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Liu S, Yue S, Guo Y, Han JY, Wang H. Sorafenib induces cardiotoxicity through RBM20-mediated alternative splicing of sarcomeric and mitochondrial genes. Pharmacol Res 2023; 198:107017. [PMID: 38006979 DOI: 10.1016/j.phrs.2023.107017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023]
Abstract
Sorafenib, a multi-targeted tyrosine kinase inhibitor, is a first-line treatment for advanced solid tumors, but it induces many adverse cardiovascular events, including myocardial infarction and heart failure. These cardiac defects can be mediated by alternative splicing of genes critical for heart function. Whether alternative splicing plays a role in sorafenib-induced cardiotoxicity remains unclear. Transcriptome of rat hearts or human cardiomyocytes treated with sorafenib was analyzed and validated to define alternatively spliced genes and their impact on cardiotoxicity. In rats, sorafenib caused severe cardiotoxicity with decreased left ventricular systolic pressure, elongated sarcomere, enlarged mitochondria and decreased ATP. This was associated with alternative splicing of hundreds of genes in the hearts, many of which were targets of a cardiac specific splicing factor, RBM20. Sorafenib inhibited RBM20 expression in both rat hearts and human cardiomyocytes. The splicing of RBM20's targets, SLC25A3 and FHOD3, was altered into fetal isoforms with decreased function. Upregulation of RBM20 during sorafenib treatment reversed the pathogenic splicing of SLC25A3 and FHOD3, and enhanced the phosphate transport into mitochondria by SLC25A3, ATP synthesis and cell survival.We envision this regulation may happen in many drug-induced cardiotoxicity, and represent a potential druggable pathway for mitigating sorafenib-induced cardiotoxicity.
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Affiliation(s)
- Songming Liu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shanshan Yue
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing 100191, China
| | - Yuxuan Guo
- Peking University Institute of Cardiovascular Sciences, Peking University Health Science Center, School of Basic Medical Sciences, Beijing 100191, China
| | - Jing-Yan Han
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing 100191, China.
| | - Huan Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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102
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Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2023:S2090-1232(23)00354-5. [PMID: 37981087 DOI: 10.1016/j.jare.2023.11.017] [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: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
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Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
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103
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Najjar R, Mustelin T. Prediction of alternative pre-mRNA splicing outcomes. Sci Rep 2023; 13:20000. [PMID: 37968320 PMCID: PMC10651857 DOI: 10.1038/s41598-023-47348-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023] Open
Abstract
To understand the biological impact of alternative pre-mRNA splicing, it is vital to know which exons are involved, what protein domains they encode, and how the translated isoforms differ. Therefore, we developed a computational pipeline (RiboSplitter) focused on functional effect prediction. It builds on event-based alternative splicing detection with additional filtering steps leading to more efficient statistical testing, and with detection of isoform-specific protein changes. A key methodological advance is reading frame prediction by translating exonic DNA in all possible frames, then finding a single open reading frame, or a single frame with matches to known proteins of the gene. This allowed unambiguous translation in 93.9% of alternative splicing events when tested on RNA-sequencing data of B cells from Sjögren's syndrome patients. RiboSplitter does not depend on reference annotations and translates events even when one or both isoform(s) are novel (unannotated). RiboSplitter's visualizations illustrate each event with translation outcomes, show event location within the gene, and align exons to protein domains.
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Affiliation(s)
- Rayan Najjar
- Division of Rheumatology, Department of Medicine, University of Washington, 750 Republican Street, Seattle, WA, 98109, USA.
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, 750 Republican Street, Seattle, WA, 98109, USA
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104
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Carrion SA, Michal JJ, Jiang Z. Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases. Genes (Basel) 2023; 14:2051. [PMID: 38002994 PMCID: PMC10671453 DOI: 10.3390/genes14112051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated importance to cell proliferation, differentiation and the transition from fetal to adult cells. While alternative exon splicing has a limited effect on protein identity, its ubiquity highlights the importance of these minor alterations, which can alter other features such as localization. The three processes are also highly interwoven, with overlapping, complementary, and competing factors, RNA polymerase II and its CTD (C-terminal domain) chief among them. Their role in development means dysregulation leads to a wide variety of disorders and cancers, with some forms of disease disproportionately affected by specific mechanisms (AES, ATS, or APA). Challenges associated with the genome-wide profiling of RNA variants and their potential solutions are also discussed in this review.
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Affiliation(s)
| | | | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620, USA; (S.A.C.); (J.J.M.)
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105
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Xie JQ, Zhou X, Jia ZC, Su CF, Zhang Y, Fernie AR, Zhang J, Du ZY, Chen MX. Alternative Splicing, An Overlooked Defense Frontier of Plants with Respect to Bacterial Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37916838 DOI: 10.1021/acs.jafc.3c04163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Disease represents a major problem in sustainable agricultural development. Plants interact closely with various microorganisms during their development and in response to the prevailing environment. In particular, pathogenic microorganisms can cause plant diseases, affecting the fertility, yield, and longevity of plants. During the long coevolution of plants and their pathogens, plants have evolved both molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) signaling networks in order to regulate host cells in response to pathogen infestation. Additionally, in the postgenomic era, alternative splicing (AS) has become uncovered as one of the major drivers of proteome diversity, and abnormal RNA splicing is closely associated with bacterial infections. Currently, the complexity of host-bacteria interactions is a much studied area of research that has shown steady progress over the past decade. Although the development of high-throughput sequencing technologies and their application in transcriptomes have revolutionized our understanding of AS, many mechanisms related to host-bacteria interactions remain still unclear. To this end, this review summarizes the changes observed in AS during host-bacteria interactions and outlines potential therapeutics for bacterial diseases based on existing studies. In doing so, we hope to provide guidelines for plant disease management in agriculture.
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Affiliation(s)
- Ji-Qin Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zi-Chang Jia
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Chang-Feng Su
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou 550025, China
| | - Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Zhi-Yan Du
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Mo-Xian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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106
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Yang Q, Tan S, Wang HL, Wang T, Cao J, Liu H, Sha Y, Zhao Y, Xia X, Guo H, Li Z. Spliceosomal protein U2B″ delays leaf senescence by enhancing splicing variant JAZ9β expression to attenuate jasmonate signaling in Arabidopsis. THE NEW PHYTOLOGIST 2023; 240:1116-1133. [PMID: 37608617 DOI: 10.1111/nph.19198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 07/23/2023] [Indexed: 08/24/2023]
Abstract
The regulatory framework of leaf senescence is gradually becoming clearer; however, the fine regulation of this process remains largely unknown. Here, genetic analysis revealed that U2 small nuclear ribonucleoprotein B (U2B″), a component of the spliceosome, is a negative regulator of leaf senescence. Mutation of U2B″ led to precocious leaf senescence, whereas overexpression of U2B″ extended leaf longevity. Transcriptome analysis revealed that the jasmonic acid (JA) signaling pathway was activated in the u2b″ mutant. U2B″ enhances the generation of splicing variant JASMONATE ZIM-DOMAIN 9β (JAZ9β) with an intron retention in the Jas motif, which compromises its interaction with CORONATINE INSENSITIVE1 and thus enhances the stability of JAZ9β protein. Moreover, JAZ9β could interact with MYC2 and obstruct its activity, thereby attenuating JA signaling. Correspondingly, overexpression of JAZ9β rescued the early senescence phenotype of the u2b″ mutant. Furthermore, JA treatment promoted expression of U2B″ that was found to be a direct target of MYC2. Overexpression of MYC2 in the u2b″ mutant resulted in a more pronounced premature senescence than that in wild-type plants. Collectively, our findings reveal that the spliceosomal protein U2B″ fine-tunes leaf senescence by enhancing the expression of JAZ9β and thereby attenuating JA signaling.
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Affiliation(s)
- Qi Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuya Tan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hou-Ling Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ting Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jie Cao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hairong Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yueqi Sha
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yaning Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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107
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Yuemaierabola A, Guo J, Sun L, Yeerkenbieke B, Liu F, Ye D, Zhai X, Guo W, Cao Y. Comprehensive analysis of CPSF4-related alternative splice genes in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:13955-13971. [PMID: 37542549 PMCID: PMC10590311 DOI: 10.1007/s00432-023-05178-z] [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: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND An important stage in controlling gene expression is RNA alternative splicing (AS), and aberrant AS can trigger the development and spread of malignancies, including hepatocellular carcinoma (HCC). A crucial component of AS is cleavage and polyadenylation-specific factor 4 (CPSF4), a component of the CPSF complex, but it is unclear how CPSF4-related AS molecules describe immune cell infiltration in the total tumor microenvironment (TME). METHODS Using RNA-sequencing data and clinical data from TCGA-LIHC from the Cancer Genome Atlas (TCGA) database, the AS genes with differential expression were found. The univariate Cox analysis, KM analysis, and Spearman analysis were used to identify the AS genes related to prognosis. Screening of key AS genes that are highly correlated with CPSF4. Key genes were screened using Cox regression analysis and stepwise regression analysis, and prognosis prediction models and the topography of TME cell infiltration were thoroughly analyzed. RESULTS A model consisting of seven AS genes (STMN1, CLSPN, MDK, RNFT2, PRR11, RNF157, GHR) was constructed that was aimed to predict prognostic condition. The outcomes of the HCC samples in the high-risk group were considerably worse than those in the lower risk group (p < 0.0001), and different risk patient groups were formed. According to the calibration curves and the area under the ROC curve (AUC) values for survival at 1, 2, and 3 years, the clinical nomogram performs well in predicting survival in HCC patients. These values were 0.76, 0.70, and 0.69, respectively. Moreover, prognostic signature was markedly related to immune infiltration and immune checkpoint genes expression. CONCLUSION By shedding light on the function of CPSF4 and the seven AS genes in the formation and progression of HCC, this research analysis contributes to the development of more useful prognostic, diagnostic, and possibly therapeutic biomarkers.
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Affiliation(s)
- Anwaier Yuemaierabola
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Jun Guo
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Lili Sun
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Buerlan Yeerkenbieke
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Fuzhong Liu
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Dilinaer Ye
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Xiaoyi Zhai
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Wenjia Guo
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China.
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China.
| | - Yan Cao
- Cancer Hospital of Xinjiang Uygur Autonomous Region (Affiliated Cancer Hospital of Xinjiang Medical University), Urumqi, 830011, China.
- Nursing School of Xinjiang Medical University, Urumqi, 830011, China.
