) to host-pathogen interaction is highlighted in mammalian studies, whereas less is known in insects. Here we presented the categorization of the PTP complement of silkworm and characterized their homologous relationship with human and fruit fly PTPs. Among the 36 PTP genes, ptp-h, which was proposed to be the origin of baculovirus ptp belongs to atypical VH1-like dual-specific PTP subset and encodes a catalytic active protein. The maximum expression level of Bmptp-h was at 5th instar and in fat body. Bombyx mori nucleopolyhedrovirus (BmNPV) infection potently induced its expression in silkworm larvae and in BmE cells. Knock-down of Bmptp-h by RNA interference significantly inhibited viral replication, and over-expression enhanced viral replication as determined by viral DNA abundance and BmNPV-GFP positive cells. These results suggest that BmPTP-h might be one of the host factors that is beneficial to baculovirus infection by promoting viral replication.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Renju Xue
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Xianyang Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Cuimei Hu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China.
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Profiles of microRNA networks in intestinal epithelial cells in a mouse model of colitis. Sci Rep 2015; 5:18174. [PMID: 26647826 PMCID: PMC4673535 DOI: 10.1038/srep18174] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) accompany a critical loss of the frontline barrier function that is achieved primarily by intestinal epithelial cells (IECs). Although the gene-regulation pathways underlying these host-defense roles of IECs presumably are deranged during IBD pathogenesis, the quantitative and qualitative alterations of posttranscriptional regulators such as microRNAs (miRNAs) within the cells largely remain to be defined. We aimed to uncover the regulatory miRNA–target gene relationships that arise differentially in inflamed small- compared with large-IECs. Whereas IBD significantly increased the expression of only a few miRNA candidates in small-IECs, numerous miRNAs were upregulated in inflamed large-IECs. These marked alterations might explain why the large, as compared with small, intestine is more sensitive to colitis and shows more severe pathology in this experimental model of IBD. Our in-depth assessment of the miRNA–mRNA expression profiles and the resulting networks prompts us to suggest that miRNAs such as miR-1224, miR-3473a, and miR-5128 represent biomarkers that appear in large-IECs upon IBD development and co-operatively repress the expression of key anti-inflammatory factors. The current study provides insight into gene-regulatory networks in IECs through which dynamic rearrangement of the involved miRNAs modulates the gene expression–regulation machinery between maintaining and disrupting gastrointestinal homeostasis.
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Affiliation(s)
- Justin J.-L. Wong
- Gene and Stem Cell Therapy Program, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
- Sydney Medical School; University of Sydney; Camperdown Australia
| | - Amy Y. M. Au
- Gene and Stem Cell Therapy Program, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
- Sydney Medical School; University of Sydney; Camperdown Australia
| | - William Ritchie
- Gene and Stem Cell Therapy Program, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
- Sydney Medical School; University of Sydney; Camperdown Australia
- Department of Bioinformatics, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
| | - John E. J. Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute; Royal Prince Alfred Hospital; Camperdown Australia
- Sydney Medical School; University of Sydney; Camperdown Australia
- Cell and Molecular Therapies; Royal Prince Alfred Hospital; Camperdown Australia
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26
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Comprehensive identification of genes driven by ERV9-LTRs reveals TNFRSF10B as a re-activatable mediator of testicular cancer cell death. Cell Death Differ 2015; 23:64-75. [PMID: 26024393 DOI: 10.1038/cdd.2015.68] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/04/2015] [Accepted: 04/16/2015] [Indexed: 12/21/2022] Open
Abstract
The long terminal repeat (LTR) of human endogenous retrovirus type 9 (ERV9) acts as a germline-specific promoter that induces the expression of a proapoptotic isoform of the tumor suppressor homologue p63, GTAp63, in male germline cells. Testicular cancer cells silence this promoter, but inhibitors of histone deacetylases (HDACs) restore GTAp63 expression and give rise to apoptosis. We show here that numerous additional transcripts throughout the genome are driven by related ERV9-LTRs. 3' Rapid amplification of cDNA ends (3'RACE) was combined with next-generation sequencing to establish a large set of such mRNAs. HDAC inhibitors induce these ERV9-LTR-driven genes but not the LTRs from other ERVs. In particular, a transcript encoding the death receptor DR5 originates from an ERV9-LTR inserted upstream of the protein coding regions of the TNFRSF10B gene, and it shows an expression pattern similar to GTAp63. When treating testicular cancer cells with HDAC inhibitors as well as the death ligand TNF-related apoptosis-inducing ligand (TRAIL), rapid cell death was observed, which depended on TNFRSF10B expression. HDAC inhibitors also cooperate with cisplatin (cDDP) to promote apoptosis in testicular cancer cells. ERV9-LTRs not only drive a large set of human transcripts, but a subset of them acts in a proapoptotic manner. We propose that this avoids the survival of damaged germ cells. HDAC inhibition represents a strategy of restoring the expression of a class of ERV9-LTR-mediated genes in testicular cancer cells, thereby re-enabling tumor suppression.
