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Tong C, Zhang K, Rong Z, Mo W, Peng Y, Zheng S, Feng QL, Deng H. Alternative splicing of POUM2 regulates embryonic cuticular formation and tanning in Bombyx mori. INSECT SCIENCE 2023; 30:1267-1281. [PMID: 36562105 DOI: 10.1111/1744-7917.13164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Insect cuticle is an apical extracellular matrix produced by the epidermis, tracheal, hind- and foregut epithelia during embryogenesis and renewed during molting and metamorphosis. However, the underlying regulatory mechanism for embryonic cuticle formation remains largely unclear. Here, we investigate the function of the transcription factor POUM2 in the embryonic cuticular formation in Bombyx mori, a model lepidopteran insect. Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein-9-mediated knockout of POUM2 resulted in the defect of cuticular deposition, pigmentation, and sclerotization in the embryos. Differentially expressed transcripts analysis of 7-d-old embryos identified 174 up- or downregulated cuticular protein transcripts, 8 upregulated chitin degradation transcripts, 2 downregulated chitin synthesis transcripts and 48 up- or downregulated transcription factor transcripts in the POUM2-/- embryos. The expression levels of the key factors of the tyrosine metabolic pathway, such as tyrosine hydroxylase (Th), Dopa decarboxylase (DDC), and arylalkylamine N-acetyltransferase (aaNAT), were significantly decreased in the POUM2-/- embryos. POUM2 isoform POUM2-L specifically bound the POU cis-regulatory element (CRE) in the Th promoter and increased the transcription of Th, whereas POUM2-S could not bind the POU CRE, although it also increased the transcription of Th. Heterogeneous nuclear ribonucleoprotein Squid-1 directly bound the POUM2 pre-mRNA (messenger RNA) and inhibited the alternative splicing of POUM2-L to POUM2-S mRNA. These results suggest that POUM2 participates in the cuticular formation by regulating the chitin and cuticular protein synthesis and metabolism, and the cuticular pigmentation and sclerotization by regulating tyrosine metabolism during embryogenesis. This study provides new insights into novel function of POUM2 in embryogenesis.
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Affiliation(s)
- Chunmei Tong
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China
| | - Kang Zhang
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zixia Rong
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wanyu Mo
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yuling Peng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China
| | - Sichun Zheng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qi-Li Feng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China
| | - Huimin Deng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China
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Yanchus C, Drucker KL, Kollmeyer TM, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo SB, Ali A, Decker PA, Kosel ML, Panda A, Al-Zahrani KN, Jiang L, Browning JWL, Lowden C, Geuenich M, Hernandez JJ, Gosio JT, Ahmed M, Loganathan SK, Berman J, Trcka D, Michealraj KA, Fortin J, Carson B, Hollingsworth EW, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He HH, Murphy DJ, Wang L, Abyzov A, Dennis JW, Maass PG, Campbell K, Wilson MD, Lachance DH, Wrensch M, Wiencke J, Mak T, Pennacchio LA, Dickel DE, Visel A, Wrana J, Taylor MD, Zadeh G, Dirks P, Eckel-Passow JE, Attisano L, Pombo A, Ida CM, Kvon EZ, Jenkins RB, Schramek D. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science 2022; 378:68-78. [PMID: 36201590 PMCID: PMC9926876 DOI: 10.1126/science.abj2890] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single-nucleotide polymorphism rs55705857, which confers a sixfold greater risk of isocitrate dehydrogenase (IDH)-mutant low-grade glioma (LGG). We reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. Mutating the orthologous mouse rs55705857 locus accelerated tumor development in an Idh1R132H-driven LGG mouse model from 472 to 172 days and increased penetrance from 30% to 75%. Our work reveals mechanisms of the heritable predisposition to lethal glioma in ~40% of LGG patients.
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Affiliation(s)
- Connor Yanchus
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristen L. Drucker
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Thomas M. Kollmeyer
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Warren Winick-Ng
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 13092 Berlin, Germany
| | - Minggao Liang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Judy Pawling
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Silvana B. De Lorenzo
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asma Ali
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul A. Decker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Matt L. Kosel
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Arijit Panda
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Khalid N. Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lingyan Jiang
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jared W. L. Browning
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Chris Lowden
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Michael Geuenich
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J. Javier Hernandez
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessica T. Gosio
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Sampath Kumar Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jacob Berman
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Daniel Trcka
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | - Jerome Fortin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Brittany Carson
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Lily Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Andrew Elia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Daniel J. Murphy
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, Scotland, UK
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, Scotland, UK
| | - Liguo Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - James W. Dennis
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Philipp G. Maass
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kieran Campbell
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael D. Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Daniel H. Lachance
- Departments of Neurology and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - John Wiencke
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Tak Mak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Diane E. Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Jeffrey Wrana
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael D. Taylor
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Gelareh Zadeh
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Peter Dirks
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ana Pombo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 13092 Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
| | - Cristiane M. Ida
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Robert B. Jenkins
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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Shafi O, Siddiqui G. Tracing the origins of glioblastoma by investigating the role of gliogenic and related neurogenic genes/signaling pathways in GBM development: a systematic review. World J Surg Oncol 2022; 20:146. [PMID: 35538578 PMCID: PMC9087910 DOI: 10.1186/s12957-022-02602-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/15/2022] [Indexed: 02/16/2023] Open
Abstract
Background Glioblastoma is one of the most aggressive tumors. The etiology and the factors determining its onset are not yet entirely known. This study investigates the origins of GBM, and for this purpose, it focuses primarily on developmental gliogenic processes. It also focuses on the impact of the related neurogenic developmental processes in glioblastoma oncogenesis. It also addresses why glial cells are at more risk of tumor development compared to neurons. Methods Databases including PubMed, MEDLINE, and Google Scholar were searched for published articles without any date restrictions, involving glioblastoma, gliogenesis, neurogenesis, stemness, neural stem cells, gliogenic signaling and pathways, neurogenic signaling and pathways, and astrocytogenic genes. Results The origin of GBM is dependent on dysregulation in multiple genes and pathways that accumulatively converge the cells towards oncogenesis. There are multiple layers of steps in glioblastoma oncogenesis including the failure of cell fate-specific genes to keep the cells differentiated in their specific cell types such as p300, BMP, HOPX, and NRSF/REST. There are genes and signaling pathways that are involved in differentiation and also contribute to GBM such as FGFR3, JAK-STAT, and hey1. The genes that contribute to differentiation processes but also contribute to stemness in GBM include notch, Sox9, Sox4, c-myc gene overrides p300, and then GFAP, leading to upregulation of nestin, SHH, NF-κB, and others. GBM mutations pathologically impact the cell circuitry such as the interaction between Sox2 and JAK-STAT pathway, resulting in GBM development and progression. Conclusion Glioblastoma originates when the gene expression of key gliogenic genes and signaling pathways become dysregulated. This study identifies key gliogenic genes having the ability to control oncogenesis in glioblastoma cells, including p300, BMP, PAX6, HOPX, NRSF/REST, LIF, and TGF beta. It also identifies key neurogenic genes having the ability to control oncogenesis including PAX6, neurogenins including Ngn1, NeuroD1, NeuroD4, Numb, NKX6-1 Ebf, Myt1, and ASCL1. This study also postulates how aging contributes to the onset of glioblastoma by dysregulating the gene expression of NF-κB, REST/NRSF, ERK, AKT, EGFR, and others.
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Affiliation(s)
- Ovais Shafi
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan.
| | - Ghazia Siddiqui
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
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Alerasool N, Leng H, Lin ZY, Gingras AC, Taipale M. Identification and functional characterization of transcriptional activators in human cells. Mol Cell 2022; 82:677-695.e7. [PMID: 35016035 DOI: 10.1016/j.molcel.2021.12.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/04/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022]
Abstract
Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-associated proteins, but how these are causally connected to transcriptional activation is poorly understood. Here, we conduct an unbiased proteome-scale screen to systematically uncover human proteins that activate transcription in a natural chromatin context. By combining interaction proteomics and chemical inhibitors, we delineate the preference of these transcriptional activators for specific co-activators, highlighting how even closely related TFs can function via distinct cofactors. We also identify potent transactivation domains among the hits and use AlphaFold2 to predict and experimentally validate interaction interfaces of two activation domains with BRD4. Finally, we show that many novel activators are partners in fusion events in tumors and functionally characterize a myofibroma-associated fusion between SRF and C3orf62, a potent p300-dependent activator. Our work provides a functional catalog of potent transactivators in the human proteome and a platform for discovering transcriptional regulators at genome scale.