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108
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Luo Q, Zhou X, Lv X, Zheng W, Geng S, Xu T, Sun Y. Identification and functional regulation of three alternative splicing isoforms of the fthl27 gene in miiuy croaker, Miichthys miiuy. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109147. [PMID: 37805112 DOI: 10.1016/j.fsi.2023.109147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Alternative splicing is an important basic mechanism for eukaryotes to control gene expression. Different forms of alternative splicing may lead to the production of protein subtypes with different functions, leading to the expansion of protein diversity in organisms, affecting cell production and metabolism, and is even related to the occurrence of many diseases. Many studies have shown that ferritin is usually associated with inflammation, vascular proliferation, and tumors, which is the focus of immunological research. It not only plays a role in iron metabolism and storage in the body, but also plays an important regulatory role in pathways related to immune and inflammatory regulation. However, there are few studies on alternative splicing events of the ferritin gene nowadays. Therefore, this study identified three different splicing isoforms in its ferritin gene fthl27 of Miichthys miiuy through Sanger sequencing, qRT-PCR, and other experimental techniques, and we found that three different splicing isoforms of the ferritin gene fthl27 in M. Miiuy cells showed an upregulation trend after being stimulated by Lipopolysaccharide (LPS) and poly (I: C). The experiment also found that the three isoforms may have different regulatory effects on the expression of inflammatory factors and antiviral immune factors, playing an important role in the innate immune response of fish.
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Affiliation(s)
- Qiang Luo
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xuefeng Zhou
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shang Geng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China.
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109
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Leal Y, Valenzuela-Muñoz V, Gallardo-Escárate C. Alternative splicing in Atlantic salmon head kidney and SHK-1 cell line during the Piscirickettsia salmonis infection: A comparative transcriptome survey. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109127. [PMID: 37813155 DOI: 10.1016/j.fsi.2023.109127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
Piscirickettsia salmonis, an intracellular bacterium in salmon aquaculture, is a big challenge because it is responsible for 54.2% of Atlantic salmon mortalities. In recent years, the high relevance of Alternative Splicing (AS) as a molecular mechanism associated with infectious conditions and host-pathogen interaction processes, especially in host immune activation, has been observed. Several studies have highlighted the role of AS in the host's immune response during viral, bacterial, and endoparasite infection. In the present study, we evaluated AS transcriptome profiles during P. salmonis infection in the two most used study models, SHK-1 cell line and salmon head kidney tissue. First, the SHK-1 cell line was exposed to P. salmonis infection at 0-, 7-, and 14-days post-infection (dpi). Following, total RNA was extracted for Illumina sequencing. On the other hand, RNA-Seq datasets of Atlantic salmon head kidney infected with the same P. salmonis strayingwase used. For both study models, the highest number of differentially alternative splicing (DAS) events was observed at 7 dpi, 16,830 DAS events derived from 9213 DAS genes in SHK-1 cells, and 13,820 DAS events from 7684 DAS genes in salmon HK. Alternative first exon (AF) was the most abundant AS type in the three infection times analyzed, representing 31% in SHK-1 cells and 228.6 in salmon HK; meanwhile, mutually exclusive exon (MX) was the least abundant. Notably, functional annotation of DAS genes in SHK-1 cells infected with P. salmonis showed a high presence of genes related to nucleotide metabolism. In contrast, the salmon head kidney exhibited many GO terms associated with immune response. Our findings reported the role of AS during P. salmonis infection in Atlantic salmon. These studies would contribute to a better understanding of the molecular bases that support the pathogen-host interaction, evidencing the contribution of AS regulating the transcriptional host response.
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Affiliation(s)
- Yeny Leal
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile.
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110
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Song YC, Chen MX, Zhang KL, Reddy ASN, Cao FL, Zhu FY. QuantAS: a comprehensive pipeline to study alternative splicing by absolute quantification of splice isoforms. THE NEW PHYTOLOGIST 2023; 240:928-939. [PMID: 37596706 DOI: 10.1111/nph.19193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/15/2023] [Indexed: 08/20/2023]
Affiliation(s)
- Yu-Chen Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Science, Nanjing Forestry University, Nanjing, 210037, China
| | - Mo-Xian Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Science, Nanjing Forestry University, Nanjing, 210037, China
| | - Kai-Lu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Science, Nanjing Forestry University, Nanjing, 210037, China
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Fu-Liang Cao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
| | - Fu-Yuan Zhu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Science, Nanjing Forestry University, Nanjing, 210037, China
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Nguyen JP, Arthur TD, Fujita K, Salgado BM, Donovan MKR, Matsui H, Kim JH, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk. Nat Commun 2023; 14:6928. [PMID: 37903777 PMCID: PMC10616100 DOI: 10.1038/s41467-023-42560-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
The impact of genetic regulatory variation active in early pancreatic development on adult pancreatic disease and traits is not well understood. Here, we generate a panel of 107 fetal-like iPSC-derived pancreatic progenitor cells (iPSC-PPCs) from whole genome-sequenced individuals and identify 4065 genes and 4016 isoforms whose expression and/or alternative splicing are affected by regulatory variation. We integrate eQTLs identified in adult islets and whole pancreas samples, which reveal 1805 eQTL associations that are unique to the fetal-like iPSC-PPCs and 1043 eQTLs that exhibit regulatory plasticity across the fetal-like and adult pancreas tissues. Colocalization with GWAS risk loci for pancreatic diseases and traits show that some putative causal regulatory variants are active only in the fetal-like iPSC-PPCs and likely influence disease by modulating expression of disease-associated genes in early development, while others with regulatory plasticity likely exert their effects in both the fetal and adult pancreas by modulating expression of different disease genes in the two developmental stages.
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Affiliation(s)
- Jennifer P Nguyen
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy D Arthur
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kyohei Fujita
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bianca M Salgado
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Ji Hyun Kim
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, South Korea
| | | | - Matteo D'Antonio
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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112
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Balasubramanian RN, Gao M, Umen J. Identification of cell-type specific alternative transcripts in the multicellular alga Volvox carteri. BMC Genomics 2023; 24:654. [PMID: 37904088 PMCID: PMC10617192 DOI: 10.1186/s12864-023-09558-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/06/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Cell type specialization is a hallmark of complex multicellular organisms and is usually established through implementation of cell-type-specific gene expression programs. The multicellular green alga Volvox carteri has just two cell types, germ and soma, that have previously been shown to have very different transcriptome compositions which match their specialized roles. Here we interrogated another potential mechanism for differentiation in V. carteri, cell type specific alternative transcript isoforms (CTSAI). METHODS We used pre-existing predictions of alternative transcripts and de novo transcript assembly with HISAT2 and Ballgown software to compile a list of loci with two or more transcript isoforms, identified a small subset that were candidates for CTSAI, and manually curated this subset of genes to remove false positives. We experimentally verified three candidates using semi-quantitative RT-PCR to assess relative isoform abundance in each cell type. RESULTS Of the 1978 loci with two or more predicted transcript isoforms 67 of these also showed cell type isoform expression biases. After curation 15 strong candidates for CTSAI were identified, three of which were experimentally verified, and their predicted gene product functions were evaluated in light of potential cell type specific roles. A comparison of genes with predicted alternative splicing from Chlamydomonas reinhardtii, a unicellular relative of V. carteri, identified little overlap between ortholog pairs with alternative splicing in both species. Finally, we interrogated cell type expression patterns of 126 V. carteri predicted RNA binding protein (RBP) encoding genes and found 40 that showed either somatic or germ cell expression bias. These RBPs are potential mediators of CTSAI in V. carteri and suggest possible pre-adaptation for cell type specific RNA processing and a potential path for generating CTSAI in the early ancestors of metazoans and plants. CONCLUSIONS We predicted numerous instances of alternative transcript isoforms in Volvox, only a small subset of which showed cell type specific isoform expression bias. However, the validated examples of CTSAI supported existing hypotheses about cell type specialization in V. carteri, and also suggested new hypotheses about mechanisms of functional specialization for their gene products. Our data imply that CTSAI operates as a minor but important component of V. carteri cellular differentiation and could be used as a model for how alternative isoforms emerge and co-evolve with cell type specialization.
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Affiliation(s)
| | - Minglu Gao
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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Alors-Pérez E, Pedraza-Arevalo S, Blázquez-Encinas R, Moreno-Montilla MT, García-Vioque V, Berbel I, Luque RM, Sainz B, Ibáñez-Costa A, Castaño JP. Splicing alterations in pancreatic ductal adenocarcinoma: a new molecular landscape with translational potential. J Exp Clin Cancer Res 2023; 42:282. [PMID: 37880792 PMCID: PMC10601233 DOI: 10.1186/s13046-023-02858-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal cancers worldwide, mainly due to its late diagnosis and lack of effective therapies, translating into a low 5-year 12% survival rate, despite extensive clinical efforts to improve outcomes. International cooperative studies have provided informative multiomic landscapes of PDAC, but translation of these discoveries into clinical advances are lagging. Likewise, early diagnosis biomarkers and new therapeutic tools are sorely needed to tackle this cancer. The study of poorly explored molecular processes, such as splicing, can provide new tools in this regard. Alternative splicing of pre-RNA allows the generation of multiple RNA variants from a single gene and thereby contributes to fundamental biological processes by finely tuning gene expression. However, alterations in alternative splicing are linked to many diseases, and particularly to cancer, where it can contribute to tumor initiation, progression, metastasis and drug resistance. Splicing defects are increasingly being associated with PDAC, including both mutations or dysregulation of components of the splicing machinery and associated factors, and altered expression of specific relevant gene variants. Such disruptions can be a key element enhancing pancreatic tumor progression or metastasis, while they can also provide suitable tools to identify potential candidate biomarkers and discover new actionable targets. In this review, we aimed to summarize the current information about dysregulation of splicing-related elements and aberrant splicing isoforms in PDAC, and to describe their relationship with the development, progression and/or aggressiveness of this dismal cancer, as well as their potential as therapeutic tools and targets.
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Affiliation(s)
- Emilia Alors-Pérez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Sergio Pedraza-Arevalo
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Ricardo Blázquez-Encinas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - María Trinidad Moreno-Montilla
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Víctor García-Vioque
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Inmaculada Berbel
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERObn), Córdoba, Spain
| | - Bruno Sainz
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, Madrid, Spain
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Area 3, Cancer, Madrid, Spain
- Gastrointestinal Tumours Research Programme, Biomedical Research Network in Cancer (CIBERONC), Madrid, Spain
| | - Alejandro Ibáñez-Costa
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.
