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Athanasopoulou K, Adamopoulos PG, Scorilas A. Structural characterization and expression analysis of novel MAPK1 transcript variants with the development of a multiplexed targeted nanopore sequencing approach. Int J Biochem Cell Biol 2022; 150:106272. [PMID: 35878809 DOI: 10.1016/j.biocel.2022.106272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/17/2022] [Accepted: 07/21/2022] [Indexed: 11/27/2022]
Abstract
Mitogen-activated protein kinases (MAPKs) represent a protein family firmly involved in many signaling cascades, regulating a vast spectrum of stimulated cellular processes. Studies have shown that alternatively spliced isoforms of MAPKs play a crucial role in determining the desired cell fate in response to specific stimulations. Although the implication of most MAPKs transcript variants in the MAPK signaling cascades has been clarified, the transcriptional profile of a pivotal member, MAPK1, has not been investigated for the existence of additional isoforms. In the current study we developed and implemented targeted long-read and short-read sequencing approaches to identify novel MAPK1 splice variants. The combination of nanopore sequencing and NGS enabled the implementation of a long-read polishing pipeline using error-rate correction algorithms, which empowered the high accuracy of the results and increased the sequencing efficiency. The utilized multiplexing option in the nanopore sequencing approach allowed not only the identification of novel MAPK1 mRNAs, but also elucidated their expression profile in multiple human malignancies and non-cancerous cell lines. Our study highlights for the first time the existence of ten previously undescribed MAPK1 mRNAs (MAPK1 v.3 - v.12) and evaluates their relative expression levels in comparison to the main MAPK1 v.1. The optimization and employment of qPCR assays revealed that MAPK1 v.3 - v.12 can be quantified in a wide spectrum of human cell lines with notable specificity. Finally, our findings suggest that the novel protein-coding mRNAs are highly expected to participate in the regulation of MAPK pathways, demonstrating differential localizations and functionalities.
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Affiliation(s)
- Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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Kim N. pH variation impacts molecular pathways associated with somatic cell reprogramming and differentiation of pluripotent stem cells. Reprod Med Biol 2021; 20:20-26. [PMID: 33488280 PMCID: PMC7812493 DOI: 10.1002/rmb2.12346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/27/2020] [Accepted: 08/10/2020] [Indexed: 12/19/2022] Open
Abstract
RATIONALE The study of somatic cell reprogramming and cell differentiation is essential for the application of recent techniques in regenerative medicine. It is, specifically, necessary to determine the appropriate conditions required for the induction of reprogramming and cell differentiation. METHODS Based on a comprehensive literature review, the effects of pH fluctuation on alternative splicing, mitochondria, plasma membrane, and phase separation, in several cell types are discussed. Additionally, the associated molecular pathways important for the induction of differentiation and reprogramming are reviewed. RESULTS While cells change their state, several factors such as cytokines and physical parameters affect cellular reprogramming and differentiation. As the extracellular and intracellular pH affects biophysical phenomena in a cell, the effects of pH fluctuation can ultimately decide the cell fate through molecular pathways. Though few studies have reported on the direct effects of culture pH on cell state, there is substantial information on the pathways related to stem cell differentiation and somatic cell reprogramming that can be stimulated by environmental pH. CONCLUSION Environmental pH fluctuations may decide cell fate through the molecular pathways associated with somatic cell reprogramming and cell differentiation.
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Affiliation(s)
- Narae Kim
- Nucleic Acid Chemistry and EngineeringOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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Osipovich AB, Long Q, Manduchi E, Gangula R, Hipkens SB, Schneider J, Okubo T, Stoeckert CJ, Takada S, Magnuson MA. Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3. Development 2014; 141:2939-49. [PMID: 25053427 PMCID: PMC4197673 DOI: 10.1242/dev.104810] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Insulinoma associated 1 (Insm1) plays an important role in regulating the development of cells in the central and peripheral nervous systems, olfactory epithelium and endocrine pancreas. To better define the role of Insm1 in pancreatic endocrine cell development we generated mice with an Insm1GFPCre reporter allele and used them to study Insm1-expressing and null populations. Endocrine progenitor cells lacking Insm1 were less differentiated and exhibited broad defects in hormone production, cell proliferation and cell migration. Embryos lacking Insm1 contained greater amounts of a non-coding Neurog3 mRNA splice variant and had fewer Neurog3/Insm1 co-expressing progenitor cells, suggesting that Insm1 positively regulates Neurog3. Moreover, endocrine progenitor cells that express either high or low levels of Pdx1, and thus may be biased towards the formation of specific cell lineages, exhibited cell type-specific differences in the genes regulated by Insm1. Analysis of the function of Ripply3, an Insm1-regulated gene enriched in the Pdx1-high cell population, revealed that it negatively regulates the proliferation of early endocrine cells. Taken together, these findings indicate that in developing pancreatic endocrine cells Insm1 promotes the transition from a ductal progenitor to a committed endocrine cell by repressing a progenitor cell program and activating genes essential for RNA splicing, cell migration, controlled cellular proliferation, vasculogenesis, extracellular matrix and hormone secretion.
