1
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Cai H, Li X, Niu X, Li J, Lan X, Lei C, Huang Y, Xu H, Li M, Chen H. Copy number variations within fibroblast growth factor 13 gene influence growth traits and alternative splicing in cattle. Anim Biotechnol 2024; 35:2314104. [PMID: 38426908 DOI: 10.1080/10495398.2024.2314104] [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: 03/02/2024]
Abstract
Previous researches revealed a copy number variation (CNV) region in the bovine fibroblast growth factor 13 (FGF13) gene. However, its effects remain unknown. This study detected the various copy number types in seven Chinese cattle breeds and analysed their population genetic characteristics and effects on growth traits and transcription levels. Copy number Loss was more frequent in Caoyuan Red cattle and Xianan cattle than in the other breeds. Association analysis between CNV and growth traits of Qinchuan indicated that the CNV was significantly related to chest depth, hip width and hucklebone width (P < 0.05). Additionally, the growth traits of individuals with copy number Loss were significantly inferior to those with copy number Gain or Median (P < 0.05). Besides, we found two splicing isoforms, AS1 and AS2, in FGF13 gene, which resulted from alternative 5' splicing sites of intron 1. These isoforms showed varied expression levels in various tissues. Moreover, CNV was significantly and negatively associated with the mRNA expression of AS1 (r = -0.525, P < 0.05). The CNVs in bovine FGF13 gene negatively regulated growth traits and gene transcription. These observations provide new insights into bovine FGF13 gene, delivering potentially useful information for future Chinese cattle breeding programs.
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Affiliation(s)
- Hanfang Cai
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Xinran Niu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Jing Li
- Animal Health Supervision Institute of Biyang, Biyang, Henan, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Hong Chen
- College of Animal Science, Xinjiang Agriculture University, Urumqi, China
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2
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Zhuravskaya A, Yap K, Hamid F, Makeyev EV. Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons. Genome Biol 2024; 25:162. [PMID: 38902825 PMCID: PMC11188260 DOI: 10.1186/s13059-024-03305-8] [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: 07/08/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identified several examples of such a regulation in developing neurons. However, the systems-level effects of AS-NMD in this context are poorly understood. RESULTS We developed an R package, factR2, which offers a comprehensive suite of AS-NMD analysis functions. Using this tool, we conducted a longitudinal analysis of gene expression in pluripotent stem cells undergoing induced neuronal differentiation. Our analysis uncovers hundreds of AS-NMD events with significant potential to regulate gene expression. Notably, this regulation is significantly overrepresented in specific functional groups of developmentally downregulated genes. Particularly strong association with gene downregulation is detected for alternative cassette exons stimulating NMD upon their inclusion into mature mRNA. By combining bioinformatic analyses with CRISPR/Cas9 genome editing and other experimental approaches we show that NMD-stimulating cassette exons regulated by the RNA-binding protein PTBP1 dampen the expression of their genes in developing neurons. We also provided evidence that the inclusion of NMD-stimulating cassette exons into mature mRNAs is temporally coordinated with NMD-independent gene repression mechanisms. CONCLUSIONS Our study provides an accessible workflow for the discovery and prioritization of AS-NMD targets. It further argues that the AS-NMD pathway plays a widespread role in developing neurons by facilitating the downregulation of functionally related non-neuronal genes.
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Affiliation(s)
- Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Karen Yap
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
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3
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Xiao MS, Damodaran AP, Kumari B, Dickson E, Xing K, On TA, Parab N, King HE, Perez AR, Guiblet WM, Duncan G, Che A, Chari R, Andresson T, Vidigal JA, Weatheritt RJ, Aregger M, Gonatopoulos-Pournatzis T. Genome-scale exon perturbation screens uncover exons critical for cell fitness. Mol Cell 2024:S1097-2765(24)00447-7. [PMID: 38917794 DOI: 10.1016/j.molcel.2024.05.024] [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: 10/01/2023] [Revised: 04/04/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.
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Affiliation(s)
- Mei-Sheng Xiao
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Arun Prasath Damodaran
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Bandana Kumari
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Ethan Dickson
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Kun Xing
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Tyler A On
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Nikhil Parab
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Helen E King
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Alexendar R Perez
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wilfried M Guiblet
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Gerard Duncan
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Anney Che
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Robert J Weatheritt
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2010, Australia
| | - Michael Aregger
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Thomas Gonatopoulos-Pournatzis
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
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Quinones-Valdez G, Amoah K, Xiao X. Long-read RNA-seq demarcates cis - and trans -directed alternative RNA splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599101. [PMID: 38915585 PMCID: PMC11195283 DOI: 10.1101/2024.06.14.599101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Genetic regulation of alternative splicing constitutes an important link between genetic variation and disease. Nonetheless, RNA splicing is regulated by both cis -acting elements and trans -acting splicing factors. Determining splicing events that are directed primarily by the cis - or trans -acting mechanisms will greatly inform our understanding of the genetic basis of disease. Here, we show that long-read RNA-seq, combined with our new method isoLASER, enables a clear segregation of cis - and trans -directed splicing events for individual samples. The genetic linkage of splicing is largely individual-specific, in stark contrast to the tissue-specific pattern of splicing profiles. Analysis of long-read RNA-seq data from human and mouse revealed thousands of cis -directed splicing events susceptible to genetic regulation. We highlight such events in the HLA genes whose analysis was challenging with short-read data. We also highlight novel cis -directed splicing events in Alzheimer's disease-relevant genes such as MAPT and BIN1 . Together, the clear demarcation of cis - and trans -directed splicing paves ways for future studies of the genetic basis of disease.
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Park J, Nam DH, Kim D, Chung YJ. RPS24 alternative splicing is a marker of cancer progression and epithelial-mesenchymal transition. Sci Rep 2024; 14:13246. [PMID: 38853173 PMCID: PMC11162997 DOI: 10.1038/s41598-024-63976-y] [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: 11/26/2023] [Accepted: 06/04/2024] [Indexed: 06/11/2024] Open
Abstract
Although alternative splicing (AS) is a major mechanism that adds diversity to gene expression patterns, its precise role in generating variability in ribosomal proteins, known as ribosomal heterogeneity, remains unclear. The ribosomal protein S24 (RPS24) gene, encoding a ribosomal component, undergoes AS; however, in-depth studies have been challenging because of three microexons between exons 4 and 6. We conducted a detailed analysis of RPS24 AS isoforms using a direct approach to investigate the splicing junctions related to these microexons, focusing on four AS isoforms. Each of these isoforms showed tissue specificity and relative differences in expression among cancer types. Significant differences in the proportions of these RPS24 AS isoforms between cancerous and normal tissues across diverse cancer types were also observed. Our study highlighted a significant correlation between the expression levels of a specific RPS24 AS isoform and the epithelial-mesenchymal transition process in lung and breast cancers. Our research contributes to a better understanding of the intricate regulatory mechanisms governing AS of ribosomal protein genes and highlights the biological implications of RPS24 AS isoforms in tissue development and tumorigenesis.
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Affiliation(s)
- Jiyeon Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea
| | - Da Hae Nam
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dokyeong Kim
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea.
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, Republic of Korea.
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6
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Bénitière F, Duret L, Necsulea A. GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes. NAR Genom Bioinform 2024; 6:lqae064. [PMID: 38867915 PMCID: PMC11167491 DOI: 10.1093/nargab/lqae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/22/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
We present GTDrift, a comprehensive data resource that enables explorations of genomic and transcriptomic characteristics alongside proxies of the intensity of genetic drift in individual species. This resource encompasses data for 1506 eukaryotic species, including 1413 animals and 93 green plants, and is organized in three components. The first two components contain approximations of the effective population size, which serve as indicators of the extent of random genetic drift within each species. In the first component, we meticulously investigated public databases to assemble data on life history traits such as longevity, adult body length and body mass for a set of 979 species. The second component includes estimations of the ratio between the rate of non-synonymous substitutions and the rate of synonymous substitutions (dN/dS) in protein-coding sequences for 1324 species. This ratio provides an estimate of the efficiency of natural selection in purging deleterious substitutions. Additionally, we present polymorphism-derived N e estimates for 66 species. The third component encompasses various genomic and transcriptomic characteristics. With this component, we aim to facilitate comparative transcriptomics analyses across species, by providing easy-to-use processed data for more than 16 000 RNA-seq samples across 491 species. These data include intron-centered alternative splicing frequencies, gene expression levels and sequencing depth statistics for each species, obtained with a homogeneous analysis protocol. To enable cross-species comparisons, we provide orthology predictions for conserved single-copy genes based on BUSCO gene sets. To illustrate the possible uses of this database, we identify the most frequently used introns for each gene and we assess how the sequencing depth available for each species affects our power to identify major and minor splice variants.
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Affiliation(s)
- Florian Bénitière
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, Villeurbanne, France
- Laboratoire d’Écologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, UMR CNRS 5023, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, Villeurbanne, France
| | - Anamaria Necsulea
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, Villeurbanne, France
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7
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Wang Y, Xu X, Zhang A, Yang S, Li H. Role of alternative splicing in fish immunity. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109601. [PMID: 38701992 DOI: 10.1016/j.fsi.2024.109601] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Alternative splicing serves as a pivotal source of complexity in the transcriptome and proteome, selectively connecting various coding elements to generate a diverse array of mRNAs. This process encodes multiple proteins with either similar or distinct functions, contributing significantly to the intricacies of cellular processes. The role of alternative splicing in mammalian immunity has been well studied. Remarkably, the immune system of fish shares substantial similarities with that of humans, and alternative splicing also emerges as a key player in the immune processes of fish. In this review, we offer an overview of alternative splicing and its associated functions in the immune processes of fish, and summarize the research progress on alternative splicing in the fish immunity. Furthermore, we review the impact of alternative splicing on the fish immune system's response to external stimuli. Finally, we present our perspectives on future directions in this field. Our aim is to provide valuable insights for the future investigations into the role of alternative splicing in immunity.
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Affiliation(s)
- Yunchao Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinyi Xu
- Hunan Fisheries Science Institute, Changsha, 410153, China
| | - Ailong Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266003, China.