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Affiliation(s)
- Nader Alerasool
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - He Leng
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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5
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Ebrahimie E, Rahimirad S, Tahsili M, Mohammadi-Dehcheshmeh M. Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis. World J Stem Cells 2021; 13:1394-1416. [PMID: 34786151 PMCID: PMC8567453 DOI: 10.4252/wjsc.v13.i10.1394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/21/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023] Open
Abstract
Alternative ribonucleic acid (RNA) splicing can lead to the assembly of different protein isoforms with distinctive functions. The outcome of alternative splicing (AS) can result in a complete loss of function or the acquisition of new functions. There is a gap in knowledge of abnormal RNA splice variants promoting cancer stem cells (CSCs), and their prospective contribution in cancer progression. AS directly regulates the self-renewal features of stem cells (SCs) and stem-like cancer cells. Notably, octamer-binding transcription factor 4A spliced variant of octamer-binding transcription factor 4 contributes to maintaining stemness properties in both SCs and CSCs. The epithelial to mesenchymal transition pathway regulates the AS events in CSCs to maintain stemness. The alternative spliced variants of CSCs markers, including cluster of differentiation 44, aldehyde dehydrogenase, and doublecortin-like kinase, α6β1 integrin, have pivotal roles in increasing self-renewal properties and maintaining the pluripotency of CSCs. Various splicing analysis tools are considered in this study. LeafCutter software can be considered as the best tool for differential splicing analysis and identification of the type of splicing events. Additionally, LeafCutter can be used for efficient mapping splicing quantitative trait loci. Altogether, the accumulating evidence re-enforces the fact that gene and protein expression need to be investigated in parallel with alternative splice variants.
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Affiliation(s)
- Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide 5005, South Australia, Australia
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne 3086, Australia
- School of Biosciences, The University of Melbourne, Melbourne 3010, Australia,
| | - Samira Rahimirad
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal H4A 3J1, Quebec, Canada
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Primate-specific stress-induced transcription factor POU2F1Z protects human neuronal cells from stress. Sci Rep 2021; 11:18808. [PMID: 34552146 PMCID: PMC8458439 DOI: 10.1038/s41598-021-98323-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
The emergence of new primate-specific genes is an essential factor in human and primate brain development and functioning. POU2F1/Oct-1 is a transcription regulator in higher eukaryotes which is involved in the regulation of development, differentiation, stress response, and other processes. We have demonstrated that the Tigger2 transposon insertion into the POU2F1 gene which occurred in the primate lineage led to the formation of an additional exon (designated the Z-exon). Z-exon-containing primate-specific Oct-1Z transcript includes a short upstream ORF (uORF) located at its 5’-end and the main ORF encoding the Oct-1Z protein isoform (Pou2F1 isoform 3, P14859-3), which differs from other Oct-1 isoforms by its N-terminal peptide. The Oct-1Z-encoding transcript is expressed mainly in human brain cortex. Under normal conditions, the translation of the ORF coding for the Oct-1Z isoform is repressed by uORF. Under various stress conditions, uORF enables a strong increase in the translation of the Oct-1Z-encoding ORF. Increased Oct-1Z expression levels in differentiating human neuroblasts activate genes controlling stress response, neural cell differentiation, brain formation, and organogenesis. We have shown that the Oct-1Z isoform of the POU2F1/Oct-1 transcription factor is an example of a primate-specific genomic element contributing to brain development and cellular stress defense.
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7
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Induction of OCT2 contributes to regulate the gene expression program in human neutrophils activated via TLR8. Cell Rep 2021; 35:109143. [PMID: 34010659 DOI: 10.1016/j.celrep.2021.109143] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/27/2021] [Accepted: 04/26/2021] [Indexed: 12/23/2022] Open
Abstract
The transcription factors (TFs) that regulate inducible genes in activated neutrophils are not yet completely characterized. Herein, we show that the genomic distribution of the histone modification H3K27Ac, as well as PU.1 and C/EBPβ, two myeloid-lineage-determining TFs (LDTFs), significantly changes in human neutrophils treated with R848, a ligand of Toll-like receptor 8 (TLR8). Interestingly, differentially acetylated and LDTF-marked regions reveal an over-representation of OCT-binding motifs that are selectively bound by OCT2/POU2F2. Analysis of OCT2 genomic distribution in primary neutrophils and of OCT2-depletion in HL-60-differentiated neutrophils proves the requirement for OCT2 in contributing to promote, along with nuclear factor κB (NF-κB) and activator protein 1 (AP-1), the TLR8-induced gene expression program in neutrophils. Altogether, our data demonstrate that neutrophils, upon activation via TLR8, profoundly reprogram their chromatin status, ultimately displaying cell-specific, prolonged transcriptome changes. Data also show an unexpected role for OCT2 in amplifying the transcriptional response to TLR8-mediated activation.
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8
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Ng AHM, Khoshakhlagh P, Rojo Arias JE, Pasquini G, Wang K, Swiersy A, Shipman SL, Appleton E, Kiaee K, Kohman RE, Vernet A, Dysart M, Leeper K, Saylor W, Huang JY, Graveline A, Taipale J, Hill DE, Vidal M, Melero-Martin JM, Busskamp V, Church GM. A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol 2021; 39:510-519. [PMID: 33257861 PMCID: PMC7610615 DOI: 10.1038/s41587-020-0742-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 10/19/2020] [Indexed: 02/06/2023]
Abstract
Human pluripotent stem cells (hPSCs) offer an unprecedented opportunity to model diverse cell types and tissues. To enable systematic exploration of the programming landscape mediated by transcription factors (TFs), we present the Human TFome, a comprehensive library containing 1,564 TF genes and 1,732 TF splice isoforms. By screening the library in three hPSC lines, we discovered 290 TFs, including 241 that were previously unreported, that induce differentiation in 4 days without alteration of external soluble or biomechanical cues. We used four of the hits to program hPSCs into neurons, fibroblasts, oligodendrocytes and vascular endothelial-like cells that have molecular and functional similarity to primary cells. Our cell-autonomous approach enabled parallel programming of hPSCs into multiple cell types simultaneously. We also demonstrated orthogonal programming by including oligodendrocyte-inducible hPSCs with unmodified hPSCs to generate cerebral organoids, which expedited in situ myelination. Large-scale combinatorial screening of the Human TFome will complement other strategies for cell engineering based on developmental biology and computational systems biology.
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Affiliation(s)
- Alex H M Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Parastoo Khoshakhlagh
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Jesus Eduardo Rojo Arias
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Giovanni Pasquini
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - Kai Wang
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Anka Swiersy
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - Seth L Shipman
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA
| | - Evan Appleton
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Kiavash Kiaee
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Richie E Kohman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Andyna Vernet
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Matthew Dysart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Kathleen Leeper
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Wren Saylor
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Jeremy Y Huang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Amanda Graveline
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - David E Hill
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marc Vidal
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Juan M Melero-Martin
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Volker Busskamp
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany.
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany.
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- GC Therapeutics, Inc, Cambridge, MA, USA.
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9
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Black JB, McCutcheon SR, Dube S, Barrera A, Klann TS, Rice GA, Adkar SS, Soderling SH, Reddy TE, Gersbach CA. Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens. Cell Rep 2020; 33:108460. [PMID: 33264623 PMCID: PMC7730023 DOI: 10.1016/j.celrep.2020.108460] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/02/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023] Open
Abstract
Technologies to reprogram cell-type specification have revolutionized the fields of regenerative medicine and disease modeling. Currently, the selection of fate-determining factors for cell reprogramming applications is typically a laborious and low-throughput process. Therefore, we use high-throughput pooled CRISPR activation (CRISPRa) screens to systematically map human neuronal cell fate regulators. We utilize deactivated Cas9 (dCas9)-based gene activation to target 1,496 putative transcription factors (TFs) in the human genome. Using a reporter of neuronal commitment, we profile the neurogenic activity of these factors in human pluripotent stem cells (PSCs), leading to a curated set of pro-neuronal factors. Activation of pairs of TFs reveals neuronal cofactors, including E2F7, RUNX3, and LHX8, that improve conversion efficiency, subtype specificity, and maturation of neuronal cell types. Finally, using multiplexed gene regulation with orthogonal CRISPR systems, we demonstrate improved neuronal differentiation with concurrent activation and repression of target genes, underscoring the power of CRISPR-based gene regulation for programming complex cellular phenotypes.
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Affiliation(s)
- Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Sean R McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Shataakshi Dube
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Tyler S Klann
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Grayson A Rice
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Shaunak S Adkar
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Scott H Soderling
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy E Reddy
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA; Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.
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10
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Farahani S, Solgi L, Bayat S, Abedin Do A, Zare-Karizi S, Safarpour Lima B, Mirfakhraie R. RAR-related orphan receptor A: One gene with multiple functions related to migraine. CNS Neurosci Ther 2020; 26:1315-1321. [PMID: 32892507 PMCID: PMC7702232 DOI: 10.1111/cns.13453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/01/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
Aims RAR‐related orphan receptor (RORA) involves in regulation of several biological processes including inflammation and circadian rhythm that probably are involved in migraine pathophysiology. In the current study, the association between RORA rs11639084 and rs4774388 variants and susceptibility to migraine were investigated in a sample of Iranian migraine patients for the first time. Methods In a case‐control study including 400 participants, 200 migraineurs and 200 healthy controls, genotyping of RORA rs4774388 and rs11639084 polymorphisms was performed using tetra‐primer amplification refractory mutation system–polymerase chain reaction (TP‐ARMS‐PCR). Results The distribution of rs4774388 C/T and T/T genotypes differed significantly between the studied groups. Moreover, an association was observed between rs4774388 and migraine under the recessive mode of inheritance (P = 0.002; OR = 1.89.; CI = 1.25‐2.87). The distribution of rs11639084 alleles and genotypes was not significantly different between migraineurs and healthy controls. Conclusion Current results suggest RORA, as a molecular link, may explain inflammation and circadian rhythm dysfunction in migraine. Further studies in different ethnicities are required to confirm the function of RORA in migraine development.