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Hatzihristidis T, Desai N, Hutchins AP, Meng TC, Tremblay ML, Miranda-Saavedra D. A Drosophila-centric view of protein tyrosine phosphatases. FEBS Lett 2015; 589:951-66. [PMID: 25771859 DOI: 10.1016/j.febslet.2015.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/02/2015] [Accepted: 03/02/2015] [Indexed: 12/30/2022]
Abstract
Most of our knowledge on protein tyrosine phosphatases (PTPs) is derived from human pathologies and mouse knockout models. These models largely correlate well with human disease phenotypes, but can be ambiguous due to compensatory mechanisms introduced by paralogous genes. Here we present the analysis of the PTP complement of the fruit fly and the complementary view that PTP studies in Drosophila will accelerate our understanding of PTPs in physiological and pathological conditions. With only 44 PTP genes, Drosophila represents a streamlined version of the human complement. Our integrated analysis places the Drosophila PTPs into evolutionary and functional contexts, thereby providing a platform for the exploitation of the fly for PTP research and the transfer of knowledge onto other model systems.
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Affiliation(s)
- Teri Hatzihristidis
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Nikita Desai
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Andrew P Hutchins
- Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Tzu-Ching Meng
- Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Michel L Tremblay
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada; Department of Biochemistry, McGill University, Montreal, Quebec, Canada.
| | - Diego Miranda-Saavedra
- World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Osaka, Japan; Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain; IE Business School, IE University, María de Molina 31 bis, 28006 Madrid, Spain.
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Zhou Y, Suzuki Y, Uchida K, Tominaga M. Identification of a splice variant of mouse TRPA1 that regulates TRPA1 activity. Nat Commun 2014; 4:2399. [PMID: 24008932 PMCID: PMC5882232 DOI: 10.1038/ncomms3399] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/02/2013] [Indexed: 02/07/2023] Open
Abstract
Transient receptor potential ankyrin 1 (TRPA1) protein is a nonselective cation channel. Although many studies suggest that TRPA1 is involved in inflammatory and neuropathic pain, its mechanism remains unclear. Here we identify an alternative splice variant of the mouse Trpa1 gene. TRPA1a (full-length) and TRPA1b (splice variant) physically interact with each other and TRPA1b increases the expression of TRPA1a in the plasma membrane. TRPA1a and TRPA1b co-expression significantly increases current density in response to different agonists without affecting their single-channel conductance. Exogenous overexpression of Trpa1b gene in wild-type and TRPA1KO DRG neurons also increases TRPA1a-mediated AITC responses. Moreover, expression levels of Trpa1a and Trpa1b mRNAs change dynamically in two pain models (complete Freund’s adjuvant-induced inflammatory pain and partial sciatic nerve ligation-induced neuropathic pain models). These results suggest that TRPA1 may be regulated through alternative splicing under these pathological conditions. TRPA1 is a transient receptor potential channel family member and is involved in the detection of nociceptive stimuli. Zhou et al. identify an alternative splice variant of TRPA1, which increases TRPA1 plasma expression and channel function, and enhances pain-like behaviour in mice.