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8
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Zhang D, Wang Z, Deng H, Yi S, Li T, Kang X, Li J, Li C, Wang T, Xiang B, Li G. Zinc oxide nanoparticles damage the prefrontal lobe in mouse: Behavioral impacts and key mechanisms. Toxicol Lett 2024; 397:129-140. [PMID: 38759938 DOI: 10.1016/j.toxlet.2024.05.009] [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: 12/14/2023] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Zinc Oxide nanoparticles (ZnO NPs) have dualistic properties due to their advantage and toxicity. However, the impact and mechanisms of ZnO NPs on the prefrontal lobe have limited research. This study investigates the behavioral changes following exposure to ZnO NPs (34 mg/kg, 30 days), integrating multiple behaviors and bioinformatics analysis to identify critical factors and regulatory mechanisms. The essential differentially expressed genes (DEGs) were identified, including ORC1, DSP, AADAT, SLITRK6, and STEAP1. Analysis of the DEGs based on fold change reveals that ZnO NPs primarily regulate cell survival, proliferation, and apoptosis in neural cells, damaging the prefrontal lobe. Moreover, disruption of cell communication, mineral absorption, and immune pathways occurs. Gene set enrichment analysis (GSEA) further shows enrichment of behavior, neuromuscular process, signal transduction in function, synapses-related, cAMP signaling, and immune pathways. Furthermore, alternative splicing (AS) genes highlight synaptic structure/function, synaptic signal transduction, immune responses, cell proliferation, and communication.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China; Department of Rehabilitation Medicine, Southwest Medical University, Luzhou, China
| | - Zhiyuan Wang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Hongmei Deng
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Simeng Yi
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Tao Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Xinjiang Kang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Jun Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Chang Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Tingting Wang
- Department of Psychiatry, Fundamental and Clinical Research on Mental Disorders Key Laboratory of Luzhou City, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, PR China.
| | - Bo Xiang
- Department of Psychiatry, Fundamental and Clinical Research on Mental Disorders Key Laboratory of Luzhou City, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, PR China.
| | - Guang Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, and Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China.
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Xing K, Li H, Wang X, Sun Y, Zhang J. A Full-Length Transcriptome and Analysis of the NHL-1 Gene Family in Neocaridina denticulata sinensis. BIOLOGY 2024; 13:366. [PMID: 38927246 PMCID: PMC11200715 DOI: 10.3390/biology13060366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024]
Abstract
Neocaridina denticulata sinensis has emerged as a promising model organism for basic studies in Decapod. However, the current transcriptome information on this species is based on next-generation sequencing technologies, which are limited by a short read length. Therefore, the present study aimed to generate a full-length transcriptome assembly of N. denticulata sinensis utilizing the PacBio Sequel Ⅱ platform. The resulting transcriptome assembly comprised 5831 transcripts with an N50 value of 3697 bp. Remarkably, 90.5% of these transcripts represented novel isoforms of known genes. The transcripts were further searched against the NR, SwissProt, KEGG, KOG, GO, NT, and Pfam databases. A total of 24.8% of the transcripts can be annotated across all seven databases. Additionally, 1236 alternative splicing events, 344 transcription factors, and 124 long non-coding RNAs (LncRNAs) were predicted. Based on the alternative splicing annotation results, a RING finger protein NHL-1 gene from N. denticulata sinensis (NdNHL-1) was identified. There are 15 transcripts in NdNHL-1. The longest transcript is 4995 bp in length and encodes a putative protein of 1665 amino acids. A phylogenetic analysis showed its close relationship with NHL-1 from other crustacean species. This report represents the full-length transcriptome of N. denticulata sinensis and will facilitate research on functional genomics and environmental adaptation in this species.
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Affiliation(s)
- Kefan Xing
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
| | - Huimin Li
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
| | - Xiongfei Wang
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
| | - Yuying Sun
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
- Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Jiquan Zhang
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
- Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
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10
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Chang CM, Chang WC, Hsieh SL. Characterization of the genetic variation and evolutionary divergence of the CLEC18 family. J Biomed Sci 2024; 31:53. [PMID: 38764023 PMCID: PMC11103991 DOI: 10.1186/s12929-024-01034-5] [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: 02/17/2024] [Accepted: 04/25/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND The C-type lectin family 18 (CLEC18) with lipid and glycan binding capabilities is important to metabolic regulation and innate immune responses against viral infection. However, human CLEC18 comprises three paralogous genes with highly similar sequences, making it challenging to distinguish genetic variations, expression patterns, and biological functions of individual CLEC18 paralogs. Additionally, the evolutionary relationship between human CLEC18 and its counterparts in other species remains unclear. METHODS To identify the sequence variation and evolutionary divergence of human CLEC18 paralogs, we conducted a comprehensive analysis using various resources, including human and non-human primate reference genome assemblies, human pangenome assemblies, and long-read-based whole-genome and -transcriptome sequencing datasets. RESULTS We uncovered paralogous sequence variants (PSVs) and polymorphic variants (PVs) of human CLEC18 proteins, and identified distinct signatures specific to each CLEC18 paralog. Furthermore, we unveiled a novel segmental duplication for human CLEC18A gene. By comparing CLEC18 across human and non-human primates, our research showed that the CLEC18 paralogy probably occurred in the common ancestor of human and closely related non-human primates, and the lipid-binding CAP/SCP/TAPS domain of CLEC18 is more diverse than its glycan-binding CTLD. Moreover, we found that certain amino acids alterations at variant positions are exclusive to human CLEC18 paralogs. CONCLUSIONS Our findings offer a comprehensive profiling of the intricate variations and evolutionary characteristics of human CLEC18.
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Affiliation(s)
- Che-Mai Chang
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nangang Dist., Taipei City, 115, Taiwan
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No.250, Wuxing St., Xinyi Dist, Taipei City, 110, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No.250, Wuxing St., Xinyi Dist, Taipei City, 110, Taiwan.
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei City, 110, Taiwan.
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei City, 116, Taiwan.
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei City, 116, Taiwan.
- Department of Pharmacology, National Defense Medical Center, Taipei City, 114, Taiwan.
| | - Shie-Liang Hsieh
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nangang Dist., Taipei City, 115, Taiwan.
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei City, 110, Taiwan.
- Immunology Research Center, National Health Research Institutes, No. 35, Keyan Rd., Zhunan Township, Miaoli County, 350, Taiwan.
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei City, 112, Taiwan.
- Department of Medical Research, Taipei Veterans General Hospital, Taipei City, 112, Taiwan.
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11
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Li F, Karimi N, Wang S, Pan T, Dong J, Wang X, Ma S, Shan Q, Liu C, Zhang Y, Li W, Feng G. mRNA isoform switches during mouse zygotic genome activation. Cell Prolif 2024:e13655. [PMID: 38764347 DOI: 10.1111/cpr.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Affiliation(s)
- Fan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Najmeh Karimi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Tianshi Pan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Jingxi Dong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Sinan Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Qingtong Shan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
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12
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Hou Z, Li X, Xu M, Meng S, Xu H, Li M, Cai H. Comparative Genome-Wide Alternative Splicing Analysis between Preadipocytes and Adipocytes. Genes (Basel) 2024; 15:640. [PMID: 38790269 PMCID: PMC11121090 DOI: 10.3390/genes15050640] [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: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Alternative splicing is a ubiquitous regulatory mechanism in gene expression that allows a single gene to generate multiple messenger RNAs (mRNAs). Adipocyte development is regulated by many processes, and recent studies have found that splicing factors also play an important role in adipogenic development. In the present study, we further investigated the differences in selective shearing during different periods of adipocyte differentiation. We identified five alternative splicing types including skipped exon, mutually exclusive exon, Alternative 5' splice site, Alternative 3' splice site, and Retained intron, with skipped exons being the most abundant type of selective shearing. In total, 641 differentially expressed selective shearing genes were obtained, enriched in 279 pathways, from which we selected and verified the accuracy of the sequencing results. Overall, RNA-seq revealed changes in the splicing and expression levels of these new candidate genes between precursor adipocytes and adipocytes, suggesting that they may be involved in adipocyte generation and differentiation.
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Affiliation(s)
- Zhongyi Hou
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Maosheng Xu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Shengbo Meng
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
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13
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Zhu N, Zhao Y, Yan W, Wei L, Sang Q, Li J, Liu B, Yu B. Characterization of alternative splicing events and prognostic signatures in gastric cancer. Cancer Cell Int 2024; 24:167. [PMID: 38734676 PMCID: PMC11088037 DOI: 10.1186/s12935-024-03348-8] [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: 01/24/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Accumulating evidences indicate that the specific alternative splicing (AS) events are linked to the occurrence and prognosis of gastric cancer (GC). Nevertheless, the impact of AS is still unclear and needed to further elucidation. METHODS The expression profile of GC and normal samples were downloaded from TCGA. AS events were achieved from SpliceSeq database. Cox regression together with LASSO analysis were employed to identify survival-associated AS events (SASEs) and calculate risk scores. PPI and pathway enrichment analysis were implemented to determine the function and pathways of these genes. Kaplan-Meier (K-M) analysis and Receiver Operating Characteristic Curves were used to evaluate the clinical significance of genes of SASEs. Q-PCR were applied to validate the hub genes on the survival prognosis in 47 GC samples. Drug sensitivity and immune cell infiltration analysis were conducted. RESULTS In total, 48 140 AS events in 10 610 genes from 361 GC and 31 normal samples were analyzed. Through univariate Cox regression, 855 SASEs in 763 genes were screened out. Further, these SASEs were analyzed by PPI and 17 hub genes were identified. Meanwhile, using Lasso and multivariate Cox regression analysis, 135 SASEs in 132 genes related to 7 AS forms were further screened and a GC prognostic model was constructed. K-M curves indicates that high-risk group has poorer prognosis. And the nomogram analysis on the basis of the multivariate Cox analysis was disclosed the interrelationships between 7 AS forms and clinical parameters in the model. Five key genes were then screened out by PPI analysis and Differential Expression Gene analysis based on TCGA and Combined-dataset, namely STAT3, RAD51B, SOCS2, POLE2 and TSR1. The expression levels of AS in STAT3, RAD51B, SOCS2, POLE2 and TSR1 were all significantly correlated with survival by qPCR verification. Nineteen drugs were sensitized to high-risk patients and eight immune cells showed significantly different infiltration between the STAD and normal groups. CONCLUSIONS In this research, the prognostic model constructed by SASEs can be applied to predict the prognosis of GC patients and the selected key genes are expected to become new biomarkers and therapeutical targets for GC treatment.
