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Honda T, Nakagawa T, Yuasa T, Tokuda Y, Nakano M, Tashiro K, Tourtas T, Schlötzer-Schrehardt U, Kruse F, Yamamoto K, Koizumi N, Okumura N. Dysregulation of the TCF4 Isoform in Corneal Endothelial Cells of Patients With Fuchs Endothelial Corneal Dystrophy. Invest Ophthalmol Vis Sci 2024; 65:27. [PMID: 38884552 PMCID: PMC11185267 DOI: 10.1167/iovs.65.6.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/03/2024] [Indexed: 06/18/2024] Open
Abstract
Purpose This study evaluated the dysregulation of TCF4 isoforms and differential exon usage (DEU) in corneal endothelial cells (CECs) of Fuchs endothelial corneal dystrophy (FECD) with or without trinucleotide repeat (TNR) expansion in the intron region of the TCF4 gene. Methods Three RNA-Seq datasets of CECs (our own and two other previously published datasets) derived from non-FECD control and FECD subjects were analyzed to identify TCF4 isoforms and DEU events dysregulated in FECD by comparing control subjects to those with FECD with TNR expansion and FECD without TNR expansion. Results Our RNA-Seq data demonstrated upregulation of three TCF4 isoforms and downregulation of two isoforms in FECD without TNR expansion compared to the controls. In FECD with TNR expansion, one isoform was upregulated and one isoform was downregulated compared to the control. Additional analysis using two other datasets identified that the TCF4-277 isoform was upregulated in common in all three datasets in FECD with TNR expansion, whereas no isoform was dysregulated in FECD without TNR expansion. DEU analysis showed that one exon (E174) upstream of the TNR, which only encompassed TCF4-277, was upregulated in common in all three datasets, whereas eight exons downstream of the TNR were downregulated in common in all three datasets in FECD with TNR expansion. Conclusions This study identified TCF4-277 as a dysregulated isoform in FECD with TNR expansion, suggesting a potential contribution of TCF4-277 to FECD pathophysiology.
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Affiliation(s)
- Tetsuro Honda
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Tatsuya Nakagawa
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Taichi Yuasa
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Yuichi Tokuda
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Theofilos Tourtas
- Department of Ophthalmology, University of Erlangen-Nürnberg, Erlangen, Germany
| | | | - Friedrich Kruse
- Department of Ophthalmology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Koji Yamamoto
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Noriko Koizumi
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Naoki Okumura
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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Kansara S, Sawant P, Kaur T, Garg M, Pandey AK. LncRNA-mediated orchestrations of alternative splicing in the landscape of breast cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195017. [PMID: 38341138 DOI: 10.1016/j.bbagrm.2024.195017] [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: 10/11/2023] [Revised: 01/19/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024]
Abstract
Alternative splicing (AS) is a fundamental post-transcriptional process in eukaryotes, enabling a single gene to generate diverse mRNA transcripts, thereby enhancing protein variability. This process involves the excision of introns and the joining of exons in pre-mRNA(s) to form mature mRNA. The resulting mature mRNAs exhibit various combinations of exons, contributing to functional diversity. Dysregulation of AS can substantially modulate protein functions, impacting the onset and progression of numerous diseases, including cancer. Non-coding RNAs (ncRNAs) are distinct from protein-coding RNAs and consist of short and long types. Long non-coding RNAs (lncRNAs) play an important role in regulating several cellular processes, particularly alternative splicing, according to new research. This review provides insight into the latest discoveries concerning how lncRNAs influence alternative splicing within the realm of breast cancer. Additionally, it explores potential therapeutic strategies focused on targeting lncRNAs.
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Affiliation(s)
- Samarth Kansara
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Prajwali Sawant
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Taranjeet Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, 382355, Gujarat, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Uttar Pradesh, Sector-125, Noida 201313, India
| | - Amit Kumar Pandey
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, 382355, Gujarat, India.
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3
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Ding W, Xiao Q, Yue Y, Chen S, She X, Pan B, Zhou L, Yin Y, Li Y, Wang S, Xu M. Deciphering alternative splicing events and their therapeutic implications in colorectal Cancer. Cell Signal 2024; 118:111134. [PMID: 38484942 DOI: 10.1016/j.cellsig.2024.111134] [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: 01/28/2024] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors with complex molecular regulatory mechanisms. Alternative splicing (AS), a fundamental regulatory process of gene expression, plays an important role in the occurrence and development of CRC. This study analyzed AS Percent Spliced In (PSI) values from 49 pairs of CRC and normal samples in the TCGA SpliceSeq database. Using Lasso and SVM, AS features that can differentiate colorectal cancer from normal were screened. Univariate COX regression analysis identified prognosis-related AS events. A risk model was constructed and validated using machine learning, Kaplan-Meier analysis, and Decision Curve Analysis. The regulatory effect of protein arginine methyltransferase 5 (PRMT5) on poly(RC) binding protein 1 (PCBP1) was verified by immunoprecipitation experiments, and the effect of PCBP1 on the AS of Obscurin (OBSCN) was verified by PCR. Five AS events, including HNF4A.59461.AP and HNF4A.59462.AP, were identified, which can distinguish CRC from normal tissue. A machine learning model using 21 key AS events accurately predicted CRC prognosis. High-risk patients had significantly shorter survival times. PRMT5 was found to regulate PCBP1 function and then influence OBSCN AS, which may drive CRC progression. The study concluded that some AS events is significantly different in CRC and normal tissues, and some of these AS events are related to the prognosis of CRC. In addition, PRMT family-driven arginine modifications play an important role in CRC-specific AS events.
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Affiliation(s)
- Wenbo Ding
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Qianni Xiao
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yanzhe Yue
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Shuyu Chen
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Xiangjian She
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Bei Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Linpeng Zhou
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yujuan Yin
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Youyue Li
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shukui Wang
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China.; Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China..
| | - Mu Xu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China..
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Zhang Z, Dong L, Tao H, Dong Y, Xiang W, Tao F, Zhao Y. RNA-binding proteins potentially regulate the alternative splicing of apoptotic genes during knee osteoarthritis progression. BMC Genomics 2024; 25:293. [PMID: 38504181 PMCID: PMC10949708 DOI: 10.1186/s12864-024-10181-w] [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: 01/19/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Alternative splicing (AS) is a principal mode of genetic regulation and one of the most widely used mechanisms to generate structurally and functionally distinct mRNA and protein variants. Dysregulation of AS may result in aberrant transcription and protein products, leading to the emergence of human diseases. Although considered important for regulating gene expression, genome-wide AS dysregulation, underlying mechanisms, and clinical relevance in knee osteoarthritis (OA) remain unelucidated. Therefore, in this study, we elucidated and validated AS events and their regulatory mechanisms during OA progression. RESULTS In this study, we identified differentially expressed genes between human OA and healthy meniscus samples. Among them, the OA-associated genes were primarily enriched in biological pathways such as extracellular matrix organization and ossification. The predominant OA-associated regulated AS (RAS) events were found to be involved in apoptosis during OA development. The expression of the apoptosis-related gene BCL2L13, XAF1, and NF2 were significantly different between OA and healthy meniscus samples. The construction of a covariation network of RNA-binding proteins (RBPs) and RAS genes revealed that differentially expressed RBP genes LAMA2 and CUL4B may regulate the apoptotic genes XAF1 and BCL2L13 to undergo AS events during OA progression. Finally, RT-qPCR revealed that CUL4B expression was significantly higher in OA meniscus samples than in normal controls and that the AS ratio of XAF1 was significantly different between control and OA samples; these findings were consistent with their expected expression and regulatory relationships. CONCLUSIONS Differentially expressed RBPs may regulate the AS of apoptotic genes during knee OA progression. XAF1 and its regulator, CUL4B, may serve as novel biomarkers and potential therapeutic targets for this disease.