- Reina Sofía University Hospital (HURS), Cordoba, Spain.
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.
- Reina Sofía University Hospital (HURS), Cordoba, Spain.
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERObn), Córdoba, Spain.
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Shah K, He S, Turner DJ, Corbo J, Rebbani K, Bateman JM, Cheloufi S, Igreja C, Valkov E, Murn J. A paradigm for regulation at the effector interface with RNA-binding proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558714. [PMID: 37790431 PMCID: PMC10542489 DOI: 10.1101/2023.09.20.558714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
RNA-binding proteins (RBPs) are key regulators of gene expression, but how RBPs convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a deeply conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by the recruiting RBP. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface, with implications for the evolution and function of RBP-operated regulatory networks.
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Affiliation(s)
- Kriti Shah
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- These authors contributed equally
| | - Shiyang He
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- These authors contributed equally
| | - David J. Turner
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
- These authors contributed equally
| | - Joshua Corbo
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, U.S.A
| | - Khadija Rebbani
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Joseph M. Bateman
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, 5 Cutcombe Road, London, SE5 9RX, U.K
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA 92521, U.S.A
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, D-72076 Tübingen, Germany
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- Lead contact
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Peng L, Zhang X, Du Y, Li F, Han J, Liu O, Dai S, Zhang X, Liu GE, Yang L, Zhou Y. New insights into transcriptome variation during cattle adipocyte adipogenesis by direct RNA sequencing. iScience 2023; 26:107753. [PMID: 37692285 PMCID: PMC10492216 DOI: 10.1016/j.isci.2023.107753] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/31/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023] Open
Abstract
We performed direct RNA sequencing (DRS) together with PCR-amplified cDNA long and short read sequencing for cattle adipocyte at different stages. We proved that the DRS was with advantages to avoid artificial transcripts and questionable exitrons. Totally, we obtained 68,124 transcripts with information of alternative splicing, poly (A) length and mRNA modification. The number of transcripts for adipogenesis was expanded by alternative splicing, which lead regulation mechanisms far more complex than ever known. We detected 891 differentially expressed genes (DEGs). However, 62.78% transcripts of DEGs were not significantly differentially expressed, and 248 transcripts showed opposite changing directions with their genes. The poly (A) tail became globally shorter in differentiated adipocyte than in primary adipocyte, and had a weak negative correlation with gene/transcript expression. Moreover, the study of different mRNA modifications implied their potential roles in gene expression and alternative splicing. Overall, our study promoted better understanding of adipogenesis mechanisms in cattle adipocytes.
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Affiliation(s)
- Lingwei Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqin Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Oujin Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Shoulu Dai
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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Pei Y, Lin C, Li H, Feng Z. Genetic background influences pig responses to porcine reproductive and respiratory syndrome virus. Front Vet Sci 2023; 10:1289570. [PMID: 37929286 PMCID: PMC10623566 DOI: 10.3389/fvets.2023.1289570] [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: 09/06/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly infectious and economically significant virus that causes respiratory and reproductive diseases in pigs. It results in reduced productivity and increased mortality in pigs, causing substantial economic losses in the industry. Understanding the factors affecting pig responses to PRRSV is crucial to develop effective control strategies. Genetic background has emerged as a significant determinant of susceptibility and resistance to PRRSV in pigs. This review provides an overview of the basic infection process of PRRSV in pigs, associated symptoms, underlying immune mechanisms, and roles of noncoding RNA and alternative splicing in PRRSV infection. Moreover, it emphasized breed-specific variations in these aspects that may have implications for individual treatment options.
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Affiliation(s)
- Yangli Pei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Chenghong Lin
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Zheng Feng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
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Li X, Zhao Y, Kong H, Song C, Liu J, Xia J. Identification of region-specific splicing QTLs in human hippocampal tissue and its distinctive role in brain disorders. iScience 2023; 26:107958. [PMID: 37810239 PMCID: PMC10558811 DOI: 10.1016/j.isci.2023.107958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/28/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Alternative splicing (AS) regulation has an essential role in complex diseases. However, the AS profiles in the hippocampal (HIPPO) region of human brain are underexplored. Here, we investigated cis-acting sQTLs of HIPPO region in 264 samples and identified thousands of significant sQTLs. By enrichment analysis and functional characterization of these sQTLs, we found that the HIPPO sQTLs were enriched among histone-marked regions, transcription factors binding sites, RNA binding proteins sites, and brain disorders-associated loci. Comparative analyses with the dorsolateral prefrontal cortex revealed the importance of AS regulation in HIPPO (rg = 0.87). Furthermore, we performed a transcriptome-wide association study of Alzheimer's disease and identified 16 significant genes whose genetically regulated splicing levels may have a causal role in Alzheimer. Overall, our study improves our knowledge of the transcriptome gene regulation in the HIPPO region and provides novel insights into elucidating the pathogenesis of potential genes associated with brain disorders.
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Affiliation(s)
- Xiaoyan Li
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Yiran Zhao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Hui Kong
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Chengcheng Song
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Jie Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Junfeng Xia
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
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Ma N, Xu H, Zhang W, Sun X, Guo R, Liu D, Zhang L, Liu Y, Zhang J, Qiao C, Chen D, Luo A, Bai J. Genome-wide analysis revealed the dysregulation of RNA binding protein-correlated alternative splicing events in myocardial ischemia reperfusion injury. BMC Med Genomics 2023; 16:251. [PMID: 37858115 PMCID: PMC10585833 DOI: 10.1186/s12920-023-01706-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Myocardial ischemia reperfusion injury (MIRI), the tissue damage which is caused by the returning of blood supply to tissue after a period of ischemia, greatly reduces the therapeutic effect of treatment of myocardial infarction. But the underlying functional mechanisms of MIRI are still unclear. METHODS We constructed mouse models of MIRI, extracted injured and healthy myocardial tissues, and performed transcriptome sequencing experiments (RNA-seq) to systematically investigate the dysregulated transcriptome of MIRI, especially the alternative splicing (AS) regulation and RNA binding proteins (RBPs). Selected RBPs and MIRI-associated AS events were then validated by RT-qPCR experiments. RESULTS The differentially expressed gene (DEG) analyses indicated that transcriptome profiles were changed by MIRI and that DEGs' enriched functions were consistent with MIRI's dysregulated pathways. Furthermore, the AS profile was synergistically regulated and showed clear differences between the mouse model and the healthy samples. The exon skipping events significantly increased in MIRI model samples, while the opposite cassette exon events significantly decreased. According to the functional analysis, regulated alternative splicing genes (RASGs) were enriched in protein transport, cell division /cell cycle, RNA splicing, and endocytosis pathways, which were associated with the development of MIRI. Meanwhile, 493 differentially expressed RBPs (DE RBPs) were detected, most of which were correlated with the changed ratios of AS events. In addition, nine DE RBP genes were validated, including Eif5, Pdia6, Tagln2, Vasp, Zfp36l2, Grsf1, Idh2, Ndrg2, and Uqcrc1. These nine DE RBPs were correlated with RASGs enriched in translation process, cell growth and division, and endocytosis pathways, highly consistent with the functions of all RASGs. Finally, we validated the AS ratio changes of five regulated alternative splicing events (RASEs) derived from important regulatory genes, including Mtmr3, Cdc42, Cd47, Fbln2, Vegfa, and Fhl2. CONCLUSION Our study emphasized the critical roles of the dysregulated AS profiles in MIRI development, investigated the potential functions of MIRI-associated RASGs, and identified regulatory RBPs involved in AS regulation. We propose that the identified RASEs and RBPs could serve as important regulators and potential therapeutic targets in MIRI treatment in the future.
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Affiliation(s)
- Ning Ma
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Hao Xu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Weihua Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Xiaoke Sun
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Ruiming Guo
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Donghai Liu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Liang Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Yang Liu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Jian Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Chenhui Qiao
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Dong Chen
- Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, 430206, Hubei, P.R. China
| | - Ailing Luo
- Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, 430206, Hubei, P.R. China
| | - Jingyun Bai
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China.
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EL-Seedy A, Pellerin L, Page G, Ladeveze V. Identification of Intron Retention in the Slc16a3 Gene Transcript Encoding the Transporter MCT4 in the Brain of Aged and Alzheimer-Disease Model (APPswePS1dE9) Mice. Genes (Basel) 2023; 14:1949. [PMID: 37895298 PMCID: PMC10606527 DOI: 10.3390/genes14101949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
The monocarboxylate transporter 4 (MCT4; Slc16a3) is expressed in the central nervous system, notably by astrocytes. It is implicated in lactate release and the regulation of glycolytic flux. Whether its expression varies during normal and/or pathological aging is unclear. As the presence of its mature transcript in the brain of young and old mice was determined, an unexpectedly longer RT-PCR fragment was detected in the mouse frontal cortex and hippocampus at 12 vs. 3 months of age. Cultured astrocytes expressed the expected 516 base pair (bp) fragment but treatment with IL-1β to mimic inflammation as can occur during aging led to the additional expression of a 928 bp fragment like that seen in aged mice. In contrast, cultured pericytes (a component of the blood-brain barrier) only exhibited the 516 bp fragment. Intriguingly, cultured endothelial cells constitutively expressed both fragments. When RT-PCR was performed on brain subregions of an Alzheimer mouse model (APPswePS1dE9), no fragment was detected at 3 months, while only the 928 bp fragment was present at 12 months. Sequencing of MCT4 RT-PCR products revealed the presence of a remaining intron between exon 2 and 3, giving rise to the longer fragment detected by RT-PCR. These results unravel the existence of intron retention for the MCT4 gene in the central nervous system. Such alternative splicing appears to increase with age in the brain and might be prominent in neurodegenerative diseases such as Alzheimer's disease. Hence, further studies in vitro and in vivo of intron 2 retention in the Slc16a3 gene transcript are required for adequate characterization concerning the biological roles of Slc16a3 isoforms in the context of aging and Alzheimer's disease pathology.