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Affiliation(s)
- Nan Zhu
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yupeng Zhao
- Gastroenterological Surgery, The affiliated Wuxi No. 2, People's Hospital of Nanjing Medical University, Wuxi, 200240, China
| | - Wenjing Yan
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lan Wei
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qingqing Sang
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianfang Li
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Bingya Liu
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Beiqin Yu
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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14
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Cesari E, Farini D, Medici V, Ehrmann I, Guerra M, Testa E, Naro C, Geloso MC, Pagliarini V, La Barbera L, D’Amelio M, Orsini T, Vecchioli SF, Tamagnone L, Fort P, Viscomi MT, Elliott DJ, Sette C. Differential expression of paralog RNA binding proteins establishes a dynamic splicing program required for normal cerebral cortex development. Nucleic Acids Res 2024; 52:4167-4184. [PMID: 38324473 PMCID: PMC11077083 DOI: 10.1093/nar/gkae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
Sam68 and SLM2 are paralog RNA binding proteins (RBPs) expressed in the cerebral cortex and display similar splicing activities. However, their relative functions during cortical development are unknown. We found that these RBPs exhibit an opposite expression pattern during development. Sam68 expression declines postnatally while SLM2 increases after birth, and this developmental pattern is reinforced by hierarchical control of Sam68 expression by SLM2. Analysis of Sam68:Slm2 double knockout (Sam68:Slm2dko) mice revealed hundreds of exons that respond to joint depletion of these proteins. Moreover, parallel analysis of single and double knockout cortices indicated that exons regulated mainly by SLM2 are characterized by a dynamic splicing pattern during development, whereas Sam68-dependent exons are spliced at relatively constant rates. Dynamic splicing of SLM2-sensitive exons is completely suppressed in the Sam68:Slm2dko developing cortex. Sam68:Slm2dko mice die perinatally with defects in neurogenesis and in neuronal differentiation, and develop a hydrocephalus, consistent with splicing alterations in genes related to these biological processes. Thus, our study reveals that developmental control of separate Sam68 and Slm2 paralog genes encoding homologous RBPs enables the orchestration of a dynamic splicing program needed for brain development and viability, while ensuring a robust redundant mechanism that supports proper cortical development.
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Affiliation(s)
- Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Donatella Farini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Vanessa Medici
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Ingrid Ehrmann
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle NE1 3BZ, UK
| | - Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Erika Testa
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Maria Concetta Geloso
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Livia La Barbera
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Marcello D’Amelio
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
- Università Campus Bio-Medico di Roma, Via Álvaro del Portillo, 21, 00128 Rome, Italy
| | - Tiziana Orsini
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC/CNR), Monterotondo, 00015 Rome, Italy
| | - Stefano Farioli Vecchioli
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC/CNR), Monterotondo, 00015 Rome, Italy
| | - Luca Tamagnone
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - Philippe Fort
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 05, France
| | - Maria Teresa Viscomi
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - David J Elliott
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle NE1 3BZ, UK
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
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Ruan L, Gu M, Geng H, Duan Z, Yu H, Shao Z, Li K, Lv M, Tang D. Achieving an optimal pregnancy outcome through the combined utilization of micro-TESE and ICSI in cryptorchidism associated with a non-canonical splicing variant in RXFP2. J Assist Reprod Genet 2024; 41:1307-1317. [PMID: 38430325 PMCID: PMC11143137 DOI: 10.1007/s10815-024-03070-4] [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: 09/11/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
PURPOSE To identify the genetic cause of a cryptorchidism patient carrying a non-canonical splicing variant highlighted by SPCards platform in RXFP2 and to provide a comprehensive overview of RXFP2 variants with cryptorchidism correlation. METHODS We identified a homozygous non-canonical splicing variant by whole-exome sequencing and Sanger sequencing in a case with cryptorchidism and non-obstructive azoospermia (NOA). As the pathogenicity of this non-canonical splicing variant remained unclear, we initially utilized the SPCards platform to predict its pathogenicity. Subsequently, we employed a minigene splicing assay to further evaluate the influence of the identified splicing variant. Microdissection testicular sperm extraction (micro-TESE) combined with intracytoplasmic sperm injection (ICSI) was performed. PubMed and Human Genome Variant Database (HGMD) were queried to search for RXFP2 variants. RESULTS We identified a homozygous non-canonical splicing variant (NM_130806: c.1376-12A > G) in RXFP2, and confirmed this variant caused aberrant splicing of exons 15 and 16 of the RXFP2 gene: 11 bases were added in front of exon 16, leading to an abnormal transcript initiation and a frameshift. Fortunately, the patient successfully obtained his biological offspring through micro-TESE combined with ICSI. Four cryptorchidism-associated variants in RXFP2 from 90 patients with cryptorchidism were identified through a literature search in PubMed and HGMD, with different inheritance patterns. CONCLUSION This is the first cryptorchidism case carrying a novel causative non-canonical splicing RXFP2 variant. The combined approach of micro-TESE and ICSI contributed to an optimal pregnancy outcome. Our literature review demonstrated that RXFP2 variants caused cryptorchidism in a recessive inheritance pattern, rather than a dominant pattern.
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Affiliation(s)
- Lewen Ruan
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Meng Gu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Hao Geng
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zongliu Duan
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
| | - Hui Yu
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zhongmei Shao
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Kuokuo Li
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China.
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
| | - Mingrong Lv
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China.
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China.
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
| | - Dongdong Tang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China.
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China.
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
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16
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Jin J, Nguyen LTG, Wassef A, Sadek R, Schmitt TM, Guo GL, Rasmussen TP, Zhong XB. Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction. Noncoding RNA 2024; 10:28. [PMID: 38668386 PMCID: PMC11053763 DOI: 10.3390/ncrna10020028] [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: 03/08/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
The long non-coding RNA (lncRNA) hepatocyte nuclear factor-1 alpha (HNF1A) antisense RNA 1 (HNF1A-AS1) is an important lncRNA for liver growth, development, cell differentiation, and drug metabolism. Like many lncRNAs, HNF1A-AS1 has multiple annotated alternative transcripts in the human genome. Several fundamental biological questions are still not solved: (1) How many transcripts really exist in biological samples, such as liver samples and liver cell lines? (2) What are the expression patterns of different alternative HNF1A-AS1 transcripts at different conditions, including during cell growth and development, after exposure to xenobiotics (such as drugs), and in disease conditions, such as metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD) cirrhosis, and obesity? (3) Does the siRNA used in previous studies knock down one or multiple transcripts? (4) Do different transcripts have the same or different functions for gene regulation? The presented data confirm the existence of several annotated HNF1A-AS1 transcripts in liver samples and cell lines, but also identify some new transcripts, which are not annotated in the Ensembl genome database. Expression patterns of the identified HNF1A-AS1 transcripts are highly correlated with the cell differentiation of matured hepatocyte-like cells from human embryonic stem cells (hESC), growth and differentiation of HepaRG cells, in response to rifampicin induction, and in various liver disease conditions. The expression levels of the HNF1A-AS1 transcripts are also highly correlated to the expression of cytochrome P450 enzymes, such as CYP3A4, during HepaRG growth, differentiation, and in response to rifampicin induction.
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Affiliation(s)
- Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Le Tra Giang Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Andrew Wassef
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
- Center of Excellence for Pharmaceutical Translational Research and Education, Rutgers University, Piscataway, NJ 08901, USA
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Ragui Sadek
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Timothy M. Schmitt
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Grace L. Guo
- Department of Pharmacology and Toxicology, Ernst Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
| | - Theodore P. Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
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17
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Damianov A, Lin CH, Huang J, Zhou L, Jami-Alahmadi Y, Peyda P, Wohlschlegel J, Black DL. The splicing regulators RBM5 and RBM10 are subunits of the U2 snRNP engaged with intron branch sites on chromatin. Mol Cell 2024; 84:1496-1511.e7. [PMID: 38537639 PMCID: PMC11057915 DOI: 10.1016/j.molcel.2024.02.039] [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: 09/08/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 04/09/2024]
Abstract
Understanding the mechanisms of pre-mRNA splicing is limited by the technical challenges to examining spliceosomes in vivo. Here, we report the isolation of RNP complexes derived from precatalytic A or B-like spliceosomes solubilized from the chromatin pellet of mammalian cell nuclei. We found that these complexes contain U2 snRNP proteins and a portion of the U2 snRNA bound with protected RNA fragments that precisely map to intronic branch sites across the transcriptome. These U2 complexes also contained the splicing regulators RBM5 and RBM10. We found RBM5 and RBM10 bound to nearly all branch site complexes and not simply those at regulated exons. The deletion of a conserved RBM5/RBM10 peptide sequence, including a zinc finger motif, disrupted U2 interaction and rendered the proteins inactive for the repression of many alternative exons. We propose a model where RBM5 and RBM10 regulate splicing as components of the U2 snRNP complex following branch site base pairing.
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Affiliation(s)
- Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeffrey Huang
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lin Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Parham Peyda
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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18
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Werner A, Kanhere A, Wahlestedt C, Mattick JS. Natural antisense transcripts as versatile regulators of gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00723-z. [PMID: 38632496 DOI: 10.1038/s41576-024-00723-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense-antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - John S Mattick
- University of New South Wales, Sydney, New South Wales, Australia
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19
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Jiao N, Xu J, Wang Y, Li D, Chen F, Chen Y, Chen J. Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera. BMC Genomics 2024; 25:372. [PMID: 38627613 PMCID: PMC11022335 DOI: 10.1186/s12864-024-10300-7] [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: 08/13/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio's SMRT technology and combined it with RNA-seq analysis (RNA sequencing on Illumina platform) after collecting xylem samples from the transition zone and the sapwood of D. odorifera. RESULTS We identified 14,938 full-length transcripts, including 9,830 novel isoforms, which has updated the D. odorifera genome annotation. Our analysis has revealed that 4,164 genes undergo APA, whereas 3,084 genes encounter AS. We have also annotated 118 lncRNAs. Furthermore, RNA-seq analysis identified 170 differential alternative splicing (DAS) events, 344 genes with differential APA site usage (DE-APA), and 6 differentially expressed lncRNAs in the transition zone when compared to the sapwood. AS, APA, and lncRNAs are differentially regulated during xylem development. Differentially expressed APA genes were enriched for terpenoid and flavonoid metabolism, indicating their role in the heartwood formation. Additionally, DE-APA genes were associated with cell wall biosynthesis and terpenoid metabolism, implying an APA's role in wood formation. A DAS gene (involved in chalcone accumulation) with a significantly greater inclusion of the last exon in the transition zone than in the sapwood was identified. We also found that differentially expressed lncRNAs targeted the genes related to terpene synthesis. CONCLUSIONS This study enhances our understanding of the molecular regulatory mechanisms underlying wood formation in D. odorifera, and provides valuable genetic resources and insights for its molecular-assisted breeding.