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Affiliation(s)
- Zheng Zhang
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China.
| | - Limei Dong
- School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, Hubei, China
| | - Hai Tao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Yusong Dong
- School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, Hubei, China
| | - Wei Xiang
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Fenghua Tao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Yingchun Zhao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
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Mehta P, Swaminathan A, Yadav A, Chattopadhyay P, Shamim U, Pandey R. Integrative genomics important to understand host-pathogen interactions. Brief Funct Genomics 2024; 23:1-14. [PMID: 35909219 DOI: 10.1093/bfgp/elac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 01/21/2024] Open
Abstract
Infectious diseases are the leading cause of morbidity and mortality worldwide. Causative pathogenic microbes readily mutate their genome and lead to outbreaks, challenging the healthcare and the medical support. Understanding how certain symptoms manifest clinically is integral for therapeutic decisions and vaccination efficacy/protection. Notably, the interaction between infecting pathogens, host response and co-presence of microbes influence the trajectories of disease progression and clinical outcome. The spectrum of observed symptomatic patients (mild, moderate and severe) and the asymptomatic infections highlight the challenges and the potential for understanding the factors driving protection/susceptibility. With the increasing repertoire of high-throughput tools, such as cutting-edge multi-omics profiling and next-generation sequencing, genetic drivers of factors linked to heterogeneous disease presentations can be investigated in tandem. However, such strategies are not without limits in terms of effectively integrating host-pathogen interactions. Nonetheless, an integrative genomics method (for example, RNA sequencing data) for exploring multiple layers of complexity in host-pathogen interactions could be another way to incorporate findings from high-throughput data. We further propose that a Holo-transcriptome-based technique to capture transcriptionally active microbial units can be used to elucidate functional microbiomes. Thus, we provide holistic perspective on investigative methodologies that can harness the same genomic data to investigate multiple seemingly independent but deeply interconnected functional domains of host-pathogen interaction that modulate disease severity and clinical outcomes.
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Carrion SA, Michal JJ, Jiang Z. Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases. Genes (Basel) 2023; 14:2051. [PMID: 38002994 PMCID: PMC10671453 DOI: 10.3390/genes14112051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated importance to cell proliferation, differentiation and the transition from fetal to adult cells. While alternative exon splicing has a limited effect on protein identity, its ubiquity highlights the importance of these minor alterations, which can alter other features such as localization. The three processes are also highly interwoven, with overlapping, complementary, and competing factors, RNA polymerase II and its CTD (C-terminal domain) chief among them. Their role in development means dysregulation leads to a wide variety of disorders and cancers, with some forms of disease disproportionately affected by specific mechanisms (AES, ATS, or APA). Challenges associated with the genome-wide profiling of RNA variants and their potential solutions are also discussed in this review.
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Affiliation(s)
| | | | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620, USA; (S.A.C.); (J.J.M.)
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Rabaya S, Nairat S, Bader K, Herzallah MM, Darwish HM. Iron metabolism in autism spectrum disorder; inference through single nucleotide polymorphisms in key iron metabolism genes. J Neurol Sci 2023; 453:120817. [PMID: 37813049 DOI: 10.1016/j.jns.2023.120817] [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: 04/24/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/11/2023]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental problems with various genetic and environmental components. The ASD diagnosis is based on symptom expression without reliance on any biomarkers. The genetic contributions in ASD remain elusive. Various studies have linked ASD with iron. Since iron plays a crucial role in brain development, neurotransmitter synthesis, neuronal myelination and mitochondrial function, we hypothesized that iron dysregulation in the brain could play a role and contribute to the pathogenesis of ASD. In this study, we investigated single nucleotide polymorphisms in ASD in various iron metabolism genes, including the Transferrin Receptor (TFRC) gene (rs11915082), the Solute Carrier Family 11 Member 2 (SLC11A2) gene (rs1048230 and rs224589), the Solute Carrier Family 40 Member 1 (SLC40A1) gene (rs1439816), and hepcidin antimicrobial peptide (HAMP) gene (rs10421768). We recruited 48 patients with ASD and 88 matched non-ASD controls. Our results revealed a significant difference between ASD and controls in the G allele of the TFRC gene rs11915082, and in the C allele of the SLC40A1 gene rs1439816. In silico analysis demonstrated potential positive role of the indicated genetic variations in ASD development and pathogenesis. These results suggest that specific genetic variations in iron metabolism genes may represent part of early genetic markers for early diagnosis of ASD. A significant effect of SNPs, groups (ASD/control) as well as interaction between SNPs and groups was revealed. Follow-up post hoc tests showed a significant difference between the ASD and control groups in rs11915082 (TFRC gene) and rs1439816 (SLC40A1 gene). Backward conditional logistic regression using both the genotype and allele data showed similar ability in detecting ASD using allel model (Nagelkerke R2 = 0.350 p = 0.967; Variables: rs1439816, rs11915082) compared to genotype model (Nagelkerke R2 = 0.347, p = 0.430; Variables: rs1439816 G, rs1439816 C, rs10421768 A). ROC curve showed 54% sensitivity in detecting ASD compared to 47% for the genotype model. Both models differentiated controls with high accuracy; the allele model had a specificity of 91% compared to 92% for the genotype model. In conclusion, our findings suggest that specific genetic variations in iron metabolism may represent early biomarkers for a diagnosis of ASD. Further research is needed to correlate these markers with specific blood iron indicators and their contribution to brain development and behavior.
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Affiliation(s)
- Sabha Rabaya
- Department of Health Sciences, Molecular Genetics and Genetic Toxicology Program, Arab American University, Ramallah,Palestine
| | - Sameera Nairat
- Palestinian Neuroscience Initiative, Al-Quds University, Abu Dis, Jerusalem, Palestine
| | - Khaldoun Bader
- Faculty of Public Health, Al-Quds University, Abu Dis, Jerusalem, Palestine
| | - Mohammad M Herzallah
- Palestinian Neuroscience Initiative, Al-Quds University, Abu Dis, Jerusalem, Palestine; Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ, USA.
| | - Hisham M Darwish
- Department of Health Sciences, Molecular Genetics and Genetic Toxicology Program, Arab American University, Ramallah,Palestine; Department of Medical Laboratory Sciences, Faculty ofAllied Medical Sciences, Arab American University, Jenin, Palestine.