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Affiliation(s)
- Sedigheh Farahani
- Department of Genetics, School of Biological Sciences, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | - Leila Solgi
- Department of Genetics, School of Biological Sciences, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | - Sahar Bayat
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Atieh Abedin Do
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Regenerative Medicine, Faculty of Medicine, GREB Dental Faculty, Laval University, Quebec, Canada
| | - Shohreh Zare-Karizi
- Department of Genetics, School of Biological Sciences, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | - Behnam Safarpour Lima
- Department of Neurology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Genomic Research Centre, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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11
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Wong CY, Chang YM, Tsai YS, Ng WV, Cheong SK, Chang TY, Chung IF, Lim YM. Decoding the differentiation of mesenchymal stem cells into mesangial cells at the transcriptomic level. BMC Genomics 2020; 21:467. [PMID: 32635896 PMCID: PMC7339572 DOI: 10.1186/s12864-020-06868-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
Background Mesangial cells play an important role in the glomerulus to provide mechanical support and maintaine efficient ultrafiltration of renal plasma. Loss of mesangial cells due to pathologic conditions may lead to impaired renal function. Mesenchymal stem cells (MSC) can differentiate into many cell types, including mesangial cells. However transcriptomic profiling during MSC differentiation into mesangial cells had not been studied yet. The aim of this study is to examine the pattern of transcriptomic changes during MSC differentiation into mesangial cells, to understand the involvement of transcription factor (TF) along the differentiation process, and finally to elucidate the relationship among TF-TF and TF-key gene or biomarkers during the differentiation of MSC into mesangial cells. Results Several ascending and descending monotonic key genes were identified by Monotonic Feature Selector. The identified descending monotonic key genes are related to stemness or regulation of cell cycle while ascending monotonic key genes are associated with the functions of mesangial cells. The TFs were arranged in a co-expression network in order of time by Time-Ordered Gene Co-expression Network (TO-GCN) analysis. TO-GCN analysis can classify the differentiation process into three stages: differentiation preparation, differentiation initiation and maturation. Furthermore, it can also explore TF-TF-key genes regulatory relationships in the muscle contraction process. Conclusions A systematic analysis for transcriptomic profiling of MSC differentiation into mesangial cells has been established. Key genes or biomarkers, TFs and pathways involved in differentiation of MSC-mesangial cells have been identified and the related biological implications have been discussed. Finally, we further elucidated for the first time the three main stages of mesangial cell differentiation, and the regulatory relationships between TF-TF-key genes involved in the muscle contraction process. Through this study, we have increased fundamental understanding of the gene transcripts during the differentiation of MSC into mesangial cells.
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Affiliation(s)
- Chee-Yin Wong
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, 43000 Kajang, Selangor, Malaysia
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Yu-Shuen Tsai
- Center for Systems and Synthetic Biology, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei, Taiwan
| | - Wailap Victor Ng
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei, Taiwan
| | - Soon-Keng Cheong
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, 43000 Kajang, Selangor, Malaysia
| | - Ting-Yu Chang
- Department of Research, ChangHua Christian Hospital, 135, Nan-Hsiao Street, ChangHua City, Taiwan
| | - I-Fang Chung
- Center for Systems and Synthetic Biology, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei, Taiwan. .,Institute of Biomedical Informatics, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei, Taiwan. .,Preventive Medicine Research Center, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei, Taiwan.
| | - Yang-Mooi Lim
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, 43000 Kajang, Selangor, Malaysia.
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12
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Fantuzzo JA, Robles DA, Mirabella VR, Hart RP, Pang ZP, Zahn JD. Development of a high-throughput arrayed neural circuitry platform using human induced neurons for drug screening applications. LAB ON A CHIP 2020; 20:1140-1152. [PMID: 32064487 PMCID: PMC7339603 DOI: 10.1039/c9lc01179j] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Proper brain function relies on the precise arrangement and flow of information between diverse neural subtypes. Developing improved human cell-based models which faithfully mimic biologically relevant connectivity patterns may improve drug screening efforts given the limited success of animal models to predict safety and efficacy of therapeutics in human clinical trials. To address this need, we have developed experimental models of defined neural circuitries through the compartmentalization of neuronal cell subtypes in a 96 well plate-based platform where each microwell is divided into two compartments connected by microchannels allowing high-throughput screening (HTS) of small molecules. We demonstrate that we can generate subtype-specific excitatory and inhibitory induced neuronal cells (iNs) from human stem cell lines and that these neurons form robust functional circuits with defined connectivity. Through the use of the genetically encoded calcium indicator GCaMP6f, we monitor calcium ion transients generated during neuronal firing between and within compartments. We further demonstrate functionality of the circuit by perturbing network activity through the addition of glutamate receptor blockers using automated liquid handling. Lastly, we show that we can stimulate network activity in defined neuronal subtypes through the expression of the designer receptor exclusively activated by designer drugs (DREADD) hM3Dq and application of the ligand clozapine-N-oxide (CNO). Our results demonstrate the formation of functional neural circuits in a high-throughput platform that is compatible with compound screening, representing an important step towards developing new screening platforms for studying and ultimately treating psychiatric brain disorders that arise from disordered neural circuit function.
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Affiliation(s)
- Joseph A Fantuzzo
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA. and Child Health Institute of New Jersey, Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, USA
| | - Denise A Robles
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA.
| | - Vincent R Mirabella
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, USA and Department of Neuroscience and Cell Biology, 675 Hoes Lane West, Research Tower, Third Floor, Piscataway, NJ 08854, USA and Pediatrics, Robert Wood Johnson Medical School, Rutgers University, One Robert Wood Johnson Place, MEB Third, PO Box 19, New Brunswick, NJ 08903, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Zhiping P Pang
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, USA and Department of Neuroscience and Cell Biology, 675 Hoes Lane West, Research Tower, Third Floor, Piscataway, NJ 08854, USA and Pediatrics, Robert Wood Johnson Medical School, Rutgers University, One Robert Wood Johnson Place, MEB Third, PO Box 19, New Brunswick, NJ 08903, USA
| | - Jeffrey D Zahn
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA.
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13
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Alexander CJ, Hammer JA. An Improved Method for Differentiating Mouse Embryonic Stem Cells into Cerebellar Purkinje Neurons. THE CEREBELLUM 2019; 18:406-421. [PMID: 30729383 DOI: 10.1007/s12311-019-1007-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While mixed primary cerebellar cultures prepared from embryonic tissue have proven valuable for dissecting structure-function relationships in cerebellar Purkinje neurons (PNs), this technique is technically challenging and often yields few cells. Recently, mouse embryonic stem cells (mESCs) have been successfully differentiated into PNs, although the published methods are very challenging as well. The focus of this study was to simplify the differentiation of mESCs into PNs. Using a recently described neural differentiation media, we generate monolayers of neural progenitor cells from mESCs and differentiate them into PN precursors using specific extrinsic factors. These PN precursors are then differentiated into mature PNs by co-culturing them with granule neuron (GN) precursors also derived from neural progenitors using different extrinsic factors. The morphology of mESC-derived PNs is indistinguishable from PNs grown in primary culture in terms of gross morphology, spine length, and spine density. Furthermore, mESC-derived PNs express Calbindin D28K, IP3R1, IRBIT, PLCβ4, PSD93, and myosin IIB-B2, all of which are either PN-specific or highly expressed in PNs. Moreover, we show that mESC-derived PNs form synapses with GN-like cells as in primary culture, express proteins driven by the PN-specific promoter Pcp2/L7, and exhibit the defect in spine ER inheritance seen in PNs isolated from dilute-lethal (myosin Va-null) mice when expressing a Pcp2/L7-driven miRNA directed against myosin Va. Finally, we define a novel extracellular matrix formulation that reproducibly yields monolayer cultures conducive for high-resolution imaging. Our improved method for differentiating mESCs into PNs should facilitate the dissection of molecular mechanisms and disease phenotypes in PNs.
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Affiliation(s)
- Christopher J Alexander
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - John A Hammer
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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14
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Masgutova G, Harris A, Jacob B, Corcoran LM, Clotman F. Pou2f2 Regulates the Distribution of Dorsal Interneurons in the Mouse Developing Spinal Cord. Front Mol Neurosci 2019; 12:263. [PMID: 31787878 PMCID: PMC6853997 DOI: 10.3389/fnmol.2019.00263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022] Open
Abstract
Spinal dorsal interneurons, which are generated during embryonic development, relay and process sensory inputs from the periphery to the central nervous system. Proper integration of these cells into neuronal circuitry depends on their correct positioning within the spinal parenchyma. Molecular cues that control neuronal migration have been extensively characterized but the genetic programs that regulate their production remain poorly investigated. Onecut (OC) transcription factors have been shown to control the migration of the dorsal interneurons (dINs) during spinal cord development. Here, we report that the OC factors moderate the expression of Pou2f2, a transcription factor essential for B-cell differentiation, in spinal dINs. Overexpression or inactivation of Pou2f2 leads to alterations in the differentiation of dI2, dI3 and Phox2a-positive dI5 populations and to defects in the distribution of dI2-dI6 interneurons. Thus, an OC-Pou2f2 genetic cascade regulates adequate diversification and distribution of dINs during embryonic development.