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Affiliation(s)
- Nanbo Jiao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Jieru Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Yue Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Dunxi Li
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Feifei Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Yu Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Jinhui Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China.
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China.
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20
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Gao M, Dekker ME, Leurs R, Vischer HF. Pharmacological characterization of seven human histamine H 3 receptor isoforms. Eur J Pharmacol 2024; 968:176450. [PMID: 38387718 DOI: 10.1016/j.ejphar.2024.176450] [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: 12/06/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
The histamine H3 receptor (H3R) regulates as a presynaptic G protein-coupled receptor the release of histamine and other neurotransmitters in the brain, and is consequently a potential therapeutic target for neuronal disorders. The human H3R encodes for seven splice variants that vary in the length of intracellular loop 3 and/or the C-terminal tail but are all able to induce heterotrimeric Gi protein signaling. The last two decades H3R drug discovery and lead optimization has been exclusively focused on the 445 amino acids-long reference isoform H3R-445. In this study, we pharmacologically characterized for the first time all seven H3R isoforms by determining their binding affinities for reference histamine H3 receptor agonists and inverse agonists. The H3R-453, H3R-415, and H3R-413 isoforms display similar binding affinities for all ligands as the H3R-445. However, increased agonist binding affinities were observed for the three shorter isoforms H3R-329, H3R-365, and H3R-373, whereas inverse agonists such as the approved anti-narcolepsy drug pitolisant (Wakix®) displayed significantly decreased binding affinities for the latter two isoforms. This opposite change in binding affinity of agonist versus inverse agonists on H3R-365 and H3R-373 is associated with their higher constitutive activity in a cAMP biosensor assay as compared to the other five isoforms. The observed differences in pharmacology between longer and shorter H3R isoforms should be considered in future drug discovery programs.
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Affiliation(s)
- Meichun Gao
- Department of Medicinal Chemistry, Amsterdam Institute of Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands
| | - Mabel E Dekker
- Department of Medicinal Chemistry, Amsterdam Institute of Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands
| | - Rob Leurs
- Department of Medicinal Chemistry, Amsterdam Institute of Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands.
| | - Henry F Vischer
- Department of Medicinal Chemistry, Amsterdam Institute of Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, the Netherlands.
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21
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de Reus AJEM, Basak O, Dykstra W, van Asperen JV, van Bodegraven EJ, Hol EM. GFAP-isoforms in the nervous system: Understanding the need for diversity. Curr Opin Cell Biol 2024; 87:102340. [PMID: 38401182 DOI: 10.1016/j.ceb.2024.102340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament (IF) protein expressed in specific types of glial cells in the nervous system. The expression of GFAP is highly regulated during brain development and in neurological diseases. The presence of distinct GFAP-isoforms in various cell types, developmental stages, and diseases indicates that GFAP (post-)transcriptional regulation has a role in glial cell physiology and pathology. GFAP-isoforms differ in sub-cellular localisation, IF-network assembly properties, and IF-dynamics which results in distinct molecular interactions and mechanical properties of the IF-network. Therefore, GFAP (post-)transcriptional regulation is likely a mechanism by which radial glia, astrocytes, and glioma cells can modulate cellular function.
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Affiliation(s)
- Alexandra J E M de Reus
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Onur Basak
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Werner Dykstra
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jessy V van Asperen
- Institut NeuroMyoGène (INMG), Unité Physiopathologie et Génétique du Neurone et du Muscle, Unversité Claude Bernard Lyon 1 CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Emma J van Bodegraven
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Elly M Hol
- Department of Translational Neuroscience, Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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22
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Liu D, Yu H, Xue N, Bao H, Gao Q, Tian Y. Alternative splicing patterns of hnrnp genes in gill tissues of rainbow trout (Oncorhynchus mykiss) during salinity changes. Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110948. [PMID: 38281704 DOI: 10.1016/j.cbpb.2024.110948] [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: 11/06/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 01/30/2024]
Abstract
Alternative splicing (AS) plays an important role in various physiological processes in eukaryotes, such as the stress response. However, patterns of AS events remain largely unexplored during salinity acclimation in fishes. In this study, we conducted AS analysis using RNA-seq datasets to explore splicing patterns in the gill tissues of rainbow trout exposed to altered salinity environments, ranging from 0 ‰ (T0) to 30 ‰ (T30). The results revealed 1441, 351, 483, 1051 and 1049 differentially alternatively spliced (DAS) events in 5 pairwise comparisons, including T6 vs. T0, T12 vs. T0, T18 vs. T0, T24 vs. T0, and T30 vs. T0, respectively. These DAS events were derived from 1290, 328, 444, 963 and 948 genes. Enrichment analysis indicated that these DAS genes were related to RNA splicing and processing. Among these, 14 DAS genes were identified as members of the large heterogeneous nuclear RNP (hnRNP) gene family. Alternative 3' splice site (A3SS), exon skipping (SE) and intron retention (RI) events resulted in the fragmentation or even loss of the functional RNA recognition motif (RRM) domains in hnrnpa0, hnrnp1a, hnrnp1b and hnrnpc genes. The incomplete RRM domains would hinder the interactions between hnRNP genes and pre-mRNAs. It would in turn influence the splicing patterns and mRNA stability of downstream target genes in response to salinity changes. The study provides insights into salinity acclimation in gill tissues of rainbow trout and serves as a significant reference on the osmoregulation mechanisms at post-transcription regulation levels in fish.
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Affiliation(s)
- Dazhi Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Han Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Na Xue
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Hancheng Bao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Qinfeng Gao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China.
| | - Yuan Tian
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China.
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23
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Liu X, Zhang J, Wang Z, Yan M, Xu M, Li G, Shender V, Wei J, Li J, Shao C, Zhang S, Kong B, Song K, Liu Z. Splicing Factor PQBP1 Curtails BAX Expression to Promote Ovarian Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306229. [PMID: 38342602 PMCID: PMC11022708 DOI: 10.1002/advs.202306229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/27/2023] [Indexed: 02/13/2024]
Abstract
Splicing factor polyglutamine binding protein-1 (PQBP1) is abundantly expressed in the central nervous system during development, and mutations in the gene cause intellectual disability. However, the roles of PQBP1 in cancer progression remain largely unknown. Here, it is shown that PQBP1 overexpression promotes tumor progression and indicates worse prognosis in ovarian cancer. Integrative analysis of spyCLIP-seq and RNA-seq data reveals that PQBP1 preferentially binds to exon regions and modulates exon skipping. Mechanistically, it is shown that PQBP1 regulates the splicing of genes related to the apoptotic signaling pathway, including BAX. PQBP1 promotes BAX exon 2 skipping to generate a truncated isoform that undergoes degradation by nonsense-mediated mRNA decay, thus making cancer cells resistant to apoptosis. In contrast, PQBP1 depletion or splice-switching antisense oligonucleotides promote exon 2 inclusion and thus increase BAX expression, leading to inhibition of tumor growth. Together, the results demonstrate an oncogenic role of PQBP1 in ovarian cancer and suggest that targeting the aberrant splicing mediated by PQBP1 has therapeutic potential in cancer treatment.
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Affiliation(s)
- Xihan Liu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
| | - Jiaojiao Zhang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Zixiang Wang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
| | - Mingyao Yan
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Meining Xu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Gaoyuan Li
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Victoria Shender
- Center for Precision Genome Editing and Genetic Technologies for BiomedicineFederal Research and Clinical Center of Physical‐Chemical Medicine of Federal Medical Biological AgencyMoscow119435Russia
| | - Jian‐jun Wei
- Department of PathologyNorthwestern University School of MedicineChicagoIL60611USA
| | - Jianqiao Li
- Department of OphthalmologyQilu HospitalShandong UniversityJinan250012China
| | - Changshun Shao
- Key Laboratory of Radiation Medicine and ProtectionInstitutes for Translational MedicineSoochow UniversitySuzhou215127China
| | - Shiqian Zhang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Beihua Kong
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Kun Song
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Zhaojian Liu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
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24
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Shi W, Tang J, Xiang J. Therapeutic strategies for aberrant splicing in cancer and genetic disorders. Clin Genet 2024; 105:345-354. [PMID: 38165092 DOI: 10.1111/cge.14478] [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: 09/21/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Accurate pre-mRNA splicing is essential for proper protein translation; however, aberrant splicing is commonly observed in the context of cancer and genetic disorders. Notably, in genetic diseases, these splicing abnormalities often play a pivotal role. Substantial challenges persist in accurately identifying and classifying disease-induced aberrant splicing, as well as in development of targeted therapeutic strategies. In this review, we examine prevalent forms of aberrant splicing and explore potential therapeutic approaches aimed at addressing these splicing-related diseases. This summary contributes to a deeper understanding of the complexities about aberrant splicing and provide a foundation for the development of effective therapeutic interventions in the field of genetic disorders and cancer.