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Affiliation(s)
- Anna B Osipovich
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qiaoming Long
- Department of Animal Science, Cornell University, Ithaca, NY 14850, USA
| | - Elisabetta Manduchi
- Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Rama Gangula
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Susan B Hipkens
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Judsen Schneider
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tadashi Okubo
- Department of Laboratory Animal Science, Kitasato University School of Medicine, Sagamihara, 252-0374, Japan
| | - Christian J Stoeckert
- Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Shinji Takada
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Mark A Magnuson
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Ma Y, Zhang X, Ma H, Ren Y, Sun Y, Wang Q, Shi J. Bioinformatic analysis of the four transcription factors used to induce pluripotent stem cells. Cytotechnology 2013; 66:967-78. [PMID: 24129607 PMCID: PMC4235945 DOI: 10.1007/s10616-013-9649-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 09/20/2013] [Indexed: 01/22/2023] Open
Abstract
Induced pluripotent stem (iPS) cells are a type of pluripotent stem cell artificially derived from non-pluripotent cells by overexpressing the transcription factors Oct4, Sox2, Klf4 and Nanog. These transcription factors play a pivotal role in stem cells; however, the function of these factors are not fully characterized. In this study, we analyzed Oct4, Sox2, Klf4 and Nanog in ten different species using bioinformatics, to provide more knowledge of the function of these genes. Nanog does not exist in the invertebrates Caenorhabditis elegans and Drosophila melanogaster, indicating that the absence of Nanog may be responsible for the developmental differences between vertebrates and invertebrates. Construction of phylogenetic trees confirmed that the function of Nanog is conserved from fish to mammals. The effect of alternative splicing on the protein domains present in Oct4, Sox2, Klf4 and Nanog were also analyzed. Examination of the expression patterns in human stem cells, iPS cells and normal tissues showed that Oct4, Sox2, Klf4 and Nanog are expressed at similar levels in iPS cells and embryonic stem cells, and expression of all four transcription factors decreases after differentiation. Expression of Klf4 reduced to the least during differentiation, and Klf4 was found to be specifically expressed in several normal tissues, especially the salivary gland. In this paper, we systematically indentified the family proteins of the four transcription factors used to induce pluripotent stem cells, and then analyzed their evolution status, composed of those protein domains, alternative splicing translation, expression status and interaction networks. Those analysis could shed a light for further research of iPS.
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Affiliation(s)
- Yuzhen Ma
- Centre of Reproductive Medicine, Inner Mongolia Hospital, Inner Mongolia, Huhhot, 010017, China
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Fu RH, Liu SP, Huang SJ, Chen HJ, Chen PR, Lin YH, Ho YC, Chang WL, Tsai CH, Shyu WC, Lin SZ. Aberrant Alternative Splicing Events in Parkinson's Disease. Cell Transplant 2013; 22:653-61. [PMID: 23127794 DOI: 10.3727/096368912x655154] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing (AS) using a sole gene to express multiple transcripts with diverse protein coding sequences and/or RNA regulatory elements raises genomic complexities. In the nervous system, several thousand AS events play important roles in ion transportation, receptor recognition, neurotransmission, memory, and learning. Not surprisingly, AS influences human physiology, development, and disease. Many research studies have focused on aberrant AS in nervous system diseases, including Parkinson's disease (PD), the second most common progressive neurodegenerative disorder of the central nervous system. PD affects the lives of several million people globally. It is caused by protein aggregation, such as in Lewy bodies, and the loss of dopamine-containing neurons in the substantia nigra of the midbrain. To our knowledge, six genes, including PARK2, SNCAIP, LRRK2, SNCA, SRRM2, and MAPT, are involved in aberrant AS events in PD patients. In this review, we highlight the relevance of aberrant AS in PD and discuss the use of an aberrant AS profile as a potential diagnostic or prognostic marker for PD and as a possible means of applying therapy.