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Affiliation(s)
- Gauhar Masgutova
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, Brussels, Belgium
| | - Audrey Harris
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, Brussels, Belgium
| | - Benvenuto Jacob
- Université catholique de Louvain, Institute of Neuroscience, System and Cognition Division, Brussels, Belgium
| | - Lynn M Corcoran
- Molecular Immunology Division and Immunology Division, The Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Frédéric Clotman
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, Brussels, Belgium
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15
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Harris A, Masgutova G, Collin A, Toch M, Hidalgo-Figueroa M, Jacob B, Corcoran LM, Francius C, Clotman F. Onecut Factors and Pou2f2 Regulate the Distribution of V2 Interneurons in the Mouse Developing Spinal Cord. Front Cell Neurosci 2019; 13:184. [PMID: 31231191 PMCID: PMC6561314 DOI: 10.3389/fncel.2019.00184] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/12/2019] [Indexed: 11/21/2022] Open
Abstract
Acquisition of proper neuronal identity and position is critical for the formation of neural circuits. In the embryonic spinal cord, cardinal populations of interneurons diversify into specialized subsets and migrate to defined locations within the spinal parenchyma. However, the factors that control interneuron diversification and migration remain poorly characterized. Here, we show that the Onecut transcription factors are necessary for proper diversification and distribution of the V2 interneurons in the developing spinal cord. Furthermore, we uncover that these proteins restrict and moderate the expression of spinal isoforms of Pou2f2, a transcription factor known to regulate B-cell differentiation. By gain- or loss-of-function experiments, we show that Pou2f2 contribute to regulate the position of V2 populations in the developing spinal cord. Thus, we uncovered a genetic pathway that regulates the diversification and the distribution of V2 interneurons during embryonic development.
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Affiliation(s)
- Audrey Harris
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Gauhar Masgutova
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Amandine Collin
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Mathilde Toch
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Maria Hidalgo-Figueroa
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Benvenuto Jacob
- Institute of Neuroscience, System and Cognition Division, Université catholique de Louvain, Brussels, Belgium
| | - Lynn M. Corcoran
- Molecular Immunology Division and Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Cédric Francius
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Frédéric Clotman
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
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16
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Tang X, Engström Y. Regulation of immune and tissue homeostasis by Drosophila POU factors. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 109:24-30. [PMID: 30954681 DOI: 10.1016/j.ibmb.2019.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 03/17/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
The innate immune system of insects deploys both cellular and humoral reactions in immunocompetent tissues for protection of insects against a variety of infections, including bacteria, fungi, and viruses. Transcriptional regulation of genes encoding antimicrobial peptides (AMPs), cytokines, and other immune effectors plays a pivotal role in maintenance of immune homeostasis both prior to and after infections. The POU/Oct transcription factor family is a subclass of the homeodomain proteins present in all metazoans. POU factors are involved in regulation of development, metabolism and immunity. Their role in regulation of immune functions has recently become evident, and involves control of tissue-specific, constitutive expression of immune effectors in barrier epithelia as well as positive and negative control of immune responses in gut and fat body. In addition, they have been shown to affect the composition of gut microbiota and play a role in regulation of intestinal stem cell activities. In this review, we summarize the current knowledge of how POU transcription factors control Drosophila immune homeostasis in healthy and infected insects. The role of POU factor isoform specific regulation of stem cell activities in Drosophila and mammals is also discussed.
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Affiliation(s)
- Xiongzhuo Tang
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691, Stockholm, Sweden
| | - Ylva Engström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691, Stockholm, Sweden.
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17
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Lin SC, Chung CH, Chung CH, Kuo MH, Hsieh CH, Chiu YF, Shieh YS, Chou YT, Wu CW. OCT4B mediates hypoxia-induced cancer dissemination. Oncogene 2018; 38:1093-1105. [PMID: 30209362 DOI: 10.1038/s41388-018-0487-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 07/04/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023]
Abstract
Hypoxia, the reduction of oxygen levels in cells or tissues, elicits a set of genes to adjust physiological and pathological demands during normal development and cancer progression. OCT4, a homeobox transcription factor, is essential for self-renewal of embryonic stem cells, but little is known about the role of OCT4 in non-germ-cell tumorigenesis. Here, we report that hypoxia stimulates a short isoform of OCT4, called OCT4B, via a HIF2α-dependent pathway to induce the epithelial-mesenchymal transition (EMT) and facilitate cancer dissemination. OCT4B overexpression decreased epithelial barrier properties, which led to an increase in cell migration and invasion in lung cancer cells. OCT4B knockdown attenuated HIF2α-induced EMT and inhibited cancer dissemination in cell-line and animal models. We observed that OCT4B bound the SLUG promoter and enhanced its expression, and SLUG silencing inhibited OCT4B-mediated EMT, accompanied with decreased cell migration and invasion. Correlation analysis revealed that OCT4B expression was significantly associated with the SLUG level in lung tumors. These results provide novel insights into OCT4B-mediated oncogenesis in cancer dissemination.
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Affiliation(s)
- Sheng-Chieh Lin
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan.,Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan
| | - Chi-Hsiu Chung
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Hung Chung
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Han Kuo
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Cheng-Han Hsieh
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.,Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Fan Chiu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Shing Shieh
- Department of Oral Diagnosis & Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Yu-Ting Chou
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan.
| | - Cheng-Wen Wu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan. .,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan. .,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan. .,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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18
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Stem Cells as Potential Targets of Polyphenols in Multiple Sclerosis and Alzheimer's Disease. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1483791. [PMID: 30112360 PMCID: PMC6077677 DOI: 10.1155/2018/1483791] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/19/2018] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) and multiple sclerosis are major neurodegenerative diseases, which are characterized by the accumulation of abnormal pathogenic proteins due to oxidative stress, mitochondrial dysfunction, impaired autophagy, and pathogens, leading to neurodegeneration and behavioral deficits. Herein, we reviewed the utility of plant polyphenols in regulating proliferation and differentiation of stem cells for inducing brain self-repair in AD and multiple sclerosis. Firstly, we discussed the genetic, physiological, and environmental factors involved in the pathophysiology of both the disorders. Next, we reviewed various stem cell therapies available and how they have proved useful in animal models of AD and multiple sclerosis. Lastly, we discussed how polyphenols utilize the potential of stem cells, either complementing their therapeutic effects or stimulating endogenous and exogenous neurogenesis, against these diseases. We suggest that polyphenols could be a potential candidate for stem cell therapy against neurodegenerative disorders.
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Sayad A, Noroozi R, Omrani MD, Taheri M, Ghafouri-Fard S. Retinoic acid-related orphan receptor alpha (RORA) variants are associated with autism spectrum disorder. Metab Brain Dis 2017; 32:1595-1601. [PMID: 28608249 DOI: 10.1007/s11011-017-0049-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/05/2017] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with various epidemiologic, genetic, epigenetic, and environmental factors being associated with it. The observed sex bias in ASD towards male has prompted investigators to propose sex-dependent mechanisms for ASD. Retinoic acid-related orphan receptor-alpha (RORA) is a new autism candidate gene that has been shown to be differentially regulated by male and female hormones. Previous studies have shown deregulation of its expression in the prefrontal cortex and the cerebellum of ASD patients. In the present study we aimed at identification of the possible associations between two functional polymorphisms in the RORA gene (rs11639084 and rs4774388) and the risk of ASD in 518 Iranian ASD patients and 472 age, gender, and ethnic-matched healthy controls by means of tetra primer-amplification refractory mutation system-PCR. The allele and genotype frequencies of rs11639084 were not significantly different between patients and controls. However, the allele frequencies of rs4774388 showed significant overrepresentation of T allele in patients compared with controls (P = 0.04, OR (95% CI) =1.21 (1.01-1.46)). The rs4774388-TT genotype was significantly higher in patients compared with controls and was associated with ASD risk in dominant inheritance model (P = 0.04, OR (95% CI) =0.77 (0.59-0.99)). Haplotype analysis showed significant association of two estimated blocks of rs11639084/ rs4774388 with ASD risk. Consequently, the present data provide further evidence for RORA participation in the pathogenesis of ASD.
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Affiliation(s)
- Arezou Sayad
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran
| | - Rezvan Noroozi
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, No 23, Shahid Labbafi Nejad Educational Hospital, Amir Ebrahimi St, Pasdaran Ave, Tehran, Iran
| | - Mohammad Taheri
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran.
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, No 23, Shahid Labbafi Nejad Educational Hospital, Amir Ebrahimi St, Pasdaran Ave, Tehran, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran.