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Affiliation(s)
- Wenhua Shi
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingqun Tang
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Juanjuan Xiang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
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25
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Sinha IR, Sandal PS, Burns GD, Mallika AP, Irwin KE, Cruz ALF, Wang V, Rodríguez JL, Wong PC, Ling JP. Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587011. [PMID: 38585725 PMCID: PMC10996699 DOI: 10.1101/2024.03.27.587011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Nuclear clearance and cytoplasmic aggregation of TDP-43 in neurons, initially identified in ALS-FTD, are hallmark pathological features observed across a spectrum of neurodegenerative diseases. We previously found that TDP-43 loss-of-function leads to the transcriptome-wide inclusion of deleterious cryptic exons in brains and biofluids post-mortem as well as during the presymptomatic stage of ALS-FTD, but upstream mechanisms that lead to TDP-43 dysregulation remain unclear. Here, we developed a web-based resource (SnapMine) to determine the levels of TDP-43 cryptic exon inclusion across hundreds of thousands of publicly available RNA sequencing datasets. We established cryptic exon inclusion across a variety of human cells and tissues to provide ground truth references for future studies on TDP-43 dysregulation. We then explored studies that were entirely unrelated to TDP-43 or neurodegeneration and found that ciclopirox olamine (CPX), an FDA-approved antifungal, can trigger the inclusion of TDP-43-associated cryptic exons in a variety of mouse and human primary cells. CPX induction of cryptic exon occurs via heavy metal toxicity and oxidative stress, suggesting that similar vulnerabilities could play a role in neurodegeneration. Our work demonstrates how diverse datasets can be linked through common biological features and underscores that public archives of sequencing data represent a vastly underutilized resource with tremendous potential for uncovering novel insights into complex biological mechanisms and diseases.
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Affiliation(s)
- Irika R Sinha
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Parker S Sandal
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Grace D Burns
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | | | - Katherine E Irwin
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Anna Lourdes F Cruz
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Vania Wang
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Philip C Wong
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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26
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Ren X, Zhao J, Hu J. Non-concordant epigenetic and transcriptional responses to acute thermal stress in western mosquitofish (Gambusia affinis). Mol Ecol 2024:e17332. [PMID: 38529738 DOI: 10.1111/mec.17332] [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: 07/17/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
Climate change is intensifying the frequency and severity of extreme temperatures. Understanding the molecular mechanisms underlying the ability to cope with acute thermal stress is key for predicting species' responses to extreme temperature events. While many studies have focused on the individual roles of gene expression, post-transcriptional processes and epigenetic modifications in response to acute thermal stress, the relative contribution of these molecular mechanisms remains unclear. The wide range of thermal limits of western mosquitofish (Gambusia affinis) provides an opportunity to explore this interplay. Here, we quantified changes in gene expression, alternative splicing, DNA methylation and microRNA (miRNA) expression in muscle tissue dissected from mosquitofish immediately after reaching high (CTmax) or low thermal limit (CTmin). Although the numbers of genes showing expression and splicing changes in response to acute temperature stress were small, we found a possibly larger and non-redundant role of splicing compared to gene expression, with more genes being differentially spliced (DSGs) than differentially expressed (DEGs), and little overlap between DSGs and DEGs. We also identified a small proportion of CpGs showing significant methylation change (i.e. differentially methylated cytosines, DMCs) in fish at thermal limits; however, there was no overlap between DEGs and genes annotated with DMCs in both CTmax and CTmin experiments. The weak interplay between epigenetic modifications and gene expression was further supported by our discoveries of no differentially expressed miRNAs. These findings provide novel insights into the relative role of different molecular mechanisms underlying immediate responses to extreme temperatures and demonstrate non-concordant responses of epigenetic and transcriptional mechanisms to acute temperature stress.
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Affiliation(s)
- Xingyue Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Junjie Zhao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
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27
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Lu D, Mihoayi M, Ablikim Y, Arikin A. RNA splicing regulator EIF3D regulates the tumor microenvironment through immunogene-related alternative splicing in head and neck squamous cell carcinoma. Aging (Albany NY) 2024; 16:5929-5948. [PMID: 38535990 PMCID: PMC11042944 DOI: 10.18632/aging.205681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/27/2024] [Indexed: 04/23/2024]
Abstract
Study finds that eukaryotic translation initiation factor 3 subunit D (EIF3D) may play an important role in aberrant alternative splicing (AS) events in tumors. AS possesses a pivotal role in both tumour progression and the constitution of the tumour microenvironment (TME). Regrettably, our current understanding of AS remains circumscribed especially in the context of immunogene-related alternative splicing (IGAS) profiles within Head and Neck Squamous Cell Carcinoma (HNSC). In this study, we comprehensively analyzed the function and mechanism of action of EIF3D by bioinformatics analysis combined with in vitro cellular experiments, and found that high expression of EIF3D in HNSC was associated with poor prognosis of overall survival (OS) and progression-free survival (PFS). The EIF3D low expression group had a higher degree of immune infiltration and better efficacy against PD1 and CTLA4 immunotherapy compared to the EIF3D high expression group. TCGA SpliceSeq analysis illustrated that EIF3D influenced differentially spliced alternative splicing (DSAS) events involving 105 differentially expressed immunogenes (DEIGs). We observed an induction of apoptosis and a suppression of cell proliferation, migration, and invasion in EIF3D knock-down FaDu cells. RNA-seq analysis unveiled that 531 genes exhibited differential expression following EIF3D knockdown in FaDu cells. These include 52 DEIGs. Furthermore, EIF3D knockdown influenced the patterns of 1923 alternative splicing events (ASEs), encompassing 129 IGASs. This study identified an RNA splicing regulator and revealed its regulatory role in IGAS and the TME of HNSC, suggesting that EIF3D may be a potential target for predicting HNSC prognosis and immunotherapeutic response.
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Affiliation(s)
- Dandan Lu
- Otolaryngology Diagnosis and Treatment Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
- Department of Otolaryngology, Shaanxi Nuclear Industry 215 Hospital, Xianyang 712000, China
| | - Mijti Mihoayi
- Otolaryngology Diagnosis and Treatment Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
| | - Yimin Ablikim
- Otolaryngology Diagnosis and Treatment Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
| | - Abdeyrim Arikin
- Otolaryngology Diagnosis and Treatment Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
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28
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Liu T, Ji W, Cheng X, Lv L, Yu X, Wang N, Li M, Hu T, Shi Z. Revealing a Novel Methylated Integrin Alpha-8 Related to Extracellular Matrix and Anoikis Resistance Using Proteomic Analysis in the Immune Microenvironment of Lung Adenocarcinoma. Mol Biotechnol 2024:10.1007/s12033-024-01114-9. [PMID: 38514598 DOI: 10.1007/s12033-024-01114-9] [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: 09/15/2023] [Accepted: 02/07/2024] [Indexed: 03/23/2024]
Abstract
Genomic epigenetics of extracellular matrix (ECM) play an important role in lung adenocarcinoma (LUAD). Our study identified a signature of potential prognostic genes associated with ECM and constructed immune risk-related prognosis model in LUAD. We downloaded mRNAs transcriptome data, miRNAs expression data, and clinical patient information for LUAD based on The Cancer Genome Atlas. "Limma, clusterProfiler, ggplot2" R packages and GSEA were used to analyze meaningful genes and explore potential biological function. A competing endogenous RNA network was constructed to reveal the mechanism of ECM-related genes. Combined with clinical LUAD patients' characteristics, univariate and multivariate Cox regression analyses were used to build prognostic immune risk model. Next, we calculated AUC value of ROC curve, and explored survival probability of different risk groups. A total of 2966 mRNAs were differently expressed in LUAD samples and normal samples. Function enrichment analyses proved mRNAs were associated with many tumor pathways, such as cell adhesion, vascular smooth muscle contraction, and cell cycle. There were 18 mRNAs related to ECM receptor signaling pathway, and 7 mRNAs expressions were correlated with EGFR expression, but only 5mRNAs were associated with the long-term prognosis. Based on Integrin alpha-8 (ITGA8) molecule, we identified potential 3 miRNAs from several databases. The promoter of ITGA8 was higher-methylated and lower-expressed in LUAD. And lower-expressed group has poor prognosis for patients. 66 immunomodulators related to ITGA8 were performed to construct immune correlation prediction model (p < 0.05). Comprehensive analyses of ITGA8 revealed it combined focal adhesion kinase to activate PI3K/AKT signaling pathway to influence the occurrence and development of LUAD. A novel immune prognostic model about ITGA8 was constructed and verified in LUAD patients. Combined with non-coding genes and genomic epigenetics, identification of potential biomarkers provided new light on therapeutic strategy for clinical patients.
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Affiliation(s)
- Tingting Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Wen Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Xue Cheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Lin Lv
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Xiaohui Yu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Na Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Mengcong Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Tinghua Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Zhihong Shi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China.
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29
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Jones EF, Haldar A, Oza VH, Lasseigne BN. Quantifying transcriptome diversity: a review. Brief Funct Genomics 2024; 23:83-94. [PMID: 37225889 DOI: 10.1093/bfgp/elad019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/14/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Following the central dogma of molecular biology, gene expression heterogeneity can aid in predicting and explaining the wide variety of protein products, functions and, ultimately, heterogeneity in phenotypes. There is currently overlapping terminology used to describe the types of diversity in gene expression profiles, and overlooking these nuances can misrepresent important biological information. Here, we describe transcriptome diversity as a measure of the heterogeneity in (1) the expression of all genes within a sample or a single gene across samples in a population (gene-level diversity) or (2) the isoform-specific expression of a given gene (isoform-level diversity). We first overview modulators and quantification of transcriptome diversity at the gene level. Then, we discuss the role alternative splicing plays in driving transcript isoform-level diversity and how it can be quantified. Additionally, we overview computational resources for calculating gene-level and isoform-level diversity for high-throughput sequencing data. Finally, we discuss future applications of transcriptome diversity. This review provides a comprehensive overview of how gene expression diversity arises, and how measuring it determines a more complete picture of heterogeneity across proteins, cells, tissues, organisms and species.
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Affiliation(s)
- Emma F Jones
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anisha Haldar
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishal H Oza
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brittany N Lasseigne
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
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30
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Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [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] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
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Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
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31
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Einson J, Minaeva M, Rafi F, Lappalainen T. The impact of genetically controlled splicing on exon inclusion and protein structure. PLoS One 2024; 19:e0291960. [PMID: 38478511 PMCID: PMC10936842 DOI: 10.1371/journal.pone.0291960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/08/2023] [Indexed: 03/17/2024] Open
Abstract
Common variants affecting mRNA splicing are typically identified though splicing quantitative trait locus (sQTL) mapping and have been shown to be enriched for GWAS signals by a similar degree to eQTLs. However, the specific splicing changes induced by these variants have been difficult to characterize, making it more complicated to analyze the effect size and direction of sQTLs, and to determine downstream splicing effects on protein structure. In this study, we catalogue sQTLs using exon percent spliced in (PSI) scores as a quantitative phenotype. PSI is an interpretable metric for identifying exon skipping events and has some advantages over other methods for quantifying splicing from short read RNA sequencing. In our set of sQTL variants, we find evidence of selective effects based on splicing effect size and effect direction, as well as exon symmetry. Additionally, we utilize AlphaFold2 to predict changes in protein structure associated with sQTLs overlapping GWAS traits, highlighting a potential new use-case for this technology for interpreting genetic effects on traits and disorders.