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Affiliation(s)
- Ayman EL-Seedy
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Alexandria University, Aflaton Street, El-Shatby, Alexandria 21545, Egypt;
- Neurovascular Unit and Cognitive Disorders (NEUVACOD), Faculty of Pharmacy (GP), Faculty of Fundamental and Applied Science (VL), University of Poitiers, Pôle Biologie Santé, 86073 Poitiers, France;
| | - Luc Pellerin
- IRMETIST, INSERM, Faculty of Medicine, University of Poitiers (U1313), CHU de Poitiers, 86021 Poitiers, France;
| | - Guylène Page
- Neurovascular Unit and Cognitive Disorders (NEUVACOD), Faculty of Pharmacy (GP), Faculty of Fundamental and Applied Science (VL), University of Poitiers, Pôle Biologie Santé, 86073 Poitiers, France;
| | - Veronique Ladeveze
- Neurovascular Unit and Cognitive Disorders (NEUVACOD), Faculty of Pharmacy (GP), Faculty of Fundamental and Applied Science (VL), University of Poitiers, Pôle Biologie Santé, 86073 Poitiers, France;
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Wang G, Chen B, Su Y, Qu N, Zhou D, Zhou W. CEP55 as a Promising Immune Intervention Marker to Regulate Tumor Progression: A Pan-Cancer Analysis with Experimental Verification. Cells 2023; 12:2457. [PMID: 37887301 PMCID: PMC10605621 DOI: 10.3390/cells12202457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
CEP55, a member of the centrosomal protein family, affects cell mitosis and promotes the progression of several malignancies. However, the relationship between CEP55 expression levels and prognosis, as well as their role in cancer progression and immune infiltration in different cancer types, remains unclear. We used a combined form of several databases to validate the expression of CEP55 in pan-cancer and its association with immune infiltration, and we further screened its targeted inhibitors with CEP55. Our results showed the expression of CEP55 was significantly higher in most tumors than in the corresponding normal tissues, and it correlated with the pathological grade and age of the patients and affected the prognosis. In breast cancer cells, CEP55 knockdown significantly decreased cell survival, proliferation, and migration, while overexpression of CEP55 significantly promoted breast cancer cell proliferation and migration. Moreover, CEP55 expression was positively correlated with immune cell infiltration, immune checkpoints, and immune-related genes in the tumor microenvironment. CD-437 was screened as a potential CEP55-targeted small-molecule compound inhibitor. In conclusion, our study highlights the prognostic value of CEP55 in cancer and further provides a potential target selection for CEP55 as a potential target for intervention in tumor immune infiltration and related immune genes.
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Affiliation(s)
- Gang Wang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing Medical University, Chongqing 400016, China
| | - Bo Chen
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing Medical University, Chongqing 400016, China
| | - Yue Su
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing Medical University, Chongqing 400016, China
| | - Na Qu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing Medical University, Chongqing 400016, China
| | - Duanfang Zhou
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing Medical University, Chongqing 400016, China
| | - Weiying Zhou
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing Medical University, Chongqing 400016, China
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Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
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Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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Khan MS, Hanif W, Alsakhen N, Jabbar B, Shamkh IM, Alsaiari AA, Almehmadi M, Alghamdi S, Shakoori A, Al Farraj DA, Almutairi SM, Hussein Issa Mohammed Y, Abouzied AS, Rehman AU, Huwaimel B. Isoform switching leads to downregulation of cytokine producing genes in estrogen receptor positive breast cancer. Front Genet 2023; 14:1230998. [PMID: 37900178 PMCID: PMC10611502 DOI: 10.3389/fgene.2023.1230998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Objective: Estrogen receptor breast cancer (BC) is characterized by the expression of estrogen receptors. It is the most common cancer among women, with an incidence rate of 2.26 million cases worldwide. The aim of this study was to identify differentially expressed genes and isoform switching between estrogen receptor positive and triple negative BC samples. Methods: The data were collected from ArrayExpress, followed by preprocessing and subsequent mapping from HISAT2. Read quantification was performed by StringTie, and then R package ballgown was used to perform differential expression analysis. Functional enrichment analysis was conducted using Enrichr, and then immune genes were shortlisted based on the ScType marker database. Isoform switch analysis was also performed using the IsoformSwitchAnalyzeR package. Results: A total of 9,771 differentially expressed genes were identified, of which 86 were upregulated and 117 were downregulated. Six genes were identified as mainly associated with estrogen receptor positive BC, while a novel set of ten genes were found which have not previously been reported in estrogen receptor positive BC. Furthermore, alternative splicing and subsequent isoform usage in the immune system related genes were determined. Conclusion: This study identified the differential usage of isoforms in the immune system related genes in cancer cells that suggest immunosuppression due to the dysregulation of CXCR chemokine receptor binding, iron ion binding, and cytokine activity.
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Affiliation(s)
| | - Waqar Hanif
- Department of Bioinformatics, Department of Sciences, School of Interdisciplinary Engineering & Science (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Nada Alsakhen
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Israa M. Shamkh
- Chemo and Bioinformatics Lab, Bio Search Research Institution, Giza, Egypt
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Afnan Shakoori
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Dunia A. Al Farraj
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Amr S. Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NOD CAR), Giza, Egypt
| | - Aziz-Ur Rehman
- Keystone Pharmacogenomics LLC, Bensalem, PA, United States
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Medical and Diagnostic Research Center, University of Hail, Hail, Saudi Arabia
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Song X, Li X, Ge Y, Song J, Wei Q, He M, Wei M, Zhang Y, Chen T, Zhao L. Alternative splicing events and function in the tumor microenvironment: New opportunities and challenges. Int Immunopharmacol 2023; 123:110718. [PMID: 37597404 DOI: 10.1016/j.intimp.2023.110718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/21/2023]
Abstract
Alternative splicing controls gene expression at the transcriptional level, producing structurally and functionally distinct protein heterodimers. Aberrant alternative splicing greatly affects cell development and plays an important role in the invasion and metastasis of many types of cancer. Recently, it has been shown that alternative splicing can alter the tumor microenvironment and regulate processes such as remodeling, immunity, and inflammation in the tumor microenvironment. However, there is no comprehensive literature review of the complex relationship between alternative splicing and the tumor microenvironment. Therefore, this review aims to collect all the latest data on this topic and provide a new perspective on the therapeutic and potential prognostic markers of cancer.
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Affiliation(s)
- Xueyi Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, PR China; Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, China Medical University, Shenyang 110122, PR China.
| | - Xuehao Li
- Department of thoracic surgery, The First Affiliated Hospital of China Medical University, Shenyang, China.
| | - Yuexin Ge
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, PR China; Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, China Medical University, Shenyang 110122, PR China.
| | - Jia Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, PR China; Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, China Medical University, Shenyang 110122, PR China.
| | - Qian Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, PR China; Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, China Medical University, Shenyang 110122, PR China.
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, PR China; Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, China Medical University, Shenyang 110122, PR China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, PR China; Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, China Medical University, Shenyang 110122, PR China.
| | - Yining Zhang
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, Shenyang, China.
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland.
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, PR China; Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, China Medical University, Shenyang 110122, PR China.
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Liu HL, Lu XM, Wang HY, Hu KB, Wu QY, Liao P, Li S, Long ZY, Wang YT. The role of RNA splicing factor PTBP1 in neuronal development. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119506. [PMID: 37263298 DOI: 10.1016/j.bbamcr.2023.119506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
Alternative pre-mRNA splicing, which produces various mRNA isoforms with distinct structures and functions from a single gene, is regulated by specific RNA-binding proteins and is an essential method for regulating gene expression in mammals. Recent studies have shown that abnormal change during neuronal development triggered by splicing mis-regulation is an important feature of various neurological diseases. Polypyrimidine tract binding protein 1 (PTBP1) is a kind of RNA-binding proteins with extensive biological functions. As a well-known splicing regulator, it affects the neuronal development process through its involvement in axon formation, synaptogenesis, and neuronal apoptosis, according to the most recent studies. Here, we summarized the mechanism of alternative splicing, structure and function of PTBP1, and the latest research progress on the role of alternative splicing events regulated by PTBP1 in axon formation, synaptogenesis and neuronal apoptosis, to reveal the mechanism of PTBP1-regulated changes in neuronal development process.
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Affiliation(s)
- Hui-Lin Liu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China; State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Kai-Bin Hu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Qing-Yun Wu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Ping Liao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Sen Li
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Zai-Yun Long
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Yong-Tang Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China.
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Vorobeva MA, Skvortsov DA, Pervouchine DD. Cooperation and Competition of RNA Secondary Structure and RNA-Protein Interactions in the Regulation of Alternative Splicing. Acta Naturae 2023; 15:23-31. [PMID: 38234601 PMCID: PMC10790352 DOI: 10.32607/actanaturae.26826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 01/19/2024] Open
Abstract
The regulation of alternative splicing in eukaryotic cells is carried out through the coordinated action of a large number of factors, including RNA-binding proteins and RNA structure. The RNA structure influences alternative splicing by blocking cis-regulatory elements, or bringing them closer or farther apart. In combination with RNA-binding proteins, it generates transcript conformations that help to achieve the necessary splicing outcome. However, the binding of regulatory proteins depends on RNA structure and, vice versa, the formation of RNA structure depends on the interaction with regulators. Therefore, RNA structure and RNA-binding proteins are inseparable components of common regulatory mechanisms. This review highlights examples of alternative splicing regulation by RNA-binding proteins, the regulation through local and long-range RNA structures, as well as how these elements work together, cooperate, and compete.
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Affiliation(s)
- M. A. Vorobeva
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. A. Skvortsov
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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126
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Feng L, Guo M, Jin C. Identification of alternative splicing and RNA-binding proteins involved in myocardial ischemia-reperfusion injury. Genome 2023; 66:261-268. [PMID: 37466303 DOI: 10.1139/gen-2022-0102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Alternative splicing (AS) and RNA-binding proteins (RBPs) have been implicated in various cardiovascular diseases. Yet, a comprehensive understanding of their role in myocardial ischemia-reperfusion injury (MIRI) remains elusive. We aimed to identify potential therapeutic targets for MIRI by studying genome-wide changes in AS events and RBPs. We analyzed RNA-seq data from ischemia-reperfusion mouse models and the control group from the GSE130217 data set using Splicing Site Usage Variation Analysis software. We identified 28 regulated alternative splicing events (RASEs) and 47 differentially expressed RBP (DE-RBP) genes in MIRI. Most variable splicing events were involved in cassette exon, alternative 5' splice, alternative 3' splice, and retained intron types. Gene Ontology and Kyoto Encyclopedia of Genes (KOBAS 2.0 server) and Genomes pathway enrichment analyses showed that the differentially expressed variable splicing and RBP genes were mainly enriched in pathways related to myocardial function. The RBP-RASE network demonstrated a common variance relationship between DE-RBPs and RASEs, indicating that RBPs regulate variable shear events in MIRI. This study systematically identified important alterations in RASEs and RBPs in MIRI, expanding our understanding of the underlying pathogenesis of MIRI.