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Tuerdimaimaiti D, Abuduaini B, Kang S, Jiao J, Li M, Madeniyati W, Tuerdi B, Aili G, Tuerhong R, Kulaxi A. Genome-wide identification and functional analysis of dysregulated alternative splicing profiles in sepsis. J Inflamm (Lond) 2023; 20:31. [PMID: 37749550 PMCID: PMC10521395 DOI: 10.1186/s12950-023-00355-w] [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: 12/29/2022] [Accepted: 08/10/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND An increasing body of evidence now shows that the long-term mortality of patients with sepsis are associated with various sepsis-related immune cell defects. Alternative splicing (AS), as a sepsis-related immune cell defect, is considered as a potential immunomodulatory therapy target to improve patient outcomes. However, our understanding of the role AS plays in sepsis is currently insufficient. AIM This study investigated possible associations between AS and the gene regulatory networks affecting immune cells. We also investigated apoptosis and AS functionality in sepsis pathophysiology. METHODS In this study, we assessed publicly available mRNA-seq data that was obtained from the NCBI GEO dataset (GSE154918), which included a healthy group (HLTY), a mild infection group (INF1), asepsis group (Seps), and a septic shock group (Shock). A total of 79 samples (excluding significant outliers) were identified by a poly-A capture method to generate RNA-seq data. The variable splicing events and highly correlated RNA binding protein (RBP) genes in each group were then systematically analyzed. RESULTS For the first time, we used systematic RNA-seq analysis of sepsis-related AS and identified 1505 variable AS events that differed significantly (p <= 0.01) across the four groups. In the sepsis group, the genes related to significant AS events, such as, SHISA5 and IFI27, were mostly enriched in the cell apoptosis pathway. Furthermore, we identified differential splicing patterns within each of the four groups. Significant differences in the expression of RNA Binding Protein(RBP) genes were observed between the control group and the sepsis group. RBP gene expression was highly correlated with variant splicing events in sepsis, as determined by co-expression analysis; The expression of DDX24, CBFA2T2, NOP, ILF3, DNMT1, FTO, PPRC1, NOLC1 RBPs were significant reduced in sepsis compared to the healthy group. Finally, we constructed an RBP-AS functional network. CONCLUSION Analysis indicated that the RBP-AS functional network serves as a critical post-transcriptional mechanism that regulates the development of sepsis. AS dysregulation is associated with alterations in the regulatory gene expression network that is involved in sepsis. Therefore, the RBP-AS expression network could be useful in refining biomarker predictions in the development of new therapeutic targets for the pathogenesis of sepsis.
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Affiliation(s)
- Dilixiati Tuerdimaimaiti
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Buzukela Abuduaini
- The Intensive Care Unit, The First Affiliated Hospital of Xinjiang Medical University, Wulumuqi, Xinjiang, 830054, China
| | - Shaotao Kang
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Jinliang Jiao
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Mengchen Li
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Wolazihan Madeniyati
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Baihetinisha Tuerdi
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China.
| | - Gulisitan Aili
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Reyila Tuerhong
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Ajiguli Kulaxi
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
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9
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Lui A, Patel RS, Krause-Hauch M, Sparks RP, Patel NA. Regulation of Human Sortilin Alternative Splicing by Glucagon-like Peptide-1 (GLP1) in Adipocytes. Int J Mol Sci 2023; 24:14324. [PMID: 37762628 PMCID: PMC10531797 DOI: 10.3390/ijms241814324] [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: 09/01/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Type 2 diabetes mellitus is a chronic metabolic disease with no cure. Adipose tissue is a major site of systemic insulin resistance. Sortilin is a central component of the glucose transporter -Glut4 storage vesicles (GSV) which translocate to the plasma membrane to uptake glucose from circulation. Here, using human adipocytes we demonstrate the presence of the alternatively spliced, truncated sortilin variant (Sort_T) whose expression is significantly increased in diabetic adipose tissue. Artificial-intelligence-based modeling, molecular dynamics, intrinsically disordered region analysis, and co-immunoprecipitation demonstrated association of Sort_T with Glut4 and decreased glucose uptake in adipocytes. The results show that glucagon-like peptide-1 (GLP1) hormone decreases Sort_T. We deciphered the molecular mechanism underlying GLP1 regulation of alternative splicing of human sortilin. Using splicing minigenes and RNA-immunoprecipitation assays, the results show that GLP1 regulates Sort_T alternative splicing via the splice factor, TRA2B. We demonstrate that targeted antisense oligonucleotide morpholinos reduces Sort_T levels and improves glucose uptake in diabetic adipocytes. Thus, we demonstrate that GLP1 regulates alternative splicing of sortilin in human diabetic adipocytes.
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Affiliation(s)
- Ashley Lui
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.L.); (M.K.-H.)
| | - Rekha S. Patel
- Research Service, James A. Haley Veterans Hospital, Tampa, FL 33612, USA; (R.S.P.); (R.P.S.)
| | - Meredith Krause-Hauch
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.L.); (M.K.-H.)
| | - Robert P. Sparks
- Research Service, James A. Haley Veterans Hospital, Tampa, FL 33612, USA; (R.S.P.); (R.P.S.)
- Department of Medicine, Division of Gastroenterology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Niketa A. Patel
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.L.); (M.K.-H.)
- Research Service, James A. Haley Veterans Hospital, Tampa, FL 33612, USA; (R.S.P.); (R.P.S.)
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10
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Varabyou A, Erdogdu B, Salzberg SL, Pertea M. Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage. NATURE COMPUTATIONAL SCIENCE 2023; 3:700-708. [PMID: 38098813 PMCID: PMC10718564 DOI: 10.1038/s43588-023-00496-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 12/17/2023]
Abstract
ORFanage is a system designed to assign open reading frames (ORFs) to known and novel gene transcripts while maximizing similarity to annotated proteins. The primary intended use of ORFanage is the identification of ORFs in the assembled results of RNA sequencing experiments, a capability that most transcriptome assembly methods do not have. Our experiments demonstrate how ORFanage can be used to find novel protein variants in RNA-seq datasets, and to improve the annotations of ORFs in tens of thousands of transcript models in the human annotation databases. Through its implementation of a highly accurate and efficient pseudo-alignment algorithm, ORFanage is substantially faster than other ORF annotation methods, enabling its application to very large datasets. When used to analyze transcriptome assemblies, ORFanage can aid in the separation of signal from transcriptional noise and the identification of likely functional transcript variants, ultimately advancing our understanding of biology and medicine.