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Affiliation(s)
- Jonah Einson
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, United States of America
- New York Genome Center, New York, NY, United States of America
| | - Mariia Minaeva
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Faiza Rafi
- New York Genome Center, New York, NY, United States of America
- Department of Biotechnology, The City College of New York, New York, NY, United States of America
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, United States of America
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, United States of America
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32
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Xiao L, Sun H, Cheng R, Yang R, Jin X, Xu Z, Cai Y, Yang Y, Pang F, Xue G, Wang P, Jiang Q, Nie H. Functional requirement of alternative splicing in epithelial-mesenchymal transition of pancreatic circulating tumor. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102129. [PMID: 38370981 PMCID: PMC10869908 DOI: 10.1016/j.omtn.2024.102129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/19/2024] [Indexed: 02/20/2024]
Abstract
Circulating tumor cells (CTCs) that undergo epithelial-to-mesenchymal transition (EMT) can provide valuable information regarding metastasis and potential therapies. However, current studies on the EMT overlook alternative splicing. Here, we used single-cell full-length transcriptome data and mRNA sequencing of CTCs to identify stage-specific alternative splicing of partial EMT and mesenchymal states during pancreatic cancer metastasis. We classified definitive tumor and normal epithelial cells via genetic aberrations and demonstrated dynamic changes in the epithelial-mesenchymal continuum in both epithelial cancer cells and CTCs. We provide the landscape of alternative splicing in CTCs at different stages of EMT, uncovering cell-type-specific splicing patterns and splicing events in cell surface proteins suitable for therapies. We show that MBNL1 governs cell fate through alternative splicing independently of changes in gene expression and affects the splicing pattern during EMT. We found a high frequency of events that contained multiple premature termination codons and were enriched with C and G nucleotides in close proximity, which influence the likelihood of stop codon readthrough and expand the range of potential therapeutic targets. Our study provides insights into the EMT transcriptome's dynamic changes and identifies potential diagnostic and therapeutic targets in pancreatic cancer.
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Affiliation(s)
- Lixing Xiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Haoxiu Sun
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Rui Cheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Rongrong Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Xiyun Jin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Zhaochun Xu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Yideng Cai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Yuexin Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Fenglan Pang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Guangfu Xue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Pingping Wang
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
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33
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Bénitière F, Necsulea A, Duret L. Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans. eLife 2024; 13:RP93629. [PMID: 38470242 DOI: 10.7554/elife.93629] [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] [Indexed: 03/13/2024] Open
Abstract
Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the number of distinct cell types) correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that 'complex' organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this 'drift barrier' theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we analyzed 3496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.
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Affiliation(s)
- Florian Bénitière
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Anamaria Necsulea
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
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34
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Bühring S, Brunner A, Heeb K, Mergard MP, Schmauck G, Jacob S. An array of signal-specific MoYpd1 isoforms determines full virulence in the pathogenic fungus Magnaporthe oryzae. Commun Biol 2024; 7:265. [PMID: 38438487 PMCID: PMC10912366 DOI: 10.1038/s42003-024-05941-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: 10/04/2023] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
Magnaporthe oryzae is placed first on a list of the world's top ten plant pathogens with the highest scientific and economic importance. The locus MGG_07173 occurs only once in the genome of M. oryzae and encodes the phosphotransfer protein MoYpd1p, which plays an important role in the high osmolarity glycerol (HOG) signaling pathway for osmoregulation. Originating from this locus, at least three MoYPD1 isoforms are produced in a signal-specific manner. The transcript levels of these MoYPD1-isoforms were individually affected by external stress. Salt (KCI) stress raised MoYPD1_T0 abundance, whereas osmotic stress by sorbitol elevates MoYPD1_T1 levels. In line with this, signal-specific nuclear translocation of green fluorescent protein-fused MoYpd1p isoforms in response to stress was observed. Mutant strains that produce only one of the MoYpd1p isoforms are less virulent, suggesting a combination thereof is required to invade the host successfully. In summary, we demonstrate signal-specific production of MoYpd1p isoforms that individually increase signal diversity and orchestrate virulence in M. oryzae.
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Affiliation(s)
- Sri Bühring
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Antonia Brunner
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Klemens Heeb
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Marius-Peter Mergard
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Greta Schmauck
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Stefan Jacob
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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35
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Reyes AV, Shrestha R, Grismer TS, Byun D, Xu SL. Impact of alternative splicing on Arabidopsis proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582853. [PMID: 38496481 PMCID: PMC10942332 DOI: 10.1101/2024.02.29.582853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Alternative splicing is an important regulatory process in eukaryotes. In plants, the major form of alternative splicing is intron retention. Despite its importance, the global impact of AS on the Arabidopsis proteome has not been investigated. In this study, we address this gap by performing a comprehensive integrated analysis of how changes in AS can affect the Arabidopsis proteome using mutants that disrupt ACINUS and PININ, two evolutionarily conserved alternative splicing factors. We used tandem mass tagging (TMT) with real-time search MS3 (RTS-SPS-MS3) coupled with extensive sample fractionations to achieve very high coverage and accurate protein quantification. We then integrated our proteomic data with transcriptomic data to assess how transcript changes and increased intron retention (IIR) affect the proteome. For differentially expressed transcripts, we have observed a weak to moderate correlation between transcript changes and protein changes. Our studies revealed that some IIRs have no effect on either transcript or protein levels, while some IIRs can significantly affect protein levels. Surprisingly, we found that IIRs have a much smaller effect on increasing protein diversity. Notably, the increased intron retention events detected in the double mutant are also detected in the WT under various biotic or abiotic stresses. We further investigated the characteristics of the retained introns. Our extensive proteomic data help to guide the phenotypic analysis and reveal that collective protein changes contribute to the observed phenotypes of the increased anthocyanin, pale green, reduced growth, and short root observed in the acinus pnn double mutant. Overall, our study provides insight into the intricate regulatory mechanism of intron retention and its impact on protein abundance in plants.
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Affiliation(s)
- Andres V Reyes
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - TaraBryn S Grismer
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Danbi Byun
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Shou-Ling Xu
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
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36
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Verta JP, Jacobs A. The evolutionary significance of post-transcriptional gene regulation. Heredity (Edinb) 2024; 132:117-119. [PMID: 38366090 PMCID: PMC10923911 DOI: 10.1038/s41437-024-00674-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| | - Arne Jacobs
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK.
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37
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Wei M, Yi P, Huang B, Naz S, Ge C, Shu-Chien AC, Wang Z, Wu X. Insights into sequence characteristics and evolutionary history of DGATs in arthropods. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101195. [PMID: 38266530 DOI: 10.1016/j.cbd.2024.101195] [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: 11/08/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Triacylglycerol (TAG) is crucial in animal energy storage and membrane biogenesis. The conversion of diacylglycerol (DAG) to triacylglycerol (TAG) is catalyzed by diacylglycerol acyltransferase enzymes (DGATs), which are encoded by genes belonging to two distinct gene families. Although arthropods are known to possess DGATs activities and utilize the glycerol-3-phosphate pathway and MAG pathway for TAG biosynthesis, the sequence characterization and evolutionary history of DGATs in arthropods remains unclear. This study aimed to comparatively evaluate genomic analyses of DGATs in 13 arthropod species and 14 outgroup species. We found that arthropods lack SOAT2 genes within the DGAT1 family, while DGAT2, MOGAT3, AWAT1, and AWAT2 were absent from in DGAT2 family. Gene structure and phylogenetic analyses revealed that DGAT1 and DGAT2 genes come from different gene families. The expression patterns of these genes were further analyzed in crustaceans, demonstrating the importance of DGAT1 in TAG biosynthesis. Additionally, we identified the DGAT1 gene in Swimming crab (P. trituberculatus) undergoes a mutually exclusive alternative splicing event in the molt stages. Our newly determined DGAT inventory data provide a more complete scenario and insights into the evolutionary dynamics and functional diversification of DGATs in arthropods.
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Affiliation(s)
- Maolei Wei
- Centre for Research on Fish Nutrition and Environmental Ecology of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Peng Yi
- Centre for Research on Fish Nutrition and Environmental Ecology of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Baoyou Huang
- Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo 315100, China; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Saira Naz
- Centre for Research on Fish Nutrition and Environmental Ecology of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Chutian Ge
- Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo 315100, China; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Alexander Chong Shu-Chien
- School of Biological Sciences, University Sains Malaysia, Minden, 11800 Penang, Malaysia; Center for Chemical Biology, University Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Zongji Wang
- Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo 315100, China; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China.