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20
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Shen Z, Kang J, Shakya A, Tabaka M, Jarboe EA, Regev A, Tantin D. Enforcement of developmental lineage specificity by transcription factor Oct1. eLife 2017; 6:20937. [PMID: 28537559 PMCID: PMC5466424 DOI: 10.7554/elife.20937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/23/2017] [Indexed: 12/26/2022] Open
Abstract
Embryonic stem cells co-express Oct4 and Oct1, a related protein with similar DNA-binding specificity. To study the role of Oct1 in ESC pluripotency and transcriptional control, we constructed germline and inducible-conditional Oct1-deficient ESC lines. ESCs lacking Oct1 show normal appearance, self-renewal and growth but manifest defects upon differentiation. They fail to form beating cardiomyocytes, generate neurons poorly, form small, poorly differentiated teratomas, and cannot generate chimeric mice. Upon RA-mediated differentiation, Oct1-deficient cells induce lineage-appropriate developmentally poised genes poorly while lineage-inappropriate genes, including extra-embryonic genes, are aberrantly expressed. In ESCs, Oct1 co-occupies a specific set of targets with Oct4, but does not occupy differentially expressed developmental targets. Instead, Oct1 occupies these targets as cells differentiate and Oct4 declines. These results identify a dynamic interplay between Oct1 and Oct4, in particular during the critical window immediately after loss of pluripotency when cells make the earliest developmental fate decisions. DOI:http://dx.doi.org/10.7554/eLife.20937.001 Humans and most other animals are composed of hundreds of different types of cell, including nerve cells, muscle cells and blood cells. Despite performing many different roles, these cells all develop from a single fertilized egg, which divides to make a particular group of cells that when studied in the laboratory are called embryonic stem cells (or ESCs for short). The ability of a cell to become a different cell type is defined as “potency”. ESCs are unique because they can specialize into any type of cell present in the adult organism, and they are therefore called “pluripotent”. However, as the embryo develops, its ESCs gradually lose their potency, and become more and more specialized. The activity of a great number of genes must be regulated during the transition from pluripotent to specialized cells, and some of the mechanisms involved in this transition are still unclear. ESCs are known to need a gene-regulating protein called Oct4 to remain pluripotent and Shen, Kang, Shakya et al. now show that a similar protein named Oct1 is essential for their transition to becoming more specialized. When the gene for Oct1 was deleted from mouse ECSs, they behaved largely like “normal” ESCs, but could not properly mature into certain cell types such as heart and nerve cells. Molecular analyses revealed that Oct4 and Oct1 compete to regulate the activity of many common genes with opposing outcomes: Oct4 keeps ESCs pluripotent while Oct1 leads them to specialize. The Oct4 protein is abundant in ESCs and prevails over Oct1, but as the cells mature, the levels of Oct4 drop, and Oct1 takes over in the regulation of their common target genes. Going forward, a better understanding of how ESCs become specialized will help basic research in the laboratory and allow scientists to tackle new questions about how the human body develops and how our organs work. In the longer-term, these findings might also have applications in the field of regenerative medicine, which aims to repair or replace a person’s cells, tissues or organs to improve their health. DOI:http://dx.doi.org/10.7554/eLife.20937.002
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Affiliation(s)
- Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Jinsuk Kang
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Arvind Shakya
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Marcin Tabaka
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Elke A Jarboe
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
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21
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Pance A. Oct-1, to go or not to go? That is the PolII question. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:820-4. [PMID: 27063953 DOI: 10.1016/j.bbagrm.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 10/22/2022]
Abstract
The Oct transcription factors recognise an octamer DNA element from which they regulate transcription of specific target genes. Oct-1 is the only member of the subfamily that is ubiquitously expressed and has a wide role in transcriptional control. Through interaction with various partner proteins, Oct-1 can modulate accessibility to the chromatin to recruit the transcription machinery and form the pre-initiation complex. The recruited PolII is induced to initiate transcription and stalled until elongation is triggered on interaction with signalling transcription factors. In this way, Oct-1 can fulfil general roles in transcription by opening the chromatin as well as transduce extracellular signals by relaying activation through various interacting partners. The emerging picture of Oct-1 is that of a complex and versatile transcription factor with fundamental functions in cell homeostasis and signal response in general as well as cell specific contexts. This article is part of a Special Issue entitled: The Oct Transcription Factor Family, edited by Dr. Dean Tantin.
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Affiliation(s)
- Alena Pance
- The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK.
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22
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Bentrari F, Chantôme A, Knights A, Jeannin JF, Pance A. Oct-2 forms a complex with Oct-1 on the iNOS promoter and represses transcription by interfering with recruitment of RNA PolII by Oct-1. Nucleic Acids Res 2015; 43:9757-65. [PMID: 26271992 PMCID: PMC4787767 DOI: 10.1093/nar/gkv829] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 08/04/2015] [Indexed: 01/09/2023] Open
Abstract
Oct-1 (POU2f1) and Oct-2 (POU2f2) are members of the POU family of transcription factors. They recognize the same DNA sequence but fulfil distinct functions: Oct-1 is ubiquitous and regulates a variety of genes while Oct-2 is restricted to B-cells and neurones. Here we examine the interplay and regulatory mechanisms of these factors to control the inducible nitric oxide synthase (iNOS, NOS2). Using two breast cancer cell lines as a comparative model, we found that MCF-7 express iNOS upon cytokine stimulation while MDA-MB-231 do not. Oct-1 is present in both cell lines but MDA-MB-231also express high levels of Oct-2. Manipulation of Oct-2 expression in these cell lines demonstrates that it is directly responsible for the repression of iNOS in MDA-MB-231. In MCF-7 cells Oct-1 binds the iNOS promoter, recruits RNA PolII and triggers initiation of transcription. In MDA-MB-231 cells, both Oct-1 and Oct-2 bind the iNOS promoter, forming a higher-order complex which fails to recruit RNA PolII, and as a consequence iNOS transcription does not proceed. Unravelling the mechanisms of transcription factor activity is paramount to the understanding of gene expression patterns that determine cell behaviour.
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Affiliation(s)
- Fatima Bentrari
- EPHE Laboratory, Faculty of Medicine, University of Bourgogne, 7 Boulevard Jeanne D'Arc, 21033 Dijon, France
| | - Aurelie Chantôme
- EPHE Laboratory, Faculty of Medicine, University of Bourgogne, 7 Boulevard Jeanne D'Arc, 21033 Dijon, France
| | - Andrew Knights
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jean-François Jeannin
- EPHE Laboratory, Faculty of Medicine, University of Bourgogne, 7 Boulevard Jeanne D'Arc, 21033 Dijon, France
| | - Alena Pance
- EPHE Laboratory, Faculty of Medicine, University of Bourgogne, 7 Boulevard Jeanne D'Arc, 21033 Dijon, France The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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23
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Abstract
The POU genes represent a diverse class of animal-specific transcription factors that play important roles in neurogenesis, pluripotency, and cell-type specification. Although previous attempts have been made to reconstruct the evolution of the POU class, these studies have been limited by a small number of representative taxa, and a lack of sequences from basally branching organisms. In this study, we performed comparative analyses on available genomes and sequences recovered through "gene fishing" to better resolve the topology of the POU gene tree. We then used ancestral state reconstruction to map the most likely changes in amino acid evolution for the conserved domains. Our work suggests that four of the six POU families evolved before the last common ancestor of living animals-doubling previous estimates-and were followed by extensive clade-specific gene loss. Amino acid changes are distributed unequally across the gene tree, consistent with a neofunctionalization model of protein evolution. We consider our results in the context of early animal evolution, and the role of POU5 genes in maintaining stem cell pluripotency.
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Affiliation(s)
- David A Gold
- Department of Ecology and Evolution, University of California, Los Angeles
| | - Ruth D Gates
- Department of Ecology and Evolution, University of California, Los Angeles
| | - David K Jacobs
- Department of Ecology and Evolution, University of California, Los Angeles
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24
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del Rosario RCH, Rayan NA, Prabhakar S. Noncoding origins of anthropoid traits and a new null model of transposon functionalization. Genome Res 2014; 24:1469-84. [PMID: 25043600 PMCID: PMC4158753 DOI: 10.1101/gr.168963.113] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions and confirmed their robust functional signatures. Of the ASC base pairs, 99.7% were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory. ASCs were highly enriched in loci associated with fetal brain development, motor coordination, neurotransmission, and vision, thus providing a large set of candidate elements for exploring the molecular basis of hallmark primate traits. We validated ASC192 as a primate-specific enhancer in proliferative zones of the developing brain. Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs, and almost all TE families showed functional potential similar to that of nonrepetitive DNA. Three L1PA repeat-derived ASCs displayed coherent eye-enhancer function, thus demonstrating that the "gene-battery" model of TE functionalization applies to enhancers in vivo. Our study provides fundamental insights into genome evolution and the origins of anthropoid phenotypes and supports an elegantly simple new null model of TE exaptation.