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Affiliation(s)
- Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Beril Erdogdu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
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11
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Soni K, Jagtap PKA, Martínez-Lumbreras S, Bonnal S, Geerlof A, Stehle R, Simon B, Valcárcel J, Sattler M. Structural basis for specific RNA recognition by the alternative splicing factor RBM5. Nat Commun 2023; 14:4233. [PMID: 37454201 PMCID: PMC10349855 DOI: 10.1038/s41467-023-39961-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The RNA-binding motif protein RBM5 belongs to a family of multi-domain RNA binding proteins that regulate alternative splicing of genes important for apoptosis and cell proliferation and have been implicated in cancer. RBM5 harbors structural modules for RNA recognition, such as RRM domains and a Zn finger, and protein-protein interactions such as an OCRE domain. Here, we characterize binding of the RBM5 RRM1-ZnF1-RRM2 domains to cis-regulatory RNA elements. A structure of the RRM1-ZnF1 region in complex with RNA shows how the tandem domains cooperate to sandwich target RNA and specifically recognize a GG dinucleotide in a non-canonical fashion. While the RRM1-ZnF1 domains act as a single structural module, RRM2 is connected by a flexible linker and tumbles independently. However, all three domains participate in RNA binding and adopt a closed architecture upon RNA binding. Our data highlight how cooperativity and conformational modularity of multiple RNA binding domains enable the recognition of distinct RNA motifs, thereby contributing to the regulation of alternative splicing. Remarkably, we observe surprising differences in coupling of the RNA binding domains between the closely related homologs RBM5 and RBM10.
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Affiliation(s)
- Komal Soni
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Pravin Kumar Ankush Jagtap
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Santiago Martínez-Lumbreras
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sophie Bonnal
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
| | - Arie Geerlof
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Ralf Stehle
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany.
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12
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Titus MB, Chang AW, Popitsch N, Ebmeier CC, Bono JM, Olesnicky EC. The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system. Front Mol Neurosci 2023; 16:1114857. [PMID: 37435576 PMCID: PMC10332324 DOI: 10.3389/fnmol.2023.1114857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 05/19/2023] [Indexed: 07/13/2023] Open
Abstract
Post-transcriptional gene regulation is a fundamental mechanism that helps regulate the development and healthy aging of the nervous system. Mutations that disrupt the function of RNA-binding proteins (RBPs), which regulate post-transcriptional gene regulation, have increasingly been implicated in neurological disorders including amyotrophic lateral sclerosis, Fragile X Syndrome, and spinal muscular atrophy. Interestingly, although the majority of RBPs are expressed widely within diverse tissue types, the nervous system is often particularly sensitive to their dysfunction. It is therefore critical to elucidate how aberrant RNA regulation that results from the dysfunction of ubiquitously expressed RBPs leads to tissue specific pathologies that underlie neurological diseases. The highly conserved RBP and alternative splicing factor Caper is widely expressed throughout development and is required for the development of Drosophila sensory and motor neurons. Furthermore, caper dysfunction results in larval and adult locomotor deficits. Nonetheless, little is known about which proteins interact with Caper, and which RNAs are regulated by Caper. Here we identify proteins that interact with Caper in both neural and muscle tissue, along with neural specific Caper target RNAs. Furthermore, we show that a subset of these Caper-interacting proteins and RNAs genetically interact with caper to regulate Drosophila gravitaxis behavior.
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Affiliation(s)
- M. Brandon Titus
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Adeline W. Chang
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Niko Popitsch
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | - Jeremy M. Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Eugenia C. Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
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13
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Singh NP, Love MI, Patro R. TreeTerminus -creating transcript trees using inferential replicate counts. iScience 2023; 26:106961. [PMID: 37378336 PMCID: PMC10291472 DOI: 10.1016/j.isci.2023.106961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
A certain degree of uncertainty is always associated with the transcript abundance estimates. The uncertainty may make many downstream analyses, such as differential testing, difficult for certain transcripts. Conversely, gene-level analysis, though less ambiguous, is often too coarse-grained. We introduce TreeTerminus, a data-driven approach for grouping transcripts into a tree structure where leaves represent individual transcripts and internal nodes represent an aggregation of a transcript set. TreeTerminus constructs trees such that, on average, the inferential uncertainty decreases as we ascend the tree topology. The tree provides the flexibility to analyze data at nodes that are at different levels of resolution in the tree and can be tuned depending on the analysis of interest. We evaluated TreeTerminus on two simulated and two experimental datasets and observed an improved performance compared to transcripts (leaves) and other methods under several different metrics.
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Affiliation(s)
- Noor Pratap Singh
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, MD, USA
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14
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Uriostegui-Arcos M, Mick ST, Shi Z, Rahman R, Fiszbein A. Splicing activates transcription from weak promoters upstream of alternative exons. Nat Commun 2023; 14:3435. [PMID: 37301863 PMCID: PMC10256964 DOI: 10.1038/s41467-023-39200-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Transcription and splicing are intrinsically coupled. Alternative splicing of internal exons can fine-tune gene expression through a recently described phenomenon called exon-mediated activation of transcription starts (EMATS). However, the association of this phenomenon with human diseases remains unknown. Here, we develop a strategy to activate gene expression through EMATS and demonstrate its potential for treatment of genetic diseases caused by loss of expression of essential genes. We first identified a catalog of human EMATS genes and provide a list of their pathological variants. To test if EMATS can be used to activate gene expression, we constructed stable cell lines expressing a splicing reporter based on the alternative splicing of motor neuron 2 (SMN2) gene. Using small molecules and antisense oligonucleotides (ASOs) currently used for treatment of spinal muscular atrophy, we demonstrated that increase of inclusion of alternative exons can trigger an activation of gene expression up to 45-fold by enhancing transcription in EMATS-like genes. We observed the strongest effects in genes under the regulation of weak human promoters located proximal to highly included skipped exons.
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Affiliation(s)
| | - Steven T Mick
- Biology Department, Boston University, Boston, 02215, USA
| | - Zhuo Shi
- Biology Department, Massachusetts Institute of Technology, Cambridge, 02139, USA
| | - Rufuto Rahman
- Biology Department, Boston University, Boston, 02215, USA
| | - Ana Fiszbein
- Biology Department, Boston University, Boston, 02215, USA.
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15
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Giarrizzo M, LaComb JF, Bialkowska AB. The Role of Krüppel-like Factors in Pancreatic Physiology and Pathophysiology. Int J Mol Sci 2023; 24:ijms24108589. [PMID: 37239940 DOI: 10.3390/ijms24108589] [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: 04/13/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Krüppel-like factors (KLFs) belong to the family of transcription factors with three highly conserved zinc finger domains in the C-terminus. They regulate homeostasis, development, and disease progression in many tissues. It has been shown that KLFs play an essential role in the endocrine and exocrine compartments of the pancreas. They are necessary to maintain glucose homeostasis and have been implicated in the development of diabetes. Furthermore, they can be a vital tool in enabling pancreas regeneration and disease modeling. Finally, the KLF family contains proteins that act as tumor suppressors and oncogenes. A subset of members has a biphasic function, being upregulated in the early stages of oncogenesis and stimulating its progression and downregulated in the late stages to allow for tumor dissemination. Here, we describe KLFs' function in pancreatic physiology and pathophysiology.