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Affiliation(s)
- Li Feng
- Department of Cardiology, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Min Guo
- Department of Cardiology, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Chunrong Jin
- Department of Cardiology, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
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Haddad-Mashadrizeh A, Mirahmadi M, Taghavizadeh Yazdi ME, Gholampour-Faroji N, Bahrami A, Zomorodipour A, Moghadam Matin M, Qayoomian M, Saebnia N. Introns and Their Therapeutic Applications in Biomedical Researches. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3316. [PMID: 38269198 PMCID: PMC10804063 DOI: 10.30498/ijb.2023.334488.3316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/23/2023] [Indexed: 01/26/2024]
Abstract
Context Although for a long time, it was thought that intervening sequences (introns) were junk DNA without any function, their critical roles and the underlying molecular mechanisms in genome regulation have only recently come to light. Introns not only carry information for splicing, but they also play many supportive roles in gene regulation at different levels. They are supposed to function as useful tools in various biological processes, particularly in the diagnosis and treatment of diseases. Introns can contribute to numerous biological processes, including gene silencing, gene imprinting, transcription, mRNA metabolism, mRNA nuclear export, mRNA localization, mRNA surveillance, RNA editing, NMD, translation, protein stability, ribosome biogenesis, cell growth, embryonic development, apoptosis, molecular evolution, genome expansion, and proteome diversity through various mechanisms. Evidence Acquisition In order to fulfill the objectives of this study, the following databases were searched: Medline, Scopus, Web of Science, EBSCO, Open Access Journals, and Google Scholar. Only articles published in English were included. Results & Conclusions The intervening sequences of eukaryotic genes have critical functions in genome regulation, as well as in molecular evolution. Here, we summarize recent advances in our understanding of how introns influence genome regulation, as well as their effects on molecular evolution. Moreover, therapeutic strategies based on intron sequences are discussed. According to the obtained results, a thorough understanding of intron functional mechanisms could lead to new opportunities in disease diagnosis and therapies, as well as in biotechnology applications.
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Affiliation(s)
- Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Mirahmadi
- Stem Cell and Regenerative Medicine Research Group, Iranian Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Nazanin Gholampour-Faroji
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmadreza Bahrami
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Maryam Moghadam Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Qayoomian
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Saebnia
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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128
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Liu X, Han W, Hu X. Post-transcriptional regulation of myeloid cell-mediated inflammatory responses. Adv Immunol 2023; 160:59-82. [PMID: 38042586 DOI: 10.1016/bs.ai.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2023]
Abstract
Myeloid cells, particularly macrophages, act as the frontline responders to infectious agents and initiate inflammation. While the molecular mechanisms driving inflammatory responses have primarily focused on pattern recognition by myeloid cells and subsequent transcriptional events, it is crucial to note that post-transcriptional regulation plays a pivotal role in this process. In addition to the transcriptional regulation of innate immune responses, additional layers of intricate network of post-transcriptional mechanisms critically determine the quantity and duration of key inflammatory products and thus the outcome of immune responses. A multitude of mechanisms governing post-transcriptional regulation in innate immunity have been uncovered, encompassing RNA alternative splicing, mRNA stability, and translational regulation. This review encapsulates the current insights into the post-transcriptional regulation of inflammatory genes within myeloid cells, with particular emphasis on translational regulation during inflammation. While acknowledging the advancements, we also shed light on the existing gaps in immunological research pertaining to post-transcriptional levels and propose perspectives that controlling post-transcriptional process may serve as potential targets for therapeutic interventions in inflammatory diseases.
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Affiliation(s)
- Xingxian Liu
- Institute for Immunology, Tsinghua University, Beijing, P.R. China; Department of Basic Medical Sciences, Tsinghua University, Beijing, P.R. China; Tsinghua-Peking Center for Life Sciences, Beijing, P.R. China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, P.R. China
| | - Weidong Han
- Department of Bio-therapeutic, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - Xiaoyu Hu
- Institute for Immunology, Tsinghua University, Beijing, P.R. China; Department of Basic Medical Sciences, Tsinghua University, Beijing, P.R. China; Tsinghua-Peking Center for Life Sciences, Beijing, P.R. China; The State Key Laboratory of Membrane Biology, Beijing, P.R. China.
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129
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Yang W, Chen SC, Wang TE, Tsai PS, Chen JC, Chen PL. L1cam alternative shorter transcripts encoding the extracellular domains were overexpressed in the intestine of L1cam knockdown mice. Gene 2023; 881:147643. [PMID: 37453721 DOI: 10.1016/j.gene.2023.147643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/25/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Hirschsprung disease (HSCR) is a congenital disorder of functional bowel obstruction due to the absence of enteric ganglia in distal bowel. Different L1cam variants were reportedly associated with L1cam syndrome and HSCR, whose phenotypes lacked predictable relevance to their genotypes. Using next-generation sequencing (NGS), we found an L1CAM de novo frameshift mutation in a female with mild hydrocephalus and skip-type HSCR. A nearly identical L1cam variant was introduced into FVB/NJ mice via the CRISPR-EZ method. A silent mutation was created via ssODN to gain an artificial Ncol restriction enzyme site for easier genotyping. Six L1cam protein-coding alternative transcripts were quantitatively measured. Immunofluorescence staining with polyclonal and monoclonal L1cam antibodies was used to characterize L1cam isoform proteins in enteric ganglia. Fifteen mice, seven males and eight females, generated via CRISPR-EZ, were confirmed to carry the L1cam frameshift variant, resulting in a premature stop codon. There was no prominent hydrocephalus nor HSCR-like presentation in these mice, but male infertility was noticed after observation for three generations in a total of 176 mice. Full-length L1cam transcripts were detected at a very low level in the intestinal tissues and almost none in the brain of these mice. Alternative shorter transcripts encoding the extracellular domains were overexpressed in the intestine of L1cam knockdown mice. Immunofluorescence confirmed no fulllength L1cam protein in enteric ganglia. These shorter L1cam isoform proteins might play a role in protecting L1cam knockdown mice from HSCR.
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Affiliation(s)
- Wendy Yang
- Department of Surgery, Chang Gung Children's Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Pediatric Research Center, Chang Gung Children's Hospital, Taoyuan, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Szu-Chieh Chen
- Pediatric Research Center, Chang Gung Children's Hospital, Taoyuan, Taiwan
| | - Tse-En Wang
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, 10617 Taipei, Taiwan
| | - Pei-Shiue Tsai
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, 10617 Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, 10617 Taipei, Taiwan
| | - Jeng-Chang Chen
- Department of Surgery, Chang Gung Children's Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Pediatric Research Center, Chang Gung Children's Hospital, Taoyuan, Taiwan.
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taiwan; Departments of Medical Genetics, National Taiwan University Hospital, Taiwan; Departments of Internal Medicine, National Taiwan University Hospital, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
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130
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McLean DT, Meudt JJ, Lopez Rivera LD, Schomberg DT, Pavelec DM, Duellman TT, Buehler DG, Schwartz PB, Graham M, Lee LM, Graff KD, Reichert JL, Bon-Durant SS, Konsitzke CM, Ronnekleiv-Kelly SM, Shanmuganayagam D, Rubinstein CD. Single-cell RNA sequencing of neurofibromas reveals a tumor microenvironment favorable for neural regeneration and immune suppression in a neurofibromatosis type 1 porcine model. Front Oncol 2023; 13:1253659. [PMID: 37817770 PMCID: PMC10561395 DOI: 10.3389/fonc.2023.1253659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Neurofibromatosis Type 1 (NF1) is one of the most common genetically inherited disorders that affects 1 in 3000 children annually. Clinical manifestations vary widely but nearly always include the development of cutaneous, plexiform and diffuse neurofibromas that are managed over many years. Recent single-cell transcriptomics profiling efforts of neurofibromas have begun to reveal cell signaling processes. However, the cell signaling networks in mature, non-cutaneous neurofibromas remain unexplored. Here, we present insights into the cellular composition and signaling within mature neurofibromas, contrasting with normal adjacent tissue, in a porcine model of NF1 using single-cell RNA sequencing (scRNA-seq) analysis and histopathological characterization. These neurofibromas exhibited classic diffuse-type histologic morphology and expected patterns of S100, SOX10, GFAP, and CD34 immunohistochemistry. The porcine mature neurofibromas closely resemble human neurofibromas histologically and contain all known cellular components of their human counterparts. The scRNA-seq confirmed the presence of all expected cell types within these neurofibromas and identified novel populations of fibroblasts and immune cells, which may contribute to the tumor microenvironment by suppressing inflammation, promoting M2 macrophage polarization, increasing fibrosis, and driving the proliferation of Schwann cells. Notably, we identified tumor-associated IDO1 +/CD274+ (PD-L1) + dendritic cells, which represent the first such observation in any NF1 animal model and suggest the role of the upregulation of immune checkpoints in mature neurofibromas. Finally, we observed that cell types in the tumor microenvironment are poised to promote immune evasion, extracellular matrix reconstruction, and nerve regeneration.