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Affiliation(s)
- Ricardo C H del Rosario
- Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, Singapore 138672
| | - Nirmala Arul Rayan
- Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, Singapore 138672
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, Singapore 138672
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25
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Thompson CL, Ng L, Menon V, Martinez S, Lee CK, Glattfelder K, Sunkin SM, Henry A, Lau C, Dang C, Garcia-Lopez R, Martinez-Ferre A, Pombero A, Rubenstein JLR, Wakeman WB, Hohmann J, Dee N, Sodt AJ, Young R, Smith K, Nguyen TN, Kidney J, Kuan L, Jeromin A, Kaykas A, Miller J, Page D, Orta G, Bernard A, Riley Z, Smith S, Wohnoutka P, Hawrylycz MJ, Puelles L, Jones AR. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron 2014; 83:309-323. [PMID: 24952961 DOI: 10.1016/j.neuron.2014.05.033] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2014] [Indexed: 11/30/2022]
Abstract
To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).
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Affiliation(s)
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Salvador Martinez
- Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain; Centro de Investigacion Biomedica en Red de Salud Mental (CIBERSAM) and IMIB-Arrixaca of Instituto de Salud Carlos III, 30120 Murcia, Spain
| | - Chang-Kyu Lee
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Alex Henry
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | | | - Ana Pombero
- Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain
| | - John L R Rubenstein
- Department of Psychiatry, Rock Hall, University of California at San Francisco, San Francisco, CA 94158, USA
| | | | - John Hohmann
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Andrew J Sodt
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Rob Young
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Jolene Kidney
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Ajamete Kaykas
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Damon Page
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Geri Orta
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Zackery Riley
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Simon Smith
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Paul Wohnoutka
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Luis Puelles
- Department of Human Anatomy and Psychobiology, University of Murcia, E30071 Murcia, Spain
| | - Allan R Jones
- Allen Institute for Brain Science, Seattle, WA 98103, USA
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26
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Kuwahara A, Sakai H, Xu Y, Itoh Y, Hirabayashi Y, Gotoh Y. Tcf3 represses Wnt-β-catenin signaling and maintains neural stem cell population during neocortical development. PLoS One 2014; 9:e94408. [PMID: 24832538 PMCID: PMC4022625 DOI: 10.1371/journal.pone.0094408] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 03/15/2014] [Indexed: 01/02/2023] Open
Abstract
During mouse neocortical development, the Wnt–β-catenin signaling pathway plays essential roles in various phenomena including neuronal differentiation and proliferation of neural precursor cells (NPCs). Production of the appropriate number of neurons without depletion of the NPC population requires precise regulation of the balance between differentiation and maintenance of NPCs. However, the mechanism that suppresses Wnt signaling to prevent premature neuronal differentiation of NPCs is poorly understood. We now show that the HMG box transcription factor Tcf3 (also known as Tcf7l1) contributes to this mechanism. Tcf3 is highly expressed in undifferentiated NPCs in the mouse neocortex, and its expression is reduced in intermediate neuronal progenitors (INPs) committed to the neuronal fate. We found Tcf3 to be a repressor of Wnt signaling in neocortical NPCs in a reporter gene assay. Tcf3 bound to the promoter of the proneural bHLH gene Neurogenin1 (Neurog1) and repressed its expression. Consistent with this, Tcf3 repressed neuronal differentiation and increased the self-renewal activity of NPCs. We also found that Wnt signal stimulation reduces the level of Tcf3, and increases those of Tcf1 (also known as Tcf7) and Lef1, positive mediators of Wnt signaling, in NPCs. Together, these results suggest that Tcf3 antagonizes Wnt signaling in NPCs, thereby maintaining their undifferentiated state in the neocortex and that Wnt signaling promotes the transition from Tcf3-mediated repression to Tcf1/Lef1-mediated enhancement of Wnt signaling, constituting a positive feedback loop that facilitates neuronal differentiation.
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Affiliation(s)
- Atsushi Kuwahara
- Laboratory of Cell Signaling, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Sakai
- Laboratory of Cell Signaling, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yuanjiang Xu
- Laboratory of Cell Signaling, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yasuhiro Itoh
- Laboratory of Cell Signaling, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke Hirabayashi
- Laboratory of Cell Signaling, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Yukiko Gotoh
- Laboratory of Cell Signaling, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
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27
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Marin-Muller C, Li D, Bharadwaj U, Li M, Chen C, Hodges SE, Fisher WE, Mo Q, Hung MC, Yao Q. A tumorigenic factor interactome connected through tumor suppressor microRNA-198 in human pancreatic cancer. Clin Cancer Res 2013; 19:5901-13. [PMID: 23989979 PMCID: PMC3920728 DOI: 10.1158/1078-0432.ccr-12-3776] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE The majority of pancreatic cancers overexpress mesothelin (MSLN), which contributes to enhanced proliferation, invasion, and migration. However, the MSLN regulatory network is still unclear. Here, we investigated the regulation of a panel of tumorigenic factors and explored the potential of MSLN-regulated miR-198 treatment in vivo. EXPERIMENTAL DESIGN The expression and functional regulation of the tumorigenic factors MSLN, NF-κB, and the homeobox transcription factors (TF) POU2F2 (OCT-2), Pre-B-cell leukemia homeobox factor 1 (PBX-1), valosin-containing protein (VCP), and miR-198 were studied in pancreatic cancer cell lines, patient tumor samples, and xenograft pancreatic cancer mouse models. RESULTS We found that miR-198 is downregulated in pancreatic cancer and is involved in an intricate reciprocal regulatory loop with MSLN, which represses miR-198 through NF-κB-mediated OCT-2 induction. Furthermore, miR-198 repression leads to overexpression of PBX-1 and VCP. The dysregulated PBX-1/VCP axis leads to increased tumorigenicity. Reconstitution of miR-198 in pancreatic cancer cells results in reduced tumor growth, metastasis, and increased survival through direct targeting MSLN, PBX-1, and VCP. Most interestingly, reduced levels of miR-198 in human tissue samples are associated with upregulation of these tumorigenic factors (MSLN, OCT-2, PBX-1, VCP) and predict poor survival. Reduced miR-198 expression links this tumor network signature and prognosticates poor patient outcome. High miR-198 disrupts the network and predicts better prognosis and increased survival. CONCLUSIONS miR-198 acts as a central tumor suppressor and modulates the molecular makeup of a critical interactome in pancreatic cancer, indicating a potential prognostic marker signature and the therapeutic potential of attacking this tumorigenic network through a central vantage point.
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MESH Headings
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Animals
- Apoptosis/drug effects
- Apoptosis/genetics
- Autocrine Communication/genetics
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/mortality
- Carcinoma, Pancreatic Ductal/pathology
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Cell Survival/genetics
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Disease Models, Animal
- Enzyme Activation
- GPI-Linked Proteins/genetics
- GPI-Linked Proteins/metabolism
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Genes, Tumor Suppressor
- Humans
- Mesothelin
- Mice
- MicroRNAs/genetics
- NF-kappa B/metabolism
- Neoplasm Metastasis
- Octamer Transcription Factor-2/metabolism
- Open Reading Frames/genetics
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/mortality
- Pancreatic Neoplasms/pathology
- Pre-B-Cell Leukemia Transcription Factor 1
- Prognosis
- Promoter Regions, Genetic
- Protein Binding
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Tumor Burden/genetics
- Tumor Necrosis Factor-alpha/pharmacology
- Valosin Containing Protein
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Affiliation(s)
- Christian Marin-Muller
- Authors' Affiliations: Molecular Surgeon Research Center, Michael E. DeBakey Department of Surgery, Department of Molecular Virology and Microbiology, Duncan Cancer Center, Baylor College of Medicine; and Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, Graduate Institute of Cancer Biology, China Medical University, Taichung, Taiwan; Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
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28
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Tantin D. Oct transcription factors in development and stem cells: insights and mechanisms. Development 2013; 140:2857-66. [PMID: 23821033 DOI: 10.1242/dev.095927] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The POU domain family of transcription factors regulates developmental processes ranging from specification of the early embryo to terminal differentiation. About half of these factors display substantial affinity for an 8 bp DNA site termed the octamer motif, and are hence known as Oct proteins. Oct4 (Pou5f1) is a well-known Oct factor, but there are other Oct proteins with varied and essential roles in development. This Primer outlines our current understanding of Oct proteins and the regulatory mechanisms that govern their role in developmental processes and concludes with the assertion that more investigation into their developmental functions is needed.
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Affiliation(s)
- Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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29
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Mayol G, Martín-Subero JI, Ríos J, Queiros A, Kulis M, Suñol M, Esteller M, Gómez S, Garcia I, de Torres C, Rodríguez E, Galván P, Mora J, Lavarino C. DNA hypomethylation affects cancer-related biological functions and genes relevant in neuroblastoma pathogenesis. PLoS One 2012; 7:e48401. [PMID: 23144874 PMCID: PMC3492354 DOI: 10.1371/journal.pone.0048401] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/01/2012] [Indexed: 02/06/2023] Open
Abstract
Neuroblastoma (NB) pathogenesis has been reported to be closely associated with numerous genetic alterations. However, underlying DNA methylation patterns have not been extensively studied in this developmental malignancy. Here, we generated microarray-based DNA methylation profiles of primary neuroblastic tumors. Stringent supervised differential methylation analyses allowed us to identify epigenetic changes characteristic for NB tumors as well as for clinical and biological subtypes of NB. We observed that gene-specific loss of DNA methylation is more prevalent than promoter hypermethylation. Remarkably, such hypomethylation affected cancer-related biological functions and genes relevant to NB pathogenesis such as CCND1, SPRR3, BTC, EGF and FGF6. In particular, differential methylation in CCND1 affected mostly an evolutionary conserved functionally relevant 3′ untranslated region, suggesting that hypomethylation outside promoter regions may play a role in NB pathogenesis. Hypermethylation targeted genes involved in cell development and proliferation such as RASSF1A, POU2F2 or HOXD3, among others. The results derived from this study provide new candidate epigenetic biomarkers associated with NB as well as insights into the molecular pathogenesis of this tumor, which involves a marked gene-specific hypomethylation.