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Affiliation(s)
- Michael Giarrizzo
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| | - Joseph F LaComb
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| | - Agnieszka B Bialkowska
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
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16
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Leung CS, Rosenzweig SJ, Yoon B, Marinelli NA, Hollingsworth EW, Maguire AM, Cowen MH, Schmidt M, Imitola J, Gamsiz Uzun ED, Lizarraga SB. Dysregulation of the chromatin environment leads to differential alternative splicing as a mechanism of disease in a human model of autism spectrum disorder. Hum Mol Genet 2023; 32:1634-1646. [PMID: 36621967 PMCID: PMC10162432 DOI: 10.1093/hmg/ddad002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/24/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023] Open
Abstract
Autism spectrum disorder (ASD) affects 1 in 44 children. Chromatin regulatory proteins are overrepresented among genes that contain high risk variants in ASD. Disruption of the chromatin environment leads to widespread dysregulation of gene expression, which is traditionally thought of as a mechanism of disease pathogenesis associated with ASD. Alternatively, alterations in chromatin dynamics could also lead to dysregulation of alternative splicing, which is understudied as a mechanism of ASD pathogenesis. The anticonvulsant valproic acid (VPA) is a well-known environmental risk factor for ASD that acts as a class I histone deacetylase inhibitor. However, the precise molecular mechanisms underlying defects in human neuronal development associated with exposure to VPA are understudied. To dissect how VPA exposure and subsequent chromatin hyperacetylation influence molecular signatures involved in ASD pathogenesis, we conducted RNA sequencing (RNA-seq) in human cortical neurons that were treated with VPA. We observed that differentially expressed genes (DEGs) were enriched for mRNA splicing, mRNA processing, histone modification and metabolism related gene sets. Furthermore, we observed widespread increases in the number and the type of alternative splicing events. Analysis of differential transcript usage (DTU) showed that exposure to VPA induces extensive alterations in transcript isoform usage across neurodevelopmentally important genes. Finally, we find that DEGs and genes that display DTU overlap with known ASD-risk genes. Altogether, these findings suggest that, in addition to differential gene expression, changes in alternative splicing correlated with alterations in the chromatin environment could act as an additional mechanism of disease in ASD.
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Affiliation(s)
- Calvin S Leung
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Shoshana J Rosenzweig
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Academic Medical Center, Providence, RI 02903, USA
| | - Brian Yoon
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Nicholas A Marinelli
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Ethan W Hollingsworth
- UCONN Health Comprehensive Multiple Sclerosis Center, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
- Division of Multiple Sclerosis and Translational Neuroimmunology, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Abbie M Maguire
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Mara H Cowen
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Michael Schmidt
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Jaime Imitola
- UCONN Health Comprehensive Multiple Sclerosis Center, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
- Division of Multiple Sclerosis and Translational Neuroimmunology, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Ece D Gamsiz Uzun
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Academic Medical Center, Providence, RI 02903, USA
| | - Sofia B Lizarraga
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
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17
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Rodrigues KS, Petroski LP, Utumi PH, Ferrasa A, Herai RH. IARA: a complete and curated atlas of the biogenesis of spliceosome machinery during RNA splicing. Life Sci Alliance 2023; 6:e202201593. [PMID: 36609432 PMCID: PMC9834665 DOI: 10.26508/lsa.202201593] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023] Open
Abstract
Splicing is one of the most important post-transcriptional processing systems and is responsible for the generation of transcriptome diversity in all living eukaryotes. Splicing is regulated by the spliceosome machinery, which is responsible for each step of primary RNA processing. However, current molecules and stages involved in RNA splicing are still spread over different studies. Thus, a curated atlas of spliceosome-related molecules and all involved stages during RNA processing can provide all researchers with a reliable resource to better investigate this important mechanism. Here, we present IARA (website access: https://pucpr-bioinformatics.github.io/atlas/), an extensively curated and constantly updated catalog of molecules involved in spliceosome machinery. IARA has a map of the steps involved in the human splicing mechanism, and it allows a detailed overview of the molecules involved throughout the distinct steps of splicing.
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Affiliation(s)
- Kelren S Rodrigues
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Luiz P Petroski
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Paulo H Utumi
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Adriano Ferrasa
- Informatics Department, Universidade Estadual de Ponta GrossaPonta Grossa, Brazil
| | - Roberto H Herai
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
- Research Division, Buko Kaesemodel Institute, Curitiba, Brazil
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18
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ElHady AK, El-Gamil DS, Abadi AH, Abdel-Halim M, Engel M. An overview of cdc2-like kinase 1 (Clk1) inhibitors and their therapeutic indications. Med Res Rev 2023; 43:343-398. [PMID: 36262046 DOI: 10.1002/med.21928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/07/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Over the past decade, Clk1 has been identified as a promising target for the treatment of various diseases, in which deregulated alternative splicing plays a role. First small molecules targeting Clk1 are in clinical trials for the treatment of solid cancer, where variants of oncogenic proteins derived from alternative splicing promote tumor progression. Since many infectious pathogens hi-jack the host cell's splicing machinery to ensure efficient replication, further indications in this area are under investigation, such as Influenza A, HIV-1 virus, and Trypanosoma infections, and more will likely be discovered in the future. In addition, Clk1 was found to contribute to the progression of Alzheimer's disease through causing an imbalance of tau splicing products. Interestingly, homozygous Clk1 knockout mice showed a rather mild phenotype, opposed to what might be expected in view of the profound role of Clk1 in alternative splicing. A major drawback of most Clk1 inhibitors is their insufficient selectivity; in particular, Dyrk kinases and haspin were frequently identified as off-targets, besides the other Clk isoforms. Only few inhibitors were shown to be selective over Dyrk1A and haspin, whereas no Clk1 inhibitor so far achieved selectivity over the Clk4 isoform. In this review, we carefully compiled all Clk1 inhibitors from the scientific literature and summarized their structure-activity relationships (SAR). In addition, we critically discuss the available selectivity data and describe the inhibitor's efficacy in cellular models, if reported. Thus, we provide a comprehensive overview on the current state of Clk1 drug discovery and highlight the most promising chemotypes.