| | - Xugan Wu
- Centre for Research on Fish Nutrition and Environmental Ecology of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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38
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Engal E, Zhang Z, Geminder O, Jaffe-Herman S, Kay G, Ben-Hur A, Salton M. The spectrum of pre-mRNA splicing in autism. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1838. [PMID: 38509732 DOI: 10.1002/wrna.1838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Disruptions in spatiotemporal gene expression can result in atypical brain function. Specifically, autism spectrum disorder (ASD) is characterized by abnormalities in pre-mRNA splicing. Abnormal splicing patterns have been identified in the brains of individuals with ASD, and mutations in splicing factors have been found to contribute to neurodevelopmental delays associated with ASD. Here we review studies that shed light on the importance of splicing observed in ASD and that explored the intricate relationship between splicing factors and ASD, revealing how disruptions in pre-mRNA splicing may underlie ASD pathogenesis. We provide an overview of the research regarding all splicing factors associated with ASD and place a special emphasis on five specific splicing factors-HNRNPH2, NOVA2, WBP4, SRRM2, and RBFOX1-known to impact the splicing of ASD-related genes. In the discussion of the molecular mechanisms influenced by these splicing factors, we lay the groundwork for a deeper understanding of ASD's complex etiology. Finally, we discuss the potential benefit of unraveling the connection between splicing and ASD for the development of more precise diagnostic tools and targeted therapeutic interventions. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
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Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zhenwei Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Jaffe-Herman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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39
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Manahan DN, Nachman MW. Alternative splicing and environmental adaptation in wild house mice. Heredity (Edinb) 2024; 132:133-141. [PMID: 38012302 PMCID: PMC10923775 DOI: 10.1038/s41437-023-00663-0] [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: 04/30/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
A major goal of evolutionary genetics is to understand the genetic and molecular mechanisms underlying adaptation. Previous work has established that changes in gene regulation may contribute to adaptive evolution, but most studies have focused on mRNA abundance and only a few studies have investigated the role of post-transcriptional processing. Here, we use a combination of exome sequences and short-read RNA-Seq data from wild house mice (Mus musculus domesticus) collected along a latitudinal transect in eastern North America to identify candidate genes for local adaptation through alternative splicing. First, we identified alternatively spliced transcripts that differ in frequency between mice from the northern-most and southern-most populations in this transect. We then identified the subset of these transcripts that exhibit clinal patterns of variation among all populations in the transect. Finally, we conducted association studies to identify cis-acting splicing quantitative trait loci (cis-sQTL), and we identified cis-sQTL that overlapped with previously ascertained targets of selection from genome scans. Together, these analyses identified a small set of alternatively spliced transcripts that may underlie environmental adaptation in house mice. Many of these genes have known phenotypes associated with body size, a trait that varies clinally in these populations. We observed no overlap between these genes and genes previously identified by changes in mRNA abundance, indicating that alternative splicing and changes in mRNA abundance may provide separate molecular mechanisms of adaptation.
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Affiliation(s)
- David N Manahan
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA.
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA
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Lai H, Lyu M, Ruan H, Liu Y, Liu T, Lei S, Xiao Y, Zhang S, Ying B. Large-scale analysis reveals splicing biomarkers for tuberculosis progression and prognosis. Comput Biol Med 2024; 171:108187. [PMID: 38402840 DOI: 10.1016/j.compbiomed.2024.108187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Emerging evidence suggests that aberrant alternative splicing (AS) may play an important role in tuberculosis (TB). However, current knowledge regarding the value of AS in TB progression and prognosis remains unclear. METHOD Public RNA-seq datasets related to TB progression and prognosis were searched and AS analyses were conducted based on SUPPA2. Percent spliced in (PSI) was used for quantifying AS events and multiple machine learning (ML) methods were employed to construct predictive models. Area under curve (AUC), sensitivity and specificity were calculated to evaluate the model performance. RESULTS A total of 1587 samples from 7 datasets were included. Among 923 TB-progression related differential AS events (DASEs), 3 events (GET1-skipping exon (SE), TPD52-alternative first exons (AF) and TIMM10-alternative 5' splice site (A5)) were selected as candidate biomarkers; however, their predictive performance was limited. For TB prognosis, 5 events (PHF23-AF, KIF1B-SE, MACROD2-alternative 3' splice site (A3), CD55-retained intron (RI) and GALNT11-AF) were selected as candidates from the 1282 DASEs. Six ML methods were used to integrate these 5 events and XGBoost outperformed than others. AUC, sensitivity and specificity of XGBoost model were 0.875, 81.1% and 83.5% in training set, while they were 0.805, 68.4% and 73.2% in test set. CONCLUSION GET1-SE, TPD52-AF and TIMM10-A5 showed limited role in predicting TB progression, while PHF23-AF, KIF1B-SE, MACROD2-A3, CD55-RI and GALNT11-AF could well predict TB prognosis and work as candidate biomarkers. This work preliminarily explored the value of AS in predicting TB progression and prognosis and offered potential targets for further research.
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Affiliation(s)
- Hongli Lai
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Mengyuan Lyu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Hongxia Ruan
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Yang Liu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Tangyuheng Liu
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Shuting Lei
- West China Medical School/West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Yuling Xiao
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China
| | - Shu Zhang
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Binwu Ying
- Department of Laboratory Medicine/Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, PR China; Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, Sichuan Province, 610041, PR China.
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Steward RA, Pruisscher P, Roberts KT, Wheat CW. Genetic constraints in genes exhibiting splicing plasticity in facultative diapause. Heredity (Edinb) 2024; 132:142-155. [PMID: 38291272 PMCID: PMC10923799 DOI: 10.1038/s41437-024-00669-2] [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: 02/26/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.
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Affiliation(s)
- Rachel A Steward
- Zoology Department, Stockholm University, Stockholm, Sweden.
- Biology Department, Lund University, Lund, Sweden.
| | - Peter Pruisscher
- Zoology Department, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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Damacena de Angelis C, Meddeb M, Chen N, Fisher SA. An antisense oligonucleotide efficiently suppresses splicing of an alternative exon in vascular smooth muscle in vivo. Am J Physiol Heart Circ Physiol 2024; 326:H860-H869. [PMID: 38276948 DOI: 10.1152/ajpheart.00745.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Targeting alternative exons for therapeutic gain has been achieved in a few instances and potentially could be applied more broadly. The myosin phosphatase (MP) enzyme is a critical hub upon which signals converge to regulate vessel tone. Alternative exon 24 of myosin phosphatase regulatory subunit (Mypt1 E24) is an ideal target as toggling between the two isoforms sets smooth muscle sensitivity to vasodilators such as nitric oxide (NO). This study aimed to develop a gene-based therapy to suppress splicing of Mypt1 E24 thereby switching MP enzyme to the NO-responsive isoform. CRISPR/Cas9 constructs were effective at editing of Mypt1 E24 in vitro; however, targeting of vascular smooth muscle in vivo with AAV9 was inefficient. In contrast, an octo-guanidine conjugated antisense oligonucleotide targeting the 5' splice site of Mypt1 E24 was highly efficient in vivo. It reduced the percent splicing inclusion of Mypt1 E24 from 80% to 10% in mesenteric arteries. The maximal and half-maximal effects occurred at 12.5 and 6.25 mg/kg, respectively. The effect persisted for at least 1 mo without toxicity. This highly effective splice-blocking antisense oligonucleotide could be developed as a novel therapy to reverse vascular dysfunction common to diseases such as hypertension and heart failure.NEW & NOTEWORTHY Alternative exon usage is a major driver of phenotypic diversity in all cell types including smooth muscle. However, the functional significance of most of the hundreds of thousands of alternative exons has not been defined, nor in most cases even tested. If their importance to vascular function were known these alternative exons could represent novel therapeutic targets. Here, we present injection of Vivo-morpholino splice-blocking antisense oligonucleotides as a simple, efficient, and cost-effective method for suppression of alternative exon usage in vascular smooth muscle in vivo.
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Affiliation(s)
| | - Mariam Meddeb
- Division of Cardiology, Department of Medicine, Baltimore, Maryland, United States
| | - Nelson Chen
- University of Maryland-Baltimore Scholars Program, Baltimore, Maryland, United States
| | - Steven A Fisher
- Division of Cardiology, Department of Medicine, Baltimore, Maryland, United States
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland, United States
- Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, United States
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43
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Liu L, Wang W, Liu W, Li X, Yi G, Adetula AA, Huang H, Tang Z. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. Int J Mol Sci 2024; 25:2874. [PMID: 38474122 DOI: 10.3390/ijms25052874] [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: 01/17/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Alternative splicing (AS) plays a crucial role in regulating gene expression, function, and diversity. However, limited reports exist on the identification and comparison of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from eight tissues, integrating information on transcription factors (TFs), selection signals, splicing factors (SFs), and quantitative trait loci (QTL) to comprehensively study alternative splicing events (ASEs) in pigs. Five ASE types were identified, with Mutually Exclusive Exon (MXE) and Skipped Exon (SE) ASEs being the most prevalent. A significant portion of genes with ASEs (ASGs) showed conservation across all eight tissues (63.21-76.13% per tissue). Differentially alternative splicing genes (DASGs) and differentially expressed genes (DEGs) exhibited tissue specificity, with blood and adipose tissues having more DASGs. Functional enrichment analysis revealed coDASG_DEGs in adipose were enriched in pathways associated with adipose deposition and immune inflammation, while coDASG_DEGs in blood were enriched in pathways related to immune inflammation and metabolism. Adipose deposition in Eastern pigs might be linked to the down-regulation of immune-inflammation-related pathways and reduced insulin resistance. The TFs, selection signals, and SFs appeared to regulate ASEs. Notably, ARID4A (TF), NSRP1 (SF), ANKRD12, IFT74, KIAA2026, CCDC18, NEXN, PPIG, and ROCK1 genes in adipose tissue showed potential regulatory effects on adipose-deposition traits. NSRP1 could promote adipogenesis by regulating alternative splicing and expression of CCDC18. Conducting an in-depth investigation into AS, this study has successfully identified key marker genes essential for pig genetic breeding and the enhancement of meat quality, which will play important roles in promoting the diversity of pork quality and meeting market demand.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wei Wang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weiwei Liu
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xingzheng Li
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guoqiang Yi
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China
| | - Adeyinka Abiola Adetula
- Reproductive Biotechnology, Department of Molecular Life Sciences, TUM School of Life Sciences, Technical University Munich, 85354 Freising, Germany
| | - Haibo Huang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zhonglin Tang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China
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Innes PA, Goebl AM, Smith CCR, Rosenberger K, Kane NC. Gene expression and alternative splicing contribute to adaptive divergence of ecotypes. Heredity (Edinb) 2024; 132:120-132. [PMID: 38071268 PMCID: PMC10924094 DOI: 10.1038/s41437-023-00665-y] [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: 02/28/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 03/10/2024] Open
Abstract
Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific gene regulatory mechanisms contribute to adaptive divergence of populations. In plants, the post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both development and abiotic stress response, making it a compelling potential target of natural selection. AS allows organisms to generate multiple different transcripts/proteins from a single gene and thus may provide a source of evolutionary novelty. Here, we examine whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation among ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, even when grown in a common environment, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for both cis and trans-regulation. Together, our results emphasize that alternative splicing has been an underappreciated mechanism providing source material for natural selection at short evolutionary time scales.