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Affiliation(s)
- Dalton T. McLean
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
- Molecular & Environmental Toxicology Program, University of Wisconsin–Madison, Madison, WI, United States
| | - Jennifer J. Meudt
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Loren D. Lopez Rivera
- Molecular & Environmental Toxicology Program, University of Wisconsin–Madison, Madison, WI, United States
| | - Dominic T. Schomberg
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Derek M. Pavelec
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Tyler T. Duellman
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Darya G. Buehler
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Patrick B. Schwartz
- Molecular & Environmental Toxicology Program, University of Wisconsin–Madison, Madison, WI, United States
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Melissa Graham
- Research Animal Resources and Compliance (RARC), Office of the Vice Chancellor for Research and Graduate Education, University of Wisconsin–Madison, Madison, WI, United States
| | - Laura M. Lee
- Research Animal Resources and Compliance (RARC), Office of the Vice Chancellor for Research and Graduate Education, University of Wisconsin–Madison, Madison, WI, United States
| | - Keri D. Graff
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Jamie L. Reichert
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Sandra S. Bon-Durant
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Charles M. Konsitzke
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Sean M. Ronnekleiv-Kelly
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Molecular & Environmental Toxicology Program, University of Wisconsin–Madison, Madison, WI, United States
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
- Center for Biomedical Swine Research and Innovation, University of Wisconsin–Madison, Madison, WI, United States
| | - C. Dustin Rubinstein
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
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131
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Zhang Q, Cao L, Song H, Lin K, Pang E. MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome. Brief Bioinform 2023; 24:bbad367. [PMID: 37833843 PMCID: PMC10576019 DOI: 10.1093/bib/bbad367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Alternative splicing (AS) is an essential post-transcriptional mechanism that regulates many biological processes. However, identifying comprehensive types of AS events without guidance from a reference genome is still a challenge. Here, we proposed a novel method, MkcDBGAS, to identify all seven types of AS events using transcriptome alone, without a reference genome. MkcDBGAS, modeled by full-length transcripts of human and Arabidopsis thaliana, consists of three modules. In the first module, MkcDBGAS, for the first time, uses a colored de Bruijn graph with dynamic- and mixed- kmers to identify bubbles generated by AS with precision higher than 98.17% and detect AS types overlooked by other tools. In the second module, to further classify types of AS, MkcDBGAS added the motifs of exons to construct the feature matrix followed by the XGBoost-based classifier with the accuracy of classification greater than 93.40%, which outperformed other widely used machine learning models and the state-of-the-art methods. Highly scalable, MkcDBGAS performed well when applied to Iso-Seq data of Amborella and transcriptome of mouse. In the third module, MkcDBGAS provides the analysis of differential splicing across multiple biological conditions when RNA-sequencing data is available. MkcDBGAS is the first accurate and scalable method for detecting all seven types of AS events using the transcriptome alone, which will greatly empower the studies of AS in a wider field.
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Affiliation(s)
- Quanbao Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lei Cao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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132
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Liu Z, Du Y, Sun Z, Cheng B, Bi Z, Yao Z, Liang Y, Zhang H, Yao R, Kang S, Shi Y, Wan H, Qin D, Xiang L, Leng L, Chen S. Manual correction of genome annotation improved alternative splicing identification of Artemisia annua. PLANTA 2023; 258:83. [PMID: 37721598 DOI: 10.1007/s00425-023-04237-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023]
Abstract
Gene annotation is essential for genome-based studies. However, algorithm-based genome annotation is difficult to fully and correctly reveal genomic information, especially for species with complex genomes. Artemisia annua L. is the only commercial resource of artemisinin production though the content of artemisinin is still to be improved. Genome-based genetic modification and breeding are useful strategies to boost artemisinin content and therefore, ensure the supply of artemisinin and reduce costs, but better gene annotation is urgently needed. In this study, we manually corrected the newly released genome annotation of A. annua using second- and third-generation transcriptome data. We found that incorrect gene information may lead to differences in structural, functional, and expression levels compared to the original expectations. We also identified alternative splicing events and found that genome annotation information impacted identifying alternative splicing genes. We further demonstrated that genome annotation information and alternative splicing could affect gene expression estimation and gene function prediction. Finally, we provided a valuable version of A. annua genome annotation and demonstrated the importance of gene annotation in future research.
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Affiliation(s)
- Zhaoyu Liu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yupeng Du
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhihao Sun
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Bohan Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zenghao Bi
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhicheng Yao
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China
| | - Yuting Liang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Huiling Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Run Yao
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shen Kang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yuhua Shi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Dou Qin
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uyghur Medicine, Urmuqi, 830000, China
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uyghur Medicine, Urmuqi, 830000, China.
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Shilin Chen
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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133
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Hınçer A, Ahan RE, Aras E, Şeker UÖŞ. Making the Next Generation of Therapeutics: mRNA Meets Synthetic Biology. ACS Synth Biol 2023; 12:2505-2515. [PMID: 37672348 PMCID: PMC10510722 DOI: 10.1021/acssynbio.3c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Indexed: 09/08/2023]
Abstract
The development of mRNA-based therapeutics centers around the natural functioning of mRNA molecules to provide the genetic information required for protein translation. To improve the efficacy of these therapeutics and minimize side effects, researchers can focus on the features of mRNA itself or the properties of the delivery agent to achieve the desired response. The tools considered for mRNA manipulation can be improved in terms of targetability, tunability, and translatability to medicine. While ongoing studies are dedicated to improving conventional approaches, innovative approaches can also be considered to unleash the full potential of mRNA-based therapeutics. Here, we discuss the opportunities that emerged from introducing synthetic biology to mRNA therapeutics. It includes a discussion of modular self-assembled mRNA nanoparticles, logic gates on a single mRNA molecule, and other possibilities.
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Affiliation(s)
- Ahmet Hınçer
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center, Bilkent
University, Ankara 06800, Turkey
| | - Recep Erdem Ahan
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center, Bilkent
University, Ankara 06800, Turkey
| | - Ebru Aras
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center, Bilkent
University, Ankara 06800, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center, Bilkent
University, Ankara 06800, Turkey
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134
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Rodriguez Gallo MC, Uhrig RG. Phosphorylation mediated regulation of RNA splicing in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1249057. [PMID: 37780493 PMCID: PMC10539000 DOI: 10.3389/fpls.2023.1249057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.
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Affiliation(s)
| | - R. Glen Uhrig
- University of Alberta, Department of Biological Sciences, Edmonton, AB, Canada
- University of Alberta, Department of Biochemistry, Edmonton, AB, Canada
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135
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Schertzer MD, Stirn A, Isaev K, Pereira L, Das A, Harbison C, Park SH, Wessels HH, Sanjana NE, Knowles DA. Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557474. [PMID: 37745416 PMCID: PMC10515814 DOI: 10.1101/2023.09.12.557474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design. To address these gaps, we developed and methodically tested a strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs that span exon-exon junctions in the mature RNA. We performed a high-throughput essentiality screen, quantitative RT-PCR assays, and PacBio long read sequencing to affirm our ability to specifically target and robustly knockdown individual RNA isoforms. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions annotated in GENCODE for multi-isoform genes and our gRNA efficacy predictions, we estimate that our junction-centric strategy can uniquely target up to 89% of human RNA isoforms, including 50,066 protein-coding and 11,415 lncRNA isoforms. Importantly, this specificity spans all splicing and transcriptional events, including exon skipping and inclusion, alternative 5' and 3' splice sites, and alternative starts and ends.
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Affiliation(s)
- Megan D Schertzer
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | - Andrew Stirn
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | - Keren Isaev
- New York Genome Center, New York, NY
- Department of Systems Biology, Columbia University, New York, NY
| | | | - Anjali Das
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | | | - Stella H Park
- New York Genome Center, New York, NY
- Department of Biomedical Engineering, Columbia University, New York, NY
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY
- Department of Biology, New York University, New York, NY
| | - Neville E Sanjana
- New York Genome Center, New York, NY
- Department of Biology, New York University, New York, NY
| | - David A Knowles
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
- Department of Systems Biology, Columbia University, New York, NY
- Data Science Institute, Columbia University, New York, NY
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136
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Lei WL, Li YY, Du Z, Su R, Meng TG, Ning Y, Hou G, Schatten H, Wang ZB, Han Z, Sun F, Qian WP, Liu C, Sun QY. SRSF1-mediated alternative splicing is required for spermatogenesis. Int J Biol Sci 2023; 19:4883-4897. [PMID: 37781512 PMCID: PMC10539708 DOI: 10.7150/ijbs.83474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023] Open
Abstract
Alternative splicing (AS) plays significant roles in a multitude of fundamental biological activities. AS is prevalent in the testis, but the regulations of AS in spermatogenesis is only little explored. Here, we report that Serine/arginine-rich splicing factor 1 (SRSF1) plays critical roles in alternative splicing and male reproduction. Male germ cell-specific deletion of Srsf1 led to complete infertility by affecting spermatogenesis. Mechanistically, by combining RNA-seq data with LACE-seq data, we showed that SRSF1 affected the AS of Stra8 in a direct manner and Dazl, Dmc1, Mre11a, Syce2 and Rif1 in an indirect manner. Our findings demonstrate that SRSF1 has crucial functions in spermatogenesis and male fertility by regulating alternative splicing.
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Affiliation(s)
- Wen-Long Lei
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, Shenzhen 518000, China
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Yuan-Yuan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zongchang Du
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruibao Su
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Tie-Gang Meng
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Yan Ning
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanmei Hou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Zhiming Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Fei Sun
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Wei-Ping Qian
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, Shenzhen 518000, China
| | - Chenli Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qing-Yuan Sun
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
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137
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Zhang Z, Bae B, Cuddleston WH, Miura P. Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing. Nat Commun 2023; 14:5506. [PMID: 37679364 PMCID: PMC10484994 DOI: 10.1038/s41467-023-41207-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Nervous system development is associated with extensive regulation of alternative splicing (AS) and alternative polyadenylation (APA). AS and APA have been extensively studied in isolation, but little is known about how these processes are coordinated. Here, the coordination of cassette exon (CE) splicing and APA in Drosophila was investigated using a targeted long-read sequencing approach we call Pull-a-Long-Seq (PL-Seq). This cost-effective method uses cDNA pulldown and Nanopore sequencing combined with an analysis pipeline to quantify inclusion of alternative exons in connection with alternative 3' ends. Using PL-Seq, we identified genes that exhibit significant differences in CE splicing depending on connectivity to short versus long 3'UTRs. Genomic long 3'UTR deletion was found to alter upstream CE splicing in short 3'UTR isoforms and ELAV loss differentially affected CE splicing depending on connectivity to alternative 3'UTRs. This work highlights the importance of considering connectivity to alternative 3'UTRs when monitoring AS events.
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Affiliation(s)
- Zhiping Zhang
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Bongmin Bae
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | | | - Pedro Miura
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Department of Biology, University of Nevada, Reno, Reno, NV, USA.
- Institute for System Genomics, University of Connecticut, Storrs, CT, USA.