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Affiliation(s)
- Ahmed K ElHady
- Department of Organic and Pharmaceutical Chemistry, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Dalia S El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.,Department of Chemistry, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Matthias Engel
- Department of Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
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19
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Genetics of mitochondrial diseases: Current approaches for the molecular diagnosis. HANDBOOK OF CLINICAL NEUROLOGY 2023; 194:141-165. [PMID: 36813310 DOI: 10.1016/b978-0-12-821751-1.00011-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Mitochondrial diseases are a genetically and phenotypically variable set of monogenic disorders. The main characteristic of mitochondrial diseases is a defective oxidative phosphorylation. Both nuclear and mitochondrial DNA encode the approximately 1500 mitochondrial proteins. Since identification of the first mitochondrial disease gene in 1988 a total of 425 genes have been associated with mitochondrial diseases. Mitochondrial dysfunctions can be caused both by pathogenic variants in the mitochondrial DNA or the nuclear DNA. Hence, besides maternal inheritance, mitochondrial diseases can follow all modes of Mendelian inheritance. The maternal inheritance and tissue specificity distinguish molecular diagnostics of mitochondrial disorders from other rare disorders. With the advances made in the next-generation sequencing technology, whole exome sequencing and even whole-genome sequencing are now the established methods of choice for molecular diagnostics of mitochondrial diseases. They reach a diagnostic rate of more than 50% in clinically suspected mitochondrial disease patients. Moreover, next-generation sequencing is delivering a constantly growing number of novel mitochondrial disease genes. This chapter reviews mitochondrial and nuclear causes of mitochondrial diseases, molecular diagnostic methodologies, and their current challenges and perspectives.
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20
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Che Y, Bai M, Lu K, Fu L. Splicing factor SRSF3 promotes the progression of cervical cancer through regulating DDX5. Mol Carcinog 2023; 62:210-223. [PMID: 36282044 DOI: 10.1002/mc.23477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/07/2022] [Accepted: 09/22/2022] [Indexed: 01/25/2023]
Abstract
Aberrant alternative splicing (AS) profoundly affects tumorigenesis and cancer progression. Serine/arginine-rich splicing factor 3 (SRSF3) regulates the AS of precursor mRNAs and acts as a proto-oncogene in many tumors, but its function and potential mechanisms in cervical cancer remain unclear. Here, we found that SRSF3 was highly expressed in cervical cancer tissues and that SRSF3 expression was correlated with prognosis after analyses of the The Cancer Genome Atlas and GEO databases. Furthermore, knockdown of SRSF3 reduced the proliferation, migration, and invasion abilities of HeLa cells, while overexpression of SRSF3 promoted proliferation, migration, and invasion of CaSki cells. Further studies showed that SRSF3 mediated the variable splicing of exon 12 of the transcriptional cofactor DEAD-box helicase 5 (DDX5). Specifically, overexpression of SRSF3 promoted the production of the pro-oncogenic spliceosome DDX5-L and repressed the production of the repressive spliceosome DDX5-S. Ultimately, both SRSF3 and DDX5-L were able to upregulate oncogenic AKT expression, while DDX5-S downregulated AKT expression. In conclusion, we found that SRSF3 increased the production of DDX5-L and decreased the production of DDX5-S by regulating the variable splicing of DDX5. This, in turn promoted the proliferation, migration, and invasion of cervical cancer by upregulating the expression level of AKT. These results reveal the oncogenic role of SRSF3 in cervical cancer and emphasize the importance of the SRSF3-DDX5-AKT axis in tumorigenesis. SRSF3 and DDX5 are new potential biomarkers and therapeutic targets for cervical cancer.
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Affiliation(s)
- Yingying Che
- School of Basic Medicine, Qingdao University, Qingdao, China.,Weihai Ocean Vocational College, Weihai, China
| | - Mixue Bai
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Kun Lu
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Lin Fu
- School of Basic Medicine, Qingdao University, Qingdao, China
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21
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Alternatively Spliced Isoforms of MUC4 and ADAM12 as Biomarkers for Colorectal Cancer Metastasis. J Pers Med 2023; 13:jpm13010135. [PMID: 36675796 PMCID: PMC9861497 DOI: 10.3390/jpm13010135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/13/2023] Open
Abstract
There is a pertinent need to develop prognostic biomarkers for practicing predictive, preventive and personalized medicine (PPPM) in colorectal cancer metastasis. The analysis of isoform expression data governed by alternative splicing provides a high-resolution picture of mRNAs in a defined condition. This information would not be available by studying gene expression changes alone. Hence, we utilized our prior data from an exon microarray and found ADAM12 and MUC4 to be strong biomarker candidates based on their alternative splicing scores and pattern. In this study, we characterized their isoform expression in a cell line model of metastatic colorectal cancer (SW480 & SW620). These two genes were found to be good prognostic indicators in two cohorts from The Cancer Genome Atlas database. We studied their exon structure using sequence information in the NCBI and ENSEMBL genome databases to amplify and validate six isoforms each for the ADAM12 and MUC4 genes. The differential expression of these isoforms was observed between normal, primary and metastatic colorectal cancer cell lines. RNA-Seq analysis further proved the differential expression of the gene isoforms. The isoforms of MUC4 and ADAM12 were found to change expression levels in response to 5-Fluorouracil (5-FU) treatment in a dose-, time- and cell line-dependent manner. Furthermore, we successfully detected the protein isoforms of ADAM12 and MUC4 in cell lysates, reflecting the differential expression at the protein level. The change in the mRNA and protein expression of MUC4 and ADAM12 in primary and metastatic cells and in response to 5-FU qualifies them to be studied as potential biomarkers. This comprehensive study underscores the importance of studying alternatively spliced isoforms and their potential use as prognostic and/or predictive biomarkers in the PPPM approach towards cancer.
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22
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Osteopontin Splicing Isoforms Contribute to Endometriotic Proliferation, Migration, and Epithelial-Mesenchymal Transition in Endometrial Epithelial Cells. Int J Mol Sci 2022; 23:ijms232315328. [PMID: 36499654 PMCID: PMC9738877 DOI: 10.3390/ijms232315328] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Osteopontin (OPN) isoforms, including OPNb and OPNc, promote malignancy and may contribute to the pathogenesis of endometriosis, a benign disorder with multiple characteristics resembling malignant tumors. In our experiments, OPNb and OPNc were significantly overexpressed in both endometriosis and adenomyosis compared to the normal endometrium. Upregulation of CD44v and the epithelial-mesenchymal transition (EMT) process was also present in endometriotic lesions. Overexpression of OPNb and OPNc splicing variants in endometriotic cells evoked morphological changes, actin remodeling, cell proliferation, cell migration, and EMT through binding OPN ligand receptors CD44 and αvβ3, subsequently activating the PI3K and NF-ĸB pathways. We elucidated the causal role of OPN splice variants in regulating endometriotic cell growth, which may promote the development of OPN-targeted therapies for patients suffering from endometriotic disorders.