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Affiliation(s)
- Peter A Innes
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA.
| | - April M Goebl
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
- Research and Conservation Department, Denver Botanic Gardens, Denver, CO, USA
| | - Chris C R Smith
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Kaylee Rosenberger
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
| | - Nolan C Kane
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
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Cui H, Shi Q, Macarios CM, Schimmel P. Metabolic regulation of mRNA splicing. Trends Cell Biol 2024:S0962-8924(24)00025-4. [PMID: 38431493 DOI: 10.1016/j.tcb.2024.02.002] [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: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.
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Affiliation(s)
- Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Qingyu Shi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Paul Schimmel
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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Ding Y, Li J, Yan K, Jin L, Fan C, Bi R, Kong H, Pan Y, Shang Q. CF2-II Alternative Splicing Isoform Regulates the Expression of Xenobiotic Tolerance-Related Cytochrome P450 CYP6CY22 in Aphis gossypii Glover. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3406-3414. [PMID: 38329423 DOI: 10.1021/acs.jafc.3c08770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The expression of P450 genes is regulated by trans-regulatory factors or cis-regulatory elements and influences how endogenous or xenobiotic substances are metabolized in an organism's tissues. In this study, we showed that overexpression of the cytochrome P450 gene, CYP6CY22, led to resistance to cyantraniliprole in Aphis gossypii. The expression of CYP6CY22 increased in the midgut and remaining carcass of the CyR strain, and after repressing the expression of CYP6CY22, the mortality of cotton aphids increased 2.08-fold after exposure to cyantraniliprole. Drosophila ectopically expressing CYP6CY22 exhibited tolerance to cyantraniliprole and cross-tolerance to xanthotoxin, quercetin, 2-tridecanone, tannic acid, and nicotine. Moreover, transcription factor CF2-II (XM_027994540.2) is transcribed only as the splicing variant isoform CF2-II-AS, which was found to be 504 nucleotides shorter than CF2-II in A. gossypii. RNAi and yeast one-hybrid (Y1H) results indicated that CF2-II-AS positively regulates CYP6CY22 and binds to cis-acting element p (-851/-842) of CYP6CY22 to regulate its overexpression. The above results indicated that CYP6CY22 was regulated by the splicing isoform CF2-II-AS, which will help us further understand the mechanism of transcriptional adaption of cross-tolerance between synthetic insecticides and plant secondary metabolites mediated by P450s.
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Affiliation(s)
- Yaping Ding
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Jianyi Li
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Kunpeng Yan
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Long Jin
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Chengcheng Fan
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Rui Bi
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, PR China
| | - Haoran Kong
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Yiou Pan
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Qingli Shang
- College of Plant Science, Jilin University, Changchun 130062, PR China
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Ruta V, Naro C, Pieraccioli M, Leccese A, Archibugi L, Cesari E, Panzeri V, Allgöwer C, Arcidiacono PG, Falconi M, Carbone C, Tortora G, Borrelli F, Attili F, Spada C, Quero G, Alfieri S, Doglioni C, Kleger A, Capurso G, Sette C. An alternative splicing signature defines the basal-like phenotype and predicts worse clinical outcome in pancreatic cancer. Cell Rep Med 2024; 5:101411. [PMID: 38325381 PMCID: PMC10897606 DOI: 10.1016/j.xcrm.2024.101411] [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: 08/03/2023] [Revised: 11/19/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by extremely poor prognosis. PDAC presents with molecularly distinct subtypes, with the basal-like one being associated with enhanced chemoresistance. Splicing dysregulation contributes to PDAC; however, its involvement in subtype specification remains elusive. Herein, we uncover a subtype-specific splicing signature associated with prognosis in PDAC and the splicing factor Quaking (QKI) as a determinant of the basal-like signature. Single-cell sequencing analyses highlight QKI as a marker of the basal-like phenotype. QKI represses splicing events associated with the classical subtype while promoting basal-like events associated with shorter survival. QKI favors a plastic, quasi-mesenchymal phenotype that supports migration and chemoresistance in PDAC organoids and cell lines, and its expression is elevated in high-grade primary tumors and metastatic lesions. These studies identify a splicing signature that defines PDAC subtypes and indicate that QKI promotes an undifferentiated, plastic phenotype, which renders PDAC cells chemoresistant and adaptable to environmental changes.
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Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy
| | - Adriana Leccese
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy
| | | | - Valentina Panzeri
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Chantal Allgöwer
- Institute for Molecular Oncology and Stem Cell Biology, Ulm University Hospital, 89081 Ulm, Germany
| | - Paolo Giorgio Arcidiacono
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy; Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Massimo Falconi
- Vita-Salute San Raffaele University, 20132 Milan, Italy; Pancreas and Transplantation Surgical Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy
| | | | - Giampaolo Tortora
- Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy; Medical Oncology, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | | | - Fabia Attili
- Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy
| | | | - Giuseppe Quero
- Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy; Gemelli Pancreatic Advanced Research Center (CRMPG), Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Sergio Alfieri
- Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy; Gemelli Pancreatic Advanced Research Center (CRMPG), Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Claudio Doglioni
- Vita-Salute San Raffaele University, 20132 Milan, Italy; Division of Pathology, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy
| | - Alexander Kleger
- Institute for Molecular Oncology and Stem Cell Biology, Ulm University Hospital, 89081 Ulm, Germany; Division of Interdisciplinary Pancreatology, Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy; Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy.
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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Dai X, Xu Z, Jia R, Zhang L, Zheng L, Zhu Z, Gao T, Xu Y, Huang X, Ren Q. Lectin diversity and their positive roles in WSSV replication through regulation of calreticulin expression and inhibiting ALFs expression. Int J Biol Macromol 2024; 258:128996. [PMID: 38151079 DOI: 10.1016/j.ijbiomac.2023.128996] [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: 09/18/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023]
Abstract
In biological evolution, gene duplication (GD) generates new genes to facilitate new functions. C-type lectins (CTLs) in crayfish have been extended by GD to expand their family members. In this study, four CTL genes generated by GD were identified from Procambarus clarkii (PcLec1-4). Among these four genes, PcLec1 can also generate new isoforms with different numbers of tandem repeats through DNA slip mispairing. PcLec1-4 was widely expressed in multiple tissues. The expression levels of PcLec1-4 were upregulated in the intestine of P. clarkii upon white spot syndrome virus (WSSV) challenge at multiple time points. Further analysis indicated that GATA transcription factor regulated PcLec1-4 expression. RNA interference and recombinant PcLec1-4 protein injection experiments suggested that PcLec1-4 promoted the expression of calreticulin (PcCRT) and negatively regulated the expression of antimicrobial peptides, thereby promoting WSSV replication. This study contributes to the understanding of the function of CTLs produced by GD during WSSV invasion in crustaceans.
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Affiliation(s)
- Xiaoling Dai
- Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Zhiqiang Xu
- Key Laboratory of Genetic Breeding and cultivation for Freshwater Crustacean, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Rui Jia
- Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Lihua Zhang
- Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Liangmin Zheng
- Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Ziyue Zhu
- Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Tianheng Gao
- Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China.
| | - Yu Xu
- Key Laboratory of Genetic Breeding and cultivation for Freshwater Crustacean, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
| | - Xin Huang
- Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China.
| | - Qian Ren
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, Jiangsu Province, 210044, China.
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Liu Y, Li Z, Meng Q, Ning A, Zhou S, Li S, Tao X, Wu Y, Chen Q, Tian T, Zhang L, Cui J, Mao L, Chu M. Identification of the consistently differential expressed hub mRNAs and proteins in lung adenocarcinoma and construction of the prognostic signature: a multidimensional analysis. Int J Surg 2024; 110:1052-1067. [PMID: 38016140 PMCID: PMC10871637 DOI: 10.1097/js9.0000000000000943] [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: 08/29/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND This study aimed to elucidate the consistency of differentially expressed hub mRNAs and proteins in lung adenocarcinoma (LUAD) across populations and to construct a comprehensive LUAD prognostic signature. METHODS The transcriptomic and proteomics data from different populations were standardized and analyzed using the same criteria to identify the consistently differential expressed mRNAs and proteins across genders and races. We then integrated prognosis-related mRNAs with clinical, pathological, and EGFR (epidermal growth factor receptor) mutation data to construct a survival model, subsequently validating it across populations. Through plasma proteomics, plasma proteins that consistently differential expressed with LUAD tissues were screened and validated, with their associations discerned by measuring expressions in tumor tissues and tumor vascular normalization. RESULTS The consistency rate of differentially expressed mRNAs and proteins was ~20-40%, with ethnic factors leading to about 40-60% consistency of differentially expressed mRNA or protein across populations. The survival model based on the identified eight hub mRNAs as well as stage, smoking status, and EGFR mutations, demonstrated good prognostic prediction capabilities in both Western and East Asian populations, with a higher number of unfavorable variables indicating poorer LUAD prognosis. Notably, GPI expression in tumor tissues was inversely correlated with vascular normalization and positively correlated with plasma GPI expression. CONCLUSION Our study underscores the significance of integrating transcriptomics and proteomics data, emphasizing the need to account for genetic diversity among ethnic groups. The developed survival model may offer a holistic perspective on LUAD progression, enhancing prognosis and therapeutic strategies.
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Affiliation(s)
- Yiran Liu
- Department of Epidemiology, School of Public Health, Nantong University
| | - Zhenyu Li
- Department of Epidemiology, School of Public Health, Nantong University
| | - Qianyao Meng
- Department of Global Health and Population, School of Public Health, Harvard University, Boston, USA
| | - Anhui Ning
- Department of Epidemiology, School of Public Health, Nantong University
| | - Shenxuan Zhou
- Department of Epidemiology, School of Public Health, Nantong University
| | - Siqi Li
- Department of Epidemiology, School of Public Health, Nantong University
| | - Xiaobo Tao
- Department of Epidemiology, School of Public Health, Nantong University
| | - Yutong Wu
- Department of Epidemiology, School of Public Health, Nantong University
| | - Qiong Chen
- Department of Epidemiology, School of Public Health, Nantong University
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University
| | - Lei Zhang
- Department of Epidemiology, School of Public Health, Nantong University
| | - Jiahua Cui
- Department of Epidemiology, School of Public Health, Nantong University
| | - Liping Mao
- Department of Oncology, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), Nantong, Jiangsu, People’s Republic of China
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University
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