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138
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Liu L, Wang B, Duan G, Wang J, Pan Z, Ou M, Bai X, Wang P, Zhao D, Nan N, Li D, Sun W. Histone Deacetylase UvHST2 Is a Global Regulator of Secondary Metabolism in Ustilaginoidea virens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13124-13136. [PMID: 37615365 DOI: 10.1021/acs.jafc.3c01782] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Ustilaginoidea virens, the causal agent of rice false smut, produces a large amount of mycotoxins, including ustilaginoidins and sorbicillinoids. However, little is known about the regulatory mechanism of mycotoxin biosynthesis inU. virens. Here, we demonstrate that the NAD+-dependent histone deacetylase UvHST2 negatively regulates ustilaginoidin biosynthesis. UvHst2 knockout caused retarded hypha growth and reduced conidiation and pathogenicity inU. virens. Transcriptome analysis revealed that the transcription factor genes, transporter genes, and other tailoring genes in eight biosynthetic gene clusters (BGCs) including ustilaginoidin and sorbicillinoid BGCs were upregulated in ΔUvhst2. Interestingly, the UvHst2 deletion affects alternative splicing. Metabolomics revealed that UvHST2 negatively regulates the biosynthesis of various mycotoxins including ustilaginoidins, sorbicillin, ochratoxin B, zearalenone, and O-M-sterigmatocystin. Combined transcriptome and metabolome analyses uncover that UvHST2 positively regulates pathogenicity but negatively modulates the expression of BGCs involved in secondary metabolism. Collectively, UvHST2 functions as a global regulator of secondary metabolism inU. virens.
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Affiliation(s)
- Ling Liu
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Bo Wang
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Guohua Duan
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Jing Wang
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Zequn Pan
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Mingming Ou
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Xiaolong Bai
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Peiying Wang
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Dan Zhao
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Nan Nan
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Dayong Li
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Wenxian Sun
- College of Plant Protection, Jilin Provincial Key Laboratory of Green Management of Crop Pests and Diseases, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
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139
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Szatkownik A, Zea DJ, Richard H, Laine E. Building alternative splicing and evolution-aware sequence-structure maps for protein repeats. J Struct Biol 2023; 215:107997. [PMID: 37453591 DOI: 10.1016/j.jsb.2023.107997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/15/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Alternative splicing of repeats in proteins provides a mechanism for rewiring and fine-tuning protein interaction networks. In this work, we developed a robust and versatile method, ASPRING, to identify alternatively spliced protein repeats from gene annotations. ASPRING leverages evolutionary meaningful alternative splicing-aware hierarchical graphs to provide maps between protein repeats sequences and 3D structures. We re-think the definition of repeats by explicitly accounting for transcript diversity across several genes/species. Using a stringent sequence-based similarity criterion, we detected over 5,000 evolutionary conserved repeats by screening virtually all human protein-coding genes and their orthologs across a dozen species. Through a joint analysis of their sequences and structures, we extracted specificity-determining sequence signatures and assessed their implication in experimentally resolved and modelled protein interactions. Our findings demonstrate the widespread alternative usage of protein repeats in modulating protein interactions and open avenues for targeting repeat-mediated interactions.
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Affiliation(s)
- Antoine Szatkownik
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France; Bioinformatics Unit, Genome Competence Center (MF1), Robert Koch Institute, 13353 Berlin, Germany
| | - Diego Javier Zea
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Hugues Richard
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France; Bioinformatics Unit, Genome Competence Center (MF1), Robert Koch Institute, 13353 Berlin, Germany.
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France.
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140
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Xue JY, Fan HY, Zeng Z, Zhou YH, Hu SY, Li SX, Cheng YJ, Meng XR, Chen F, Shao ZQ, Van de Peer Y. Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato. HORTICULTURE RESEARCH 2023; 10:uhad147. [PMID: 37691964 PMCID: PMC10483172 DOI: 10.1093/hr/uhad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/15/2023] [Indexed: 09/12/2023]
Abstract
MicroTom has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g. arbuscular mycorrhizal symbiosis and fruit development. Additionally, non-coding RNAs, including miRNAs, lncRNAs, and circRNAs were also identified, together with their potential targets. Interacting networks between different types of non-coding RNAs (miRNA-lncRNA), and non-coding RNAs and genes (miRNA-mRNA and lncRNA-mRNA) were constructed as well. Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit. Lastly, we established a database (http://eplant.njau.edu.cn/microTomBase/) with genomic and transcriptomic data, as well as details of gene co-expression and interacting networks on MicroTom, and this database should be of great value to those who want to adopt MicroTom as a model plant for research.
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Affiliation(s)
- Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai-Yun Fan
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yu-Han Zhou
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Sai-Xi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ying-Juan Cheng
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiang-Ru Meng
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Chen
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biotechnology and Bioinformatics, VIB-UGent Center for Plant Systems Biology, Ghent University, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
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141
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田 学, 陈 婵, 王 雄. [Tau Protein Induces Aberrant Alternative Splicing Changes in PS19 Transgenic Mice]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:874-883. [PMID: 37866941 PMCID: PMC10579071 DOI: 10.12182/20230960501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Indexed: 10/24/2023]
Abstract
Objective To explore through big data analysis whether aberrant alternative splicing (AS) events precede tau P301S-induced neurodegenerative phenotype in 6-month-old PS19 mice. Methods The original sequencing files of the GSE182170 dataset was downloaded from the European Nucleotide Archive (ENA) database with axel, aligned to the reference genome of the ENSEMBL database by using STAR software, and common AS event analysis and visualization were performed with rMATS and rmats2sashimiplot R packages. RSEM software was utilized for gene transcript quantification, Deseq2, edgeR, and limma R packages were used for differential expression analysis, and clusterProfiler R package was applied for GO enrichment analysis. String and Cytoscape were used for protein-protein interaction (PPI) analysis. Gene expression correlation analysis was performed with ggcorrplot R package. AS events were validated using PCR followed by agarose electrophoresis. Results A total of 8 079 AS events were identified with rMATS and 117 significant AS events (ΔPSI>0.1, sequencing coverage >1) were selected eventually. The most frequent type of AS event was skipped exon (SE) (50.43%), followed by alternative 3' splice site (A3SS) and mutually exclusive exons (MXE). GO enrichment analysis revealed that synapse organization genes were aberrantly spliced in SE events and spliceosome genes were spliced in A3SS events. PPI and correlation analyses showed that the splicing factor Snrpn was significantly associated with the largest number of transcripts. Agarose electrophoresis confirmed the aberrant AS event of the Lrp8 gene in PS19 mice. Conclusion Dysregulated splicing factors may contribute to tau P301S-induced aberrant AS changes. The study also increases the understanding of the cycling of tau protein and splicing factors in tauopathies.
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Affiliation(s)
- 学文 田
- 华中科技大学同济医学院附属同济医院 检验科 (武汉 430030)Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - 婵 陈
- 华中科技大学同济医学院附属同济医院 检验科 (武汉 430030)Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - 雄 王
- 华中科技大学同济医学院附属同济医院 检验科 (武汉 430030)Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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142
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Das S, Mallick D, Sarkar S, Billington N, Sellers JR, Jana SS. A brain specific alternatively spliced isoform of nonmuscle myosin IIA lacks its mechanoenzymatic activities. J Biol Chem 2023; 299:105143. [PMID: 37562567 PMCID: PMC10480317 DOI: 10.1016/j.jbc.2023.105143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Recent genomic studies reported that 90 to 95% of human genes can undergo alternative splicing, by which multiple isoforms of proteins are synthesized. However, the functional consequences of most of the isoforms are largely unknown. Here, we report a novel alternatively spliced isoform of nonmuscle myosin IIA (NM IIA), called NM IIA2, which is generated by the inclusion of 21 amino acids near the actin-binding region (loop 2) of the head domain of heavy chains. Expression of NM IIA2 is found exclusively in the brain tissue, where it reaches a maximum level at 24 h during the circadian rhythm. The actin-dependent Mg2+-ATPase activity and in vitro motility assays reveal that NM IIA2 lacks its motor activities but localizes with actin filaments in cells. Interestingly, NM IIA2 can also make heterofilaments with NM IIA0 (noninserted isoform of NM IIA) and can retard the in vitro motility of NM IIA, when the two are mixed. Altogether, our findings provide the functional importance of a previously unknown alternatively spliced isoform, NM IIA2, and its potential physiological role in regulating NM IIA activity in the brain.
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Affiliation(s)
- Samprita Das
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Ditipriya Mallick
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Sourav Sarkar
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Neil Billington
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - James R Sellers
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
| | - Siddhartha S Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India.
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143
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Khan AH, Bagley JR, LaPierre N, Gonzalez-Figueroa C, Spencer TC, Choudhury M, Xiao X, Eskin E, Jentsch JD, Smith DJ. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice. Cell Rep 2023; 42:112856. [PMID: 37481717 PMCID: PMC10530068 DOI: 10.1016/j.celrep.2023.112856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
To identify addiction genes, we evaluate intravenous self-administration of cocaine or saline in 84 inbred and recombinant inbred mouse strains over 10 days. We integrate the behavior data with brain RNA-seq data from 41 strains. The self-administration of cocaine and that of saline are genetically distinct. We maximize power to map loci for cocaine intake by using a linear mixed model to account for this longitudinal phenotype while correcting for population structure. A total of 15 unique significant loci are identified in the genome-wide association study. A transcriptome-wide association study highlights the Trpv2 ion channel as a key locus for cocaine self-administration as well as identifying 17 additional genes, including Arhgef26, Slc18b1, and Slco5a1. We find numerous instances where alternate splice site selection or RNA editing altered transcript abundance. Our work emphasizes the importance of Trpv2, an ionotropic cannabinoid receptor, for the response to cocaine.
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Affiliation(s)
- Arshad H Khan
- Department of Molecular and Medical Pharmacology, Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jared R Bagley
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Nathan LaPierre
- Department of Computer Science, UCLA, Los Angeles, CA 90095, USA
| | | | - Tadeo C Spencer
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Eleazar Eskin
- Department of Computational Medicine, UCLA, Los Angeles, CA 90095, USA
| | - James D Jentsch
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Desmond J Smith
- Department of Molecular and Medical Pharmacology, Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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144
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Han N, Liu Z. Targeting alternative splicing in cancer immunotherapy. Front Cell Dev Biol 2023; 11:1232146. [PMID: 37635865 PMCID: PMC10450511 DOI: 10.3389/fcell.2023.1232146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Tumor immunotherapy has made great progress in cancer treatment but still faces several challenges, such as a limited number of targetable antigens and varying responses among patients. Alternative splicing (AS) is an essential process for the maturation of nearly all mammalian mRNAs. Recent studies show that AS contributes to expanding cancer-specific antigens and modulating immunogenicity, making it a promising solution to the above challenges. The organoid technology preserves the individual immune microenvironment and reduces the time/economic costs of the experiment model, facilitating the development of splicing-based immunotherapy. Here, we summarize three critical roles of AS in immunotherapy: resources for generating neoantigens, targets for immune-therapeutic modulation, and biomarkers to guide immunotherapy options. Subsequently, we highlight the benefits of adopting organoids to develop AS-based immunotherapies. Finally, we discuss the current challenges in studying AS-based immunotherapy in terms of existing bioinformatics algorithms and biological technologies.