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23
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Das AS, Sherry EC, Vaughan RM, Henderson ML, Zieba J, Uhl KL, Koehn O, Bupp CP, Rajasekaran S, Li X, Chhetri SB, Nissim S, Williams CL, Prokop JW. The complex, dynamic SpliceOme of the small GTPase transcripts altered by technique, sex, genetics, tissue specificity, and RNA base editing. Front Cell Dev Biol 2022; 10:1033695. [PMID: 36467401 PMCID: PMC9714508 DOI: 10.3389/fcell.2022.1033695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/01/2022] [Indexed: 04/04/2024] Open
Abstract
The small GTPase family is well-studied in cancer and cellular physiology. With 162 annotated human genes, the family has a broad expression throughout cells of the body. Members of the family have multiple exons that require splicing. Yet, the role of splicing within the family has been underexplored. We have studied the splicing dynamics of small GTPases throughout 41,671 samples by integrating Nanopore and Illumina sequencing techniques. Within this work, we have made several discoveries. 1). Using the GTEx long read data of 92 samples, each small GTPase gene averages two transcripts, with 83 genes (51%) expressing two or more isoforms. 2). Cross-tissue analysis of GTEx from 17,382 samples shows 41 genes (25%) expressing two or more protein-coding isoforms. These include protein-changing transcripts in genes such as RHOA, RAB37, RAB40C, RAB4B, RAB5C, RHOC, RAB1A, RAN, RHEB, RAC1, and KRAS. 3). The isolation and library technique of the RNAseq influences the abundance of non-sense-mediated decay and retained intron transcripts of small GTPases, which are observed more often in genes than appreciated. 4). Analysis of 16,243 samples of "Blood PAXgene" identified seven genes (3.7%; RHOA, RAB40C, RAB4B, RAB37, RAB5B, RAB5C, RHOC) with two or more transcripts expressed as the major isoform (75% of the total gene), suggesting a role of genetics in altering splicing. 5). Rare (ARL6, RAB23, ARL13B, HRAS, NRAS) and common variants (GEM, RHOC, MRAS, RAB5B, RERG, ARL16) can influence splicing and have an impact on phenotypes and diseases. 6). Multiple genes (RAB9A, RAP2C, ARL4A, RAB3A, RAB26, RAB3C, RASL10A, RAB40B, and HRAS) have sex differences in transcript expression. 7). Several exons are included or excluded for small GTPase genes (RASEF, KRAS, RAC1, RHEB, ARL4A, RHOA, RAB30, RHOBTB1, ARL16, RAP1A) in one or more forms of cancer. 8). Ten transcripts are altered in hypoxia (SAR1B, IFT27, ARL14, RAB11A, RAB10, RAB38, RAN, RIT1, RAB9A) with RHOA identified to have a transient 3'UTR RNA base editing at a conserved site found in all of its transcripts. Overall, we show a remarkable and dynamic role of splicing within the small GTPase family that requires future explorations.
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Affiliation(s)
- Akansha S. Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Biology, Washington and Jefferson College, Washington, PA, United States
| | - Emily C. Sherry
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, United States
| | - Robert M. Vaughan
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Marian L. Henderson
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- The Department of Biology, Calvin University, Grand Rapids, MI, United States
| | - Jacob Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI, United States
| | - Katie L. Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Olivia Koehn
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Medical Genetics, Spectrum Health and Helen DeVos Children’s Hospital, Grand Rapids, MI, United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Pediatric Critical Care Medicine, Helen DeVos Children’s Hospital Spectrum Health, Grand Rapids, MI, United States
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Surya B. Chhetri
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MA, United States
| | - Sahar Nissim
- Genetics and Gastroenterology Divisions, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, United States
| | - Carol L. Williams
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
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24
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Gao C, Lu S, Zhou R, Ding J, Fan J, Han B, Chen M, Wang B, Cao Y. Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family. BMC Genomics 2022; 23:744. [DOI: 10.1186/s12864-022-08956-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Alternative splicing (AS) is an important channel for gene expression regulation and protein diversification, in addition to a major reason for the considerable differences in the number of genes and proteins in eukaryotes. In plants, U2 small nuclear ribonucleoprotein B″ (U2B″), a component of splicing complex U2 snRNP, plays an important role in AS. Currently, few studies have investigated plant U2B″, and its mechanism remains unclear.
Result
Phylogenetic analysis, including gene and protein structures, revealed that U2B″ is highly conserved in plants and typically contains two RNA recognition motifs. Subcellular localisation showed that OsU2B″ is located in the nucleus and cytoplasm, indicating that it has broad functions throughout the cell. Elemental analysis of the promoter region showed that it responded to numerous external stimuli, including hormones, stress, and light. Subsequent qPCR experiments examining response to stress (cold, salt, drought, and heavy metal cadmium) corroborated the findings. The prediction results of protein–protein interactions showed that its function is largely through a single pathway, mainly through interaction with snRNP proteins.
Conclusion
U2B″ is highly conserved in the plant kingdom, functions in the nucleus and cytoplasm, and participates in a wide range of processes in plant growth and development.
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25
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Exploration of Tools for the Interpretation of Human Non-Coding Variants. Int J Mol Sci 2022; 23:ijms232112977. [PMID: 36361767 PMCID: PMC9654743 DOI: 10.3390/ijms232112977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
The advent of Whole Genome Sequencing (WGS) broadened the genetic variation detection range, revealing the presence of variants even in non-coding regions of the genome, which would have been missed using targeted approaches. One of the most challenging issues in WGS analysis regards the interpretation of annotated variants. This review focuses on tools suitable for the functional annotation of variants falling into non-coding regions. It couples the description of non-coding genomic areas with the results and performance of existing tools for a functional interpretation of the effect of variants in these regions. Tools were tested in a controlled genomic scenario, representing the ground-truth and allowing us to determine software performance.
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26
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Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van Bemmel J, Hüttenhain R, Vedantham V, Conklin BR, Black BL, Bruneau BG, Steinmetz L, Krogan NJ, Pollard KS, Srivastava D. Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors. Circulation 2022; 146:770-787. [PMID: 35938400 PMCID: PMC9452483 DOI: 10.1161/circulationaha.121.057620] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND GATA4 (GATA-binding protein 4), a zinc finger-containing, DNA-binding transcription factor, is essential for normal cardiac development and homeostasis in mice and humans, and mutations in this gene have been reported in human heart defects. Defects in alternative splicing are associated with many heart diseases, yet relatively little is known about how cell type- or cell state-specific alternative splicing is achieved in the heart. Here, we show that GATA4 regulates cell type-specific splicing through direct interaction with RNA and the spliceosome in human induced pluripotent stem cell-derived cardiac progenitors. METHODS We leveraged a combination of unbiased approaches including affinity purification of GATA4 and mass spectrometry, enhanced cross-linking with immunoprecipitation, electrophoretic mobility shift assays, in vitro splicing assays, and unbiased transcriptomic analysis to uncover GATA4's novel function as a splicing regulator in human induced pluripotent stem cell-derived cardiac progenitors. RESULTS We found that GATA4 interacts with many members of the spliceosome complex in human induced pluripotent stem cell-derived cardiac progenitors. Enhanced cross-linking with immunoprecipitation demonstrated that GATA4 also directly binds to a large number of mRNAs through defined RNA motifs in a sequence-specific manner. In vitro splicing assays indicated that GATA4 regulates alternative splicing through direct RNA binding, resulting in functionally distinct protein products. Correspondingly, knockdown of GATA4 in human induced pluripotent stem cell-derived cardiac progenitors resulted in differential alternative splicing of genes involved in cytoskeleton organization and calcium ion import, with functional consequences associated with the protein isoforms. CONCLUSIONS This study shows that in addition to its well described transcriptional function, GATA4 interacts with members of the spliceosome complex and regulates cell type-specific alternative splicing via sequence-specific interactions with RNA. Several genes that have splicing regulated by GATA4 have functional consequences and many are associated with dilated cardiomyopathy, suggesting a novel role for GATA4 in achieving the necessary cardiac proteome in normal and stress-responsive conditions.