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Affiliation(s)
- Gemma Mayol
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - José I. Martín-Subero
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain
| | - José Ríos
- Laboratory of Biostatistics and Epidemiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Clinical Pharmacology Service, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - Ana Queiros
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain
| | - Marta Kulis
- Hematopathology Unit, Hospital Clinic, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL),L'Hospitalet, Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Soledad Gómez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Idoia Garcia
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Eva Rodríguez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Patricia Galván
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
- * E-mail:
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Maioli M, Rinaldi S, Santaniello S, Castagna A, Pigliaru G, Gualini S, Cavallini C, Fontani V, Ventura C. Radio electric conveyed fields directly reprogram human dermal skin fibroblasts toward cardiac, neuronal, and skeletal muscle-like lineages. Cell Transplant 2012; 22:1227-35. [PMID: 23057961 DOI: 10.3727/096368912x657297] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Somatic cells can be directly reprogrammed to alternative differentiated fates without first becoming stem/progenitor cells. Nevertheless, the initial need for viral-mediated gene delivery renders this strategy unsafe in humans. Here, we provide evidence that exposure of human skin fibroblasts to a Radio Electric Asymmetric Conveyer (REAC), an innovative device delivering radio electric conveyed fields at a radiofrequency of 2.4 GHz, afforded remarkable commitment toward cardiac, neuronal, and skeletal muscle lineages. REAC induced the transcription of tissue-restricted genes, including Mef2c, Tbx5, GATA4, Nkx2.5, and prodynorphin for cardiac reprogramming, as well as myoD, and neurogenin 1 for skeletal myogenesis and neurogenesis, respectively. Conversely, REAC treatment elicited a biphasic effect on a number of stemness-related genes, leading to early transcriptional increase of Oct4, Sox2, cMyc, Nanog, and Klf4 within 6-20 h, followed by a downregulation at later times. The REAC action bypassed a persistent reprogramming toward an induced pluripotent stem cell-like state and involved the transcriptional induction of the NADPH oxidase subunit Nox4. Our results show for the first time the feasibility of using a physical stimulus to afford the expression of pluripotentiality in human adult somatic cells up to the attainment of three major target lineages for regenerative medicine.
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Affiliation(s)
- Margherita Maioli
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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Xing Y, Li A, Borok Z, Li C, Minoo P. NOTCH1 is required for regeneration of Clara cells during repair of airway injury. Stem Cells 2012; 30:946-55. [PMID: 22331706 DOI: 10.1002/stem.1059] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The airways of the mammalian lung are lined with highly specialized epithelial cell types that are the targets of airborne toxicants and injury. Notch signaling plays an important role in the ontogeny of airway epithelial cells, but its contributions to recruitment, expansion or differentiation of resident progenitor/stem cells, and repair and re-establishment of the normal composition of airway epithelium following injury have not been addressed. In this study, the role of a specific Notch receptor, Notch1, was investigated by targeted inactivation in the embryonic lung epithelium using the epithelial-specific Gata5-Cre driver line. Notch1-deficient mice are viable without discernible defects in pulmonary epithelial cell-fate determination and differentiation. However, in an experimental model of airway injury, activity of Notch1 is found to be required for normal repair of the airway epithelium. Absence of Notch1 reduced the ability of a population of cells distinguished by expression of PGP9.5, otherwise a marker of pulmonary neuroendocrine cells, which appears to serve as a reservoir for regeneration of Clara cells. Hairy/enhancer of split-5 (Hes5) and paired-box-containing gene 6 (Pax6) were found to be downstream targets of Notch1. Both Hes5 and Pax6 expressions were significantly increased in association with Clara cell regeneration in wild-type lungs. Ablation of Notch1 reduced Hes5 and Pax6 and inhibited airway epithelial repair. Thus, although dispensable in developmental ontogeny of airway epithelial cells, normal activity of Notch1 is required for repair of the airway epithelium. The signaling pathway by which Notch1 regulates the repair process includes stimulation of Hes5 and Pax6 gene expression.
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Affiliation(s)
- Yiming Xing
- Department of Pediatrics, Division of Neonatology, Will Rogers Institute Pulmonary Research Center, University of Southern California, Keck School of Medicine, Los Angeles, California, USA
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Chen CK, Chen WY, Chien CT. The POU-domain protein Pdm3 regulates axonal targeting of R neurons in the Drosophila ellipsoid body. Dev Neurobiol 2012; 72:1422-32. [PMID: 22190420 DOI: 10.1002/dneu.22003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 11/06/2022]
Abstract
The ability of axons to project correctly to the target is essential for the formation of complex neural networks. The intrinsic regulation of this process is still unclear. Here, we show that POU domain motif 3 (Pdm3) is required in ring (R) neurons to control precise axon targeting to the Drosophila ellipsoid body (EB). Pdm3 is expressed in neurons of the central nervous system in larvae and adults and required for the normal development of the EB of the central complex in the adult brain. The normal EB structure is abolished in pdm3 mutants, and this phenotype is rescued by pdm3 expression in R neurons, suggesting that the defect in axonal targeting of R neurons is the major cause in EB malformation in pdm3 mutants. We show that cell fate determination, dendritic arborization, and initial axon projection of R neurons are normal while the axonal targeting to the EB is defective in pdm3 mutants.
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Affiliation(s)
- Chien-Kuo Chen
- Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
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33
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Alternative splicing: decoding an expansive regulatory layer. Curr Opin Cell Biol 2012; 24:323-32. [DOI: 10.1016/j.ceb.2012.03.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/27/2012] [Accepted: 03/08/2012] [Indexed: 12/14/2022]
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Affiliation(s)
- Mary Johnson
- Synatom Research, Princeton, New Jersey, United States
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35
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Abstract
Genome-wide analyses of metazoan transcriptomes have revealed an unexpected level of mRNA diversity that is generated by alternative splicing. Recently, regulatory networks have been identified through which splicing promotes dynamic remodelling of the transcriptome to promote physiological changes, which involve robust and coordinated alternative splicing transitions. The regulation of splicing in yeast, worms, flies and vertebrates affects a variety of biological processes. The functional classes of genes that are regulated by alternative splicing include both those with widespread homeostatic activities and those with cell-type-specific functions. Alternative splicing can drive determinative physiological change or can have a permissive role by providing mRNA variability that is used by other regulatory mechanisms.
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36
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Synthesis and biological evaluation of a novel human stem/progenitor cells proliferation activator: 4-(4-(5-mercapto-1,3,4-oxadiazol-2-yl)phenyl) thiosemicarbazide (Stemazole). Eur J Med Chem 2011; 46:2930-6. [DOI: 10.1016/j.ejmech.2011.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/21/2011] [Accepted: 04/04/2011] [Indexed: 02/05/2023]
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37
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Carén H, Djos A, Nethander M, Sjöberg RM, Kogner P, Enström C, Nilsson S, Martinsson T. Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma. BMC Cancer 2011; 11:66. [PMID: 21314941 PMCID: PMC3045360 DOI: 10.1186/1471-2407-11-66] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 02/11/2011] [Indexed: 11/27/2022] Open
Abstract
Background Epigenetic mechanisms such as DNA methylation and histone modifications are important regulators of gene expression and are frequently involved in silencing tumor suppressor genes. Methods In order to identify genes that are epigenetically regulated in neuroblastoma tumors, we treated four neuroblastoma cell lines with the demethylating agent 5-Aza-2'-deoxycytidine (5-Aza-dC) either separately or in conjunction with the histone deacetylase inhibitor trichostatin A (TSA). Expression was analyzed using whole-genome expression arrays to identify genes activated by the treatment. These data were then combined with data from genome-wide DNA methylation arrays to identify candidate genes silenced in neuroblastoma due to DNA methylation. Results We present eight genes (KRT19, PRKCDBP, SCNN1A, POU2F2, TGFBI, COL1A2, DHRS3 and DUSP23) that are methylated in neuroblastoma, most of them not previously reported as such, some of which also distinguish between biological subsets of neuroblastoma tumors. Differential methylation was observed for the genes SCNN1A (p < 0.001), PRKCDBP (p < 0.001) and KRT19 (p < 0.01). Among these, the mRNA expression of KRT19 and PRKCDBP was significantly lower in patients that have died from the disease compared with patients with no evidence of disease (fold change -8.3, p = 0.01 for KRT19 and fold change -2.4, p = 0.04 for PRKCDBP). Conclusions In our study, a low methylation frequency of SCNN1A, PRKCDBP and KRT19 is significantly associated with favorable outcome in neuroblastoma. It is likely that analysis of specific DNA methylation will be one of several methods in future patient therapy stratification protocols for treatment of childhood neuroblastomas.