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Affiliation(s)
- Ru-Huei Fu
- Center for Neuropsychiatry, China Medical University Hospital, Taichung, Taiwan, ROC
- Graduate Institute of Immunology, China Medical University, Taichung, Taiwan, ROC
| | - Shih-Ping Liu
- Center for Neuropsychiatry, China Medical University Hospital, Taichung, Taiwan, ROC
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan, ROC
| | - Shyh-Jer Huang
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan, ROC
| | - Hung-Jen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan, ROC
| | - Pin-Ru Chen
- Graduate Institute of Immunology, China Medical University, Taichung, Taiwan, ROC
| | - Ya-Hsien Lin
- Graduate Institute of Immunology, China Medical University, Taichung, Taiwan, ROC
| | - Yu-Chen Ho
- Graduate Institute of Immunology, China Medical University, Taichung, Taiwan, ROC
| | - Wen-Lin Chang
- Graduate Institute of Immunology, China Medical University, Taichung, Taiwan, ROC
| | - Chang-Hai Tsai
- Department of Pediatrics, China Medical University Hospital, Taichung, Taiwan, ROC
- Department of Healthcare Administration, Asia University, Taichung, Taiwan, ROC
| | - Woei-Cherng Shyu
- Center for Neuropsychiatry, China Medical University Hospital, Taichung, Taiwan, ROC
- Graduate Institute of Immunology, China Medical University, Taichung, Taiwan, ROC
| | - Shinn-Zong Lin
- Center for Neuropsychiatry, China Medical University Hospital, Taichung, Taiwan, ROC
- Graduate Institute of Immunology, China Medical University, Taichung, Taiwan, ROC
- Department of Healthcare Administration, Asia University, Taichung, Taiwan, ROC
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Affiliation(s)
- Shinn-Zong Lin
- Center for Neuropsychiatry and Department of Neurosurgery, China Medical University Hospital, Taichung, Taiwan
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Lin JC, Tarn WY. RBM4 down-regulates PTB and antagonizes its activity in muscle cell-specific alternative splicing. ACTA ACUST UNITED AC 2011; 193:509-20. [PMID: 21518792 PMCID: PMC3087008 DOI: 10.1083/jcb.201007131] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RBM4 activates exon skipping of PTB transcripts to suppress PTB expression and counteracts PTB-mediated inhibition of alternative splicing during myogenesis. Alternative splicing contributes largely to cell differentiation and functional specification. We previously reported that the RNA-binding protein RBM4 antagonizes the activity of splicing factor PTB to modulate muscle cell–specific exon selection of α-tropomyosin. Here we show that down-regulation of PTB and its neuronal analogue nPTB during muscle cell differentiation may involve alternative splicing-coupled nonsense-mediated mRNA decay. RBM4 regulates PTB/nPTB expression by activating exon skipping of their transcripts during myogenesis. Moreover, RBM4 and PTB target a common set of transcripts that undergo muscle cell–specific alternative splicing. Overexpression of RBM4 invariably promoted expression of muscle cell–specific isoforms, which recapitulated in vivo alternative splicing changes during muscle differentiation, whereas PTB acted oppositely to RBM4 in expression of mRNA isoforms specific for late-stage differentiation. Therefore, RBM4 may synergize its effect on muscle cell–specific alternative splicing by down-regulating PTB expression and antagonizing the activity of PTB in exon selection, which highlights a hierarchical role for RBM4 in a splicing cascade that regulates myogenesis.
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Affiliation(s)
- Jung-Chun Lin
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan
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Eve DJ, Fillmore RW, Borlongan CV, Sanberg PR. Stem cell research in cell transplantation: sources, geopolitical influence, and transplantation. Cell Transplant 2010; 19:1493-509. [PMID: 21054954 DOI: 10.3727/096368910x540612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
If the rapidly progressing field of stem cell research reaches its full potential, successful treatments and enhanced understanding of many diseases are the likely results. However, the full potential of stem cell science will only be reached if all possible avenues can be explored and on a worldwide scale. Until 2009, the US had a highly restrictive policy on obtaining cells from human embryos and fetal tissue, a policy that pushed research toward the use of adult-derived cells. Currently, US policy is still in flux, and retrospective analysis does show the US lagging behind the rest of the world in the proportional increase in embryonic/fetal stem cell research. The majority of US studies being on either a limited number of cell lines, or on cells derived elsewhere (or funded by other sources than Federal) rather than on freshly isolated embryonic or fetal material. Neural, mesenchymal, and the mixed stem cell mononuclear fraction are the most commonly investigated types, which can generally be classified as adult-derived stem cells, although roughly half of the neural stem cells are fetal derived. Other types, such as embryonic and fat-derived stem cells, are increasing in their prominence, suggesting that new types of stem cells are still being pursued. Sixty percent of the reported stem cell studies involved transplantation, of which over three quarters were allogeneic transplants. A high proportion of the cardiovascular systems articles were on allogeneic transplants in a number of different species, including several autologous studies. A number of pharmaceutical grade stem cell products have also recently been tested and reported on. Stem cell research shows considerable promise for the treatment of a number of disorders, some of which have entered clinical trials; over the next few years it will be interesting to see how these treatments progress in the clinic.
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Affiliation(s)
- David J Eve
- Center of Excellence for Aging & Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, FL 33612, USA.
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Affiliation(s)
- Shinn-Zong Lin
- Scientific Committee Professor of Neurosurgery, China Medical University Superintendent, China Medical University Beigan Hospital
- China Medical University Hospital Taichung, Taiwan
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