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Affiliation(s)
- Yiming Zhou
- Division of Cell Signaling, Okazaki Institute for Integrative Bioscience (National Institute for Physiological Sciences), National Institutes of Natural Sciences, Okazaki, Japan
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Sankhala RS, Lokareddy RK, Cingolani G. Structure of human PIR1, an atypical dual-specificity phosphatase. Biochemistry 2014; 53:862-71. [PMID: 24447265 PMCID: PMC3985963 DOI: 10.1021/bi401240x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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PIR1 is an atypical dual-specificity
phosphatase (DSP) that dephosphorylates
RNA with a higher specificity than phosphoproteins. Here we report
the atomic structure of a catalytically inactive mutant (C152S) of
the human PIR1 phosphatase core (PIR1-core, residues 29–205),
refined at 1.20 Å resolution. PIR1-core shares structural similarities
with DSPs related to Vaccinia virus VH1 and with
RNA 5′-phosphatases such as the baculovirus RNA triphosphatase
and the human mRNA capping enzyme. The PIR1 active site cleft is wider
and deeper than that of VH1 and contains two bound ions: a phosphate
trapped above the catalytic cysteine C152 exemplifies the binding
mode expected for the γ-phosphate of RNA, and ∼6 Å
away, a chloride ion coordinates the general base R158. Two residues
in the PIR1 phosphate-binding loop (P-loop), a histidine (H154) downstream
of C152 and an asparagine (N157) preceding R158, make close contacts
with the active site phosphate, and their nonaliphatic side chains
are essential for phosphatase activity in vitro.
These residues are conserved in all RNA 5′-phosphatases that,
analogous to PIR1, lack a “general acid” residue. Thus,
a deep active site crevice, two active site ions, and conserved P-loop
residues stabilizing the γ-phosphate of RNA are defining features
of atypical DSPs that specialize in dephosphorylating 5′-RNA.
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Affiliation(s)
- Rajeshwer Singh Sankhala
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University , 233 South 10th Street, Philadelphia, Pennsylvania 19107, United States
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Tafforeau L, Zorbas C, Langhendries JL, Mullineux ST, Stamatopoulou V, Mullier R, Wacheul L, Lafontaine D. The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors. Mol Cell 2013; 51:539-51. [DOI: 10.1016/j.molcel.2013.08.011] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/06/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
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Gassling V, Hampe J, Açil Y, Braesen JH, Wiltfang J, Häsler R. Disease-associated miRNA-mRNA networks in oral lichen planus. PLoS One 2013; 8:e63015. [PMID: 23723971 PMCID: PMC3664564 DOI: 10.1371/journal.pone.0063015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 03/27/2013] [Indexed: 12/20/2022] Open
Abstract
Background A large number of pathophysiological mechanisms are regulated by microRNAs (miRNAs), which represent a new class of posttranscriptional regulators of gene expression. To date, little is known about their role in oral lichen planus (OLP), a chronic inflammatory mucocutaneous disease of unknown etiology which is being discussed as a potentially premalignant condition of oropharyngeal cancer. The aim of the present investigation was to assess the pathophysiological impact of miRNAs and to determine regulatory miRNA networks which are directly linked to potentially disease-associated target transcripts in OLP. Methods Native tissue samples were collected from the oral mucosa of seven patients with OLP. The control group was composed of native tissue from elective oral surgery. The mRNA profiling was performed using the Affymetrix Human Gene 1.0 ST Array while miRNA profiling was performed using the microRNA Galaxy Array. Subsequent validation of initial results was carried out using TaqMan real time PCR. Results We identified 24 differentially regulated miRNA and 2,694 regulated transcripts. Linking the miRNAs to their potential targets we found 11 potential miRNA-mRNA pairs, of which several are functionally related to premalignant as well as to inflammatory events. Conclusions Our data shows miRNA associated with transcripts which are regulated when comparing OLP patients with healthy control individuals. This suggests that miRNAs may potentially regulate disease-relevant transcripts, proposing the concept of therapeutic interventions based on miRNAs.