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Affiliation(s)
- Nan Han
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoqi Liu
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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145
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Kolapalli SP, Nielsen TM, Frankel LB. Post-transcriptional dynamics and RNA homeostasis in autophagy and cancer. Cell Death Differ 2023:10.1038/s41418-023-01201-5. [PMID: 37558732 DOI: 10.1038/s41418-023-01201-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/22/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Autophagy is an essential recycling and quality control pathway which preserves cellular and organismal homeostasis. As a catabolic process, autophagy degrades damaged and aged intracellular components in response to conditions of stress, including nutrient deprivation, oxidative and genotoxic stress. Autophagy is a highly adaptive and dynamic process which requires an intricately coordinated molecular control. Here we provide an overview of how autophagy is regulated post-transcriptionally, through RNA processing events, epitranscriptomic modifications and non-coding RNAs. We further discuss newly revealed RNA-binding properties of core autophagy machinery proteins and review recent indications of autophagy's ability to impact cellular RNA homeostasis. From a physiological perspective, we examine the biological implications of these emerging regulatory layers of autophagy, particularly in the context of nutrient deprivation and tumorigenesis.
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Affiliation(s)
| | | | - Lisa B Frankel
- Danish Cancer Institute, Copenhagen, Denmark.
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
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146
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Manabile MA, Hull R, Khanyile R, Molefi T, Damane BP, Mongan NP, Bates DO, Dlamini Z. Alternative Splicing Events and Their Clinical Significance in Colorectal Cancer: Targeted Therapeutic Opportunities. Cancers (Basel) 2023; 15:3999. [PMID: 37568815 PMCID: PMC10417810 DOI: 10.3390/cancers15153999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) ranks as one of the top causes of cancer mortality worldwide and its incidence is on the rise, particularly in low-middle-income countries (LMICs). There are several factors that contribute to the development and progression of CRC. Alternative splicing (AS) was found to be one of the molecular mechanisms underlying the development and progression of CRC. With the advent of genome/transcriptome sequencing and large patient databases, the broad role of aberrant AS in cancer development and progression has become clear. AS affects cancer initiation, proliferation, invasion, and migration. These splicing changes activate oncogenes or deactivate tumor suppressor genes by producing altered amounts of normally functional or new proteins with different, even opposing, functions. Thus, identifying and characterizing CRC-specific alternative splicing events and variants might help in designing new therapeutic splicing disrupter drugs. CRC-specific splicing events can be used as diagnostic and prognostic biomarkers. In this review, alternatively spliced events and their role in CRC development will be discussed. The paper also reviews recent research on alternatively spliced events that might be exploited as prognostic, diagnostic, and targeted therapeutic indicators. Of particular interest is the targeting of protein arginine methyltransferase (PMRT) isoforms for the development of new treatments and diagnostic tools. The potential challenges and limitations in translating these discoveries into clinical practice will also be addressed.
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Affiliation(s)
- Mosebo Armstrong Manabile
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Rodney Hull
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
| | - Richard Khanyile
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Thulo Molefi
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Botle Precious Damane
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa;
| | - Nigel Patrick Mongan
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2QL, UK;
| | - David Owen Bates
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Centre for Cancer Sciences, Division of Cancer and Stem Cells, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
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147
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Feng Y, Zhu S, Liu T, Zhi G, Shao B, Liu J, Li B, Jiang C, Feng Q, Wu P, Wang D. Surmounting Cancer Drug Resistance: New Perspective on RNA-Binding Proteins. Pharmaceuticals (Basel) 2023; 16:1114. [PMID: 37631029 PMCID: PMC10458901 DOI: 10.3390/ph16081114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
RNA-binding proteins (RBPs), being pivotal elements in both physiological and pathological processes, possess the ability to directly impact RNA, thereby exerting a profound influence on cellular life. Furthermore, the dysregulation of RBPs not only induces alterations in the expression levels of genes associated with cancer but also impairs the occurrence of post-transcriptional regulatory mechanisms. Consequently, these circumstances can give rise to aberrations in cellular processes, ultimately resulting in alterations within the proteome. An aberrant proteome can disrupt the equilibrium between oncogenes and tumor suppressor genes, promoting cancer progression. Given their significant role in modulating gene expression and post-transcriptional regulation, directing therapeutic interventions towards RBPs represents a viable strategy for combating drug resistance in cancer treatment. RBPs possess significant potential as diagnostic and prognostic markers for diverse cancer types. Gaining comprehensive insights into the structure and functionality of RBPs, along with delving deeper into the molecular mechanisms underlying RBPs in tumor drug resistance, can enhance cancer treatment strategies and augment the prognostic outcomes for individuals afflicted with cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peijie Wu
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
| | - Dong Wang
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
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148
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Huang H, Kuang X, Zou Y, Zeng J, Du H, Tang H, Long C, Mao Y, Yu X, Wen C, Yan J, Shen H. MAP4K4 is involved in the neuronal development of retinal photoreceptors. Exp Eye Res 2023; 233:109524. [PMID: 37290629 DOI: 10.1016/j.exer.2023.109524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/10/2023]
Abstract
Mitogen-activated protein kinase kinase kinase kinase-4 (MAP4K4) is a potential regulator of photoreceptor development. To investigate the mechanisms underlying MAP4K4 during the neuronal development of retinal photoreceptors, we generated knockout models of C57BL/6j mice in vivo and 661 W cells in vitro. Our findings revealed homozygous lethality and neural tube malformation in mice subjected to Map4k4 DNA ablation, providing evidence for the involvement of MAP4K4 in early stage embryonic neural formation. Furthermore, our study demonstrated that the ablation of Map4k4 DNA led to the vulnerability of photoreceptor neurites during induced neuronal development. By monitoring transcriptional and protein variations in mitogen-activated protein kinase (MAPK) signaling pathway-related factors, we discovered an imbalance in neurogenesis-related factors in Map4k4 -/- cells. Specifically, MAP4K4 promotes jun proto-oncogene (c-JUN) phosphorylation and recruits other factors related to nerve growth, ultimately leading to the robust formation of photoreceptor neurites. These data suggest that MAP4K4 plays a decisive role in regulating the fate of retinal photoreceptors through molecular modulation and contributes to our understanding of vision formation.
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Affiliation(s)
- Hao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Department of Ophthalmology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412000, China
| | - Xielan Kuang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Biobank of Eye, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yuxiu Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Jingshu Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Han Du
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Han Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Chongde Long
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yan Mao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Xinyue Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Chaojuan Wen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Jianhua Yan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
| | - Huangxuan Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Biobank of Eye, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
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149
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Verdile V, Riccioni V, Guerra M, Ferrante G, Sette C, Valle C, Ferri A, Paronetto MP. An impaired splicing program underlies differentiation defects in hSOD1 G93A neural progenitor cells. Cell Mol Life Sci 2023; 80:236. [PMID: 37524863 PMCID: PMC11072603 DOI: 10.1007/s00018-023-04893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult devastating neurodegenerative disease characterized by the loss of upper and lower motor neurons (MNs), resulting in progressive paralysis and death. Genetic animal models of ALS have highlighted dysregulation of synaptic structure and function as a pathogenic feature of ALS-onset and progression. Alternative pre-mRNA splicing (AS), which allows expansion of the coding power of genomes by generating multiple transcript isoforms from each gene, is widely associated with synapse formation and functional specification. Deciphering the link between aberrant splicing regulation and pathogenic features of ALS could pave the ground for novel therapeutic opportunities. Herein, we found that neural progenitor cells (NPCs) derived from the hSOD1G93A mouse model of ALS displayed increased proliferation and propensity to differentiate into neurons. In parallel, hSOD1G93A NPCs showed impaired splicing patterns in synaptic genes, which could contribute to the observed phenotype. Remarkably, master splicing regulators of the switch from stemness to neural differentiation are de-regulated in hSOD1G93A NPCs, thus impacting the differentiation program. Our data indicate that hSOD1G93A mutation impacts on neurogenesis by increasing the NPC pool in the developing mouse cortex and affecting their intrinsic properties, through the establishment of a specific splicing program.
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Affiliation(s)
- Veronica Verdile
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135, Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
| | - Veronica Riccioni
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
| | - Marika Guerra
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gabriele Ferrante
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
| | - Claudio Sette
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, 00168, Rome, Italy
| | - Cristiana Valle
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
- Institute of Translational Pharmacology (IFT), Consiglio Nazionale delle Ricerche (CNR), 00133, Rome, Italy
| | - Alberto Ferri
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
- Institute of Translational Pharmacology (IFT), Consiglio Nazionale delle Ricerche (CNR), 00133, Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135, Rome, Italy.
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy.
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150
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Chao KH, Mao A, Salzberg SL, Pertea M. Splam: a deep-learning-based splice site predictor that improves spliced alignments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550754. [PMID: 37546880 PMCID: PMC10402160 DOI: 10.1101/2023.07.27.550754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The process of splicing messenger RNA to remove introns plays a central role in creating genes and gene variants. Here we describe Splam, a novel method for predicting splice junctions in DNA based on deep residual convolutional neural networks. Unlike some previous models, Splam looks at a relatively limited window of 400 base pairs flanking each splice site, motivated by the observation that the biological process of splicing relies primarily on signals within this window. Additionally, Splam introduces the idea of training the network on donor and acceptor pairs together, based on the principle that the splicing machinery recognizes both ends of each intron at once. We compare Splam's accuracy to recent state-of-the-art splice site prediction methods, particularly SpliceAI, another method that uses deep neural networks. Our results show that Splam is consistently more accurate than SpliceAI, with an overall accuracy of 96% at predicting human splice junctions. Splam generalizes even to non-human species, including distant ones like the flowering plant Arabidopsis thaliana. Finally, we demonstrate the use of Splam on a novel application: processing the spliced alignments of RNA-seq data to identify and eliminate errors. We show that when used in this manner, Splam yields substantial improvements in the accuracy of downstream transcriptome analysis of both poly(A) and ribo-depleted RNA-seq libraries. Overall, Splam offers a faster and more accurate approach to detecting splice junctions, while also providing a reliable and efficient solution for cleaning up erroneous spliced alignments.
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Affiliation(s)
- Kuan-Hao Chao
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alan Mao
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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