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Affiliation(s)
- Helena Carén
- Department of Clinical Genetics, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, SE-41345 Gothenburg, Sweden.
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Korade Z, Xu L, Shelton R, Porter NA. Biological activities of 7-dehydrocholesterol-derived oxysterols: implications for Smith-Lemli-Opitz syndrome. J Lipid Res 2010; 51:3259-69. [PMID: 20702862 DOI: 10.1194/jlr.m009365] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Smith-Lemli-Opitz syndrome (SLOS) is a metabolic and developmental disorder caused by mutations in the gene encoding the enzyme 7-dehydrocholesterol reductase (Dhcr7). This reductase catalyzes the last step in cholesterol biosynthesis, and levels of 7-dehydrocholesterol (7-DHC), the substrate for this enzyme, are elevated in SLOS patients as a result of this defect. Our group has previously shown that 7-DHC is extremely prone to free radical autoxidation, and we identified about a dozen different oxysterols formed from oxidation of 7-DHC. We report here that 7-DHC-derived oxysterols reduce cell viability in a dose- and time-dependent manner, some of the compounds showing activity at sub-micromolar concentrations. The reduction of cell survival is caused by a combination of reduced proliferation and induced differentiation of the Neuro2a cells. The complex 7-DHC oxysterol mixture added to control Neuro2a cells also triggers the gene expression changes that were previously identified in Dhcr7-deficient Neuro2a cells. Based on the identification of overlapping gene expression changes in Dhcr7-deficient and 7-DHC oxysterol-treated Neuro2a cells, we hypothesize that some of the pathophysiological findings in the mouse SLOS model and SLOS patients might be due to accumulated 7-DHC oxysterols.
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Affiliation(s)
- Zeljka Korade
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
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Garnier D, Milsom C, Magnus N, Meehan B, Weitz J, Yu J, Rak J. Role of the tissue factor pathway in the biology of tumor initiating cells. Thromb Res 2010; 125 Suppl 2:S44-50. [PMID: 20434004 DOI: 10.1016/s0049-3848(10)70012-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Oncogenic transformation and aberrant cellular differentiation are regarded as key processes leading to malignancy. They produce heterogenous cellular populations including subsets of tumour initiating cells (TICs), also known as cancer stem cells (CSCs). Intracellular events involved in these changes profoundly impact the extracellular and systemic constituents of cancer progression, including those dependent on the vascular system. This includes angiogenesis, vasculogenesis, activation of the coagulation system and formation of CSC-related and premetastatic niches. Tissue factor (TF) is a unique cell-associated receptor for coagulation factor VIIa, initiator of blood coagulation, and mediator of cellular signalling, all of which influence vascular homeostasis. Our studies established a link between oncogenic events, angiogenesis and the elevated expression of TF in several types of cancer cells. The latter suggests that cancer coagulopathy and cellular events attributed to the coagulation system may have cancer-specific and genetic causes. Indeed, in human glioma cells, a transforming mutant of the epidermal growth factor receptor (EGFRvIII) triggers not only the expression of TF, but also of its ligand (factor VII) and protease activated receptors (PAR-1 and PAR-2). Consequently, tumour cells expressing EGFRvIII become hypersensitive to contact with blood borne proteases (VIIa, thrombin), which upregulate their production of angiogenic factors (VEGF and IL-8), and contribute to formation of the growth promoting microenvironment (niche). Moreover, TF overexpression accompanies features of cellular aggressiveness such as markers of CSCs (CD133), epithelial-to-mesenchymal transition (EMT) and expression of the angiogenic and prometastatic phenotype. Conversely, TF blocking antibodies inhibit tumour growth, angiogenesis, and especially tumour initiation upon injection of threshold numbers of tumourigenic cells. Likewise, TF depletion in the host compartment (e.g. in low-TF mice) perturbs tumour initiation. These observations suggest that both cancer cells and their adjacent host stroma contribute TF activity to the tumour microenvironment. We postulate that the TF pathway may play an important role in formation of the vascular niche for tumour initiating CSCs, through its procoagulant and signalling effects. Therapeutic blockade of these mechanisms could hamper tumour initiation processes, which are dependent on CSCs and participate in tumour onset, recurrence, drug resistance and metastasis.
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Massouras A, Decouttere F, Hens K, Deplancke B. WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data. Nucleic Acids Res 2010; 38:W378-84. [PMID: 20501601 PMCID: PMC2896179 DOI: 10.1093/nar/gkq431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users.
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Affiliation(s)
- Andreas Massouras
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Alternative splicing in stem cell self-renewal and diferentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 695:92-104. [PMID: 21222201 DOI: 10.1007/978-1-4419-7037-4_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This chapter provides a review of recent advances in understanding the importance of alternative pre-messenger RNA splicing in stem cell biology. The majority of transcribed pre-mRNAs undergo RNA splicing where introns are excised and exons are juxtaposed to form mature messenger RNA sequences. This regulated, selective removal of whole or portions of exons by alternative splicing provides avenues for control of RNA abundance and proteome diversity. We discuss several examples of key alternative splicing events in stem cell biology and provide an overview of recently developed microarray and sequencing technologies that enable systematic and genome-wide assessment of the extent of alternative splicing during stem cell differentiation.
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Milsom C, Magnus N, Meehan B, Al-Nedawi K, Garnier D, Rak J. Tissue factor and cancer stem cells: is there a linkage? Arterioscler Thromb Vasc Biol 2009; 29:2005-14. [PMID: 19628788 DOI: 10.1161/atvbaha.108.177444] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A common feature in the progression of multiple human malignancies is the protracted deregulation of the coagulation system, often referred to as cancer coagulopathy. Indeed, cancer cells and their vascular stroma often exhibit procoagulant properties, of which deregulation of tissue factor (TF) expression is a notable, although not the sole example. These changes can be traced to oncogenic influences affecting epidermal growth factor receptor (EGFR), EGFRvIII, K-ras, p53, PTEN, and probably many other proto-oncogenes and tumor suppressors in tumor parenchyma. Cancer stem cells (CSCs)/tumor initiating cells (TICs) are thought to represent the primary target and the main cellular effector through which oncogenic mutations exert their tumor-inducing effects. In so doing, CSCs/TICs depend on interactions with the tumor vasculature, which forms supportive niches for their clonal growth. We postulate that TF contributes to these interactions (directly or indirectly) through procoagulant and signaling effects, the latter executed in concert with juxtaposed protease activated receptors (mainly PAR-1 and PAR-2). TF/PAR system acts as a "blood sensing" mechanism, whereby cancer cells, including CSCs/TICs, may respond to plasma proteases (Factors VIIa, Xa, and IIa) and their related microenvironmental changes (fibrin deposition, activation of platelets). A growing body of still largely circumstantial evidence suggests that these events may contribute to the CSC/TIC niche, which could influence tumor initiation, metastasis, recurrence, and therapeutic intractability. Indeed, certain types of cancer cells harboring markers of CSCs (CD133) exhibit elevated TF expression and depend on this receptor to efficiently initiate tumor growth. We propose that both tumor cell-associated and host-related TF could influence the properties of CSCs, and that agents targeting the TF/PAR system may represent a hitherto unappreciated therapeutic opportunity to control cancer progression by influencing the CSC/TIC compartment.
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Affiliation(s)
- Chloe Milsom
- Montreal Children's Hospital, McGill University, QC, Canada
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Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M. Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev 2009; 23:1351-63. [PMID: 19487574 DOI: 10.1101/gad.1781909] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Complex biological processes are often regulated, at least in part, by the binding of transcription factors to their targets. Recently, considerable effort has been made to analyze the binding of relevant factors to the suite of targets they regulate, thereby generating a regulatory circuit map. However, for most studies the dynamics of binding have not been analyzed, and thus the temporal order of events and mechanisms by which this occurs are poorly understood. We globally analyzed in detail the temporal order of binding of several key factors involved in the salt response of yeast to their target genes. Analysis of Yap4 and Sko1 binding to their target genes revealed multiple temporal classes of binding patterns: (1) constant binding, (2) rapid induction, (3) slow induction, and (4) transient induction. These results demonstrate that individual transcription factors can have multiple binding patterns and help define the different types of temporal binding patterns used in eukaryotic gene regulation. To investigate these binding patterns further, we also analyzed the binding of seven other key transcription factors implicated in osmotic regulation, including Hot1, Msn1, Msn2, Msn4, Skn7, and Yap6, and found significant coassociation among the different factors at their gene targets. Moreover, the binding of several key factors was correlated with distinct classes of Yap4- and Sko1-binding patterns and with distinct types of genes. Gene expression studies revealed association of Yap4, Sko1, and other transcription factor-binding patterns with different gene expression patterns. The integration and analysis of binding and expression information reveals a complex dynamic and hierarchical circuit in which specific combinations of transcription factors target distinct sets of genes at discrete times to coordinate a rapid and important biological response.
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Affiliation(s)
- Li Ni
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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