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Affiliation(s)
- Volker Gassling
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jochen Hampe
- Department of Internal Medicine I, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Yahya Açil
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jan Hinrich Braesen
- Department of Pathology, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jörg Wiltfang
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
- * E-mail:
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Mills JD, Nalpathamkalam T, Jacobs HI, Janitz C, Merico D, Hu P, Janitz M. RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism. Neurosci Lett 2013; 536:90-5. [DOI: 10.1016/j.neulet.2012.12.042] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 12/25/2012] [Indexed: 11/26/2022]
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Zhang ZH, Zhao XJ, Song YZ, Tang XM, Zha QB. Cloning and sequence analysis of SLC25A13 transcripts in human amniocytes. Transl Pediatr 2012; 1:85-90. [PMID: 26835269 PMCID: PMC4728883 DOI: 10.3978/j.issn.2224-4336.2012.02.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE To amplify the entire ORF of SLC25A13 cDNA which encodes citrin, a liver-type mitochondrial aspartate-glutamate carrier, and to investigate sequence feature of the transcripts for this gene in cultured human amniocytes. This study will provide laboratory evidences for prenatal diagnosis of NICCD at mRNA level. METHODS Total RNA was extracted from cultured amniocytes, and cDNA was synthesized, and then nest PCR was performed to amplify the entire ORF sequences of SLC25A13. The PCR products were purified, cloned, sequenced, and aligned with the genomic DNA of SLC25A13 to analyze the alternative splicing pattern. RESULTS The entire ORF of SLC25A13 gene was successfully amplified. Three splice variants of SLC25A13, i.e., SLCA (normal mRNA), SLCB (CAG insertion between exon 9-10) and SLCC (exon 5-11 skipping), were identified in the subjects. However, no abnormal mRNA from the allele with mutation 851del4 was detected in the amniocytes cultured from a carrier fetus of this mutation. CONCLUSIONS This study demonstrated that the entire ORF of SLC25A13 cDNA can be successfully amplified from cultured human amniocytes, and revealed exon 5-11 skipping as a novel SLC25A13 transcript. Normal mRNA occupied majority of the transcripts in normal control and heterozygous amniocytes which contained normal allele and 851del4 mutation, indicating that the two fetuses wouldn't suffer from NICCD. These SLC25A13 transcription features provided laboratory evidences for prenatal diagnosis of NICCD.
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Affiliation(s)
- Zhan-Hui Zhang
- 1 Department of Pediatrics, 2 Department of Obstetrics and Gynecology, 3 Department of Fetal Medicine, the First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Xin-Jing Zhao
- 1 Department of Pediatrics, 2 Department of Obstetrics and Gynecology, 3 Department of Fetal Medicine, the First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Yuan-Zong Song
- 1 Department of Pediatrics, 2 Department of Obstetrics and Gynecology, 3 Department of Fetal Medicine, the First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Xiao-Mei Tang
- 1 Department of Pediatrics, 2 Department of Obstetrics and Gynecology, 3 Department of Fetal Medicine, the First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Qing-Bing Zha
- 1 Department of Pediatrics, 2 Department of Obstetrics and Gynecology, 3 Department of Fetal Medicine, the First Affiliated Hospital, Jinan University, Guangzhou 510630, China
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Becker ST, Beck-Broichsitter BE, Graetz C, Dörfer CE, Wiltfang J, Häsler R. Peri-Implantitis versus Periodontitis: Functional Differences Indicated by Transcriptome Profiling. Clin Implant Dent Relat Res 2012; 16:401-11. [DOI: 10.1111/cid.12001] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Stephan T. Becker
- Department of Oral and Maxillofacial Surgery; Christian-Albrechts University of Kiel; Kiel Germany
| | | | - Christian Graetz
- Department of Conservative Dentistry and Periodontology; Christian-Albrechts University of Kiel; Kiel Germany
| | - Christof E. Dörfer
- Department of Conservative Dentistry and Periodontology; Christian-Albrechts University of Kiel; Kiel Germany
| | - Jörg Wiltfang
- Department of Oral and Maxillofacial Surgery; Christian-Albrechts University of Kiel; Kiel Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology; Christian-Albrechts University of Kiel; Kiel Germany
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Mena de la Cruz R, López-Lera A, López-Trascasa M. Analysis of SERPING1 expression on hereditary angioedema patients: Quantitative analysis of full-length and exon 3 splicing variants. Immunol Lett 2012; 141:158-64. [DOI: 10.1016/j.imlet.2011.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 06/17/2011] [Accepted: 07/07/2011] [Indexed: 10/17/2022]
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