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Affiliation(s)
- Lili Zhu
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | | | - Barbara Gonzalez-Teran
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Yen-Sin Ang
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | | | - Nicole R. Stone
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Lei Liu
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Ping Zhou
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Palo Alto, CA, USA
| | - Hongmei Ruan
- Department of Medicine, University of California, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Yu Huang
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Shibo Jin
- Division of Cellular and Developmental Biology, Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, CA, USA
| | - Angelo Pelonero
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Frances Koback
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Nandhini Sadagopan
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Austin Hsu
- Gladstone Institutes, San Francisco, CA, USA
| | - Mauro W. Costa
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Casey A. Gifford
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Joke van Bemmel
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
| | - Vasanth Vedantham
- Department of Medicine, University of California, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Bruce R. Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Brian L. Black
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Benoit G. Bruneau
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Lars Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Nevan J. Krogan
- Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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27
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Athanasopoulou K, Adamopoulos PG, Daneva GN, Scorilas A. Decoding the concealed transcriptional signature of the apoptosis-related BCL2 antagonist/killer 1 (BAK1) gene in human malignancies. Apoptosis 2022; 27:869-882. [DOI: 10.1007/s10495-022-01753-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
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28
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Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 2022; 11:73888. [PMID: 35695373 PMCID: PMC9236610 DOI: 10.7554/elife.73888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
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Affiliation(s)
- Jayashree Kumar
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United States
| | - Justin M Waldern
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
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29
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Kwiatkowski M, Hotze M, Schumacher J, Asif AR, Pittol JMR, Brenig B, Ramljak S, Zischler H, Herlyn H. Protein speciation is likely to increase the chance of proteins to be determined in 2‐DE/MS. Electrophoresis 2022; 43:1203-1214. [DOI: 10.1002/elps.202000393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 11/30/2021] [Accepted: 02/02/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Marcel Kwiatkowski
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | - Madlen Hotze
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | | | - Abdul R. Asif
- Department of Clinical Chemistry/UMG‐Laboratories University Medical Center Göttingen Germany
| | - Jose Miguel Ramos Pittol
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | - Bertram Brenig
- Department of Molecular Biology of Livestock Institute of Veterinary Medicine University of Göttingen Göttingen Germany
| | | | - Hans Zischler
- Institute of Organismic and Molecular Evolution, Anthropology University of Mainz Mainz Germany
| | - Holger Herlyn
- Institute of Organismic and Molecular Evolution, Anthropology University of Mainz Mainz Germany
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30
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Smirnov D, Schlieben LD, Peymani F, Berutti R, Prokisch H. Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes. Hum Mutat 2022; 43:1056-1070. [DOI: 10.1002/humu.24416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Lea D. Schlieben
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Fatemeh Peymani
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
| | - Riccardo Berutti
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Holger Prokisch
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
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31
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Chang JJY, Gleeson J, Rawlinson D, De Paoli-Iseppi R, Zhou C, Mordant FL, Londrigan SL, Clark MB, Subbarao K, Stinear TP, Coin LJM, Pitt ME. Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection. Front Immunol 2022; 13:832223. [PMID: 35464437 PMCID: PMC9019466 DOI: 10.3389/fimmu.2022.832223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative to help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) using Oxford Nanopore Technologies (ONT) long-reads to measure differential host gene expression, transcript polyadenylation and isoform usage within various epithelial cell lines permissive and non-permissive for SARS-CoV-2 infection. SARS-CoV-2-infected and mock-infected Vero (African green monkey kidney epithelial cells), Calu-3 (human lung adenocarcinoma epithelial cells), Caco-2 (human colorectal adenocarcinoma epithelial cells) and A549 (human lung carcinoma epithelial cells) were analyzed over time (0, 2, 24, 48 hours). Differential polyadenylation was found to occur in both infected Calu-3 and Vero cells during a late time point (48 hpi), with Gene Ontology (GO) terms such as viral transcription and translation shown to be significantly enriched in Calu-3 data. Poly(A) tails showed increased lengths in the majority of the differentially polyadenylated transcripts in Calu-3 and Vero cell lines (up to ~101 nt in mean poly(A) length, padj = 0.029). Of these genes, ribosomal protein genes such as RPS4X and RPS6 also showed downregulation in expression levels, suggesting the importance of ribosomal protein genes during infection. Furthermore, differential transcript usage was identified in Caco-2, Calu-3 and Vero cells, including transcripts of genes such as GSDMB and KPNA2, which have previously been implicated in SARS-CoV-2 infections. Overall, these results highlight the potential role of differential polyadenylation and transcript usage in host immune response or viral manipulation of host mechanisms during infection, and therefore, showcase the value of long-read sequencing in identifying less-explored host responses to disease.
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Affiliation(s)
- Jessie J-Y Chang
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Josie Gleeson
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Daniel Rawlinson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Ricardo De Paoli-Iseppi
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Chenxi Zhou
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Francesca L Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sarah L Londrigan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Michael B Clark
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Disease, Imperial College London, London, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Miranda E Pitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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32
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Splicing Modulation as a Promising Therapeutic Strategy for Lysosomal Storage Disorders: The Mucopolysaccharidoses Example. Life (Basel) 2022; 12:life12050608. [PMID: 35629276 PMCID: PMC9146820 DOI: 10.3390/life12050608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
Over recent decades, the many functions of RNA have become more evident. This molecule has been recognized not only as a carrier of genetic information, but also as a specific and essential regulator of gene expression. Different RNA species have been identified and novel and exciting roles have been unveiled. Quite remarkably, this explosion of novel RNA classes has increased the possibility for new therapeutic strategies that tap into RNA biology. Most of these drugs use nucleic acid analogues and take advantage of complementary base pairing to either mimic or antagonize the function of RNAs. Among the most successful RNA-based drugs are those that act at the pre-mRNA level to modulate or correct aberrant splicing patterns, which are caused by specific pathogenic variants. This approach is particularly tempting for monogenic disorders with associated splicing defects, especially when they are highly frequent among affected patients worldwide or within a specific population. With more than 600 mutations that cause disease affecting the pre-mRNA splicing process, we consider lysosomal storage diseases (LSDs) to be perfect candidates for this type of approach. Here, we introduce the overall rationale and general mechanisms of splicing modulation approaches and highlight the currently marketed formulations, which have been developed for non-lysosomal genetic disorders. We also extensively reviewed the existing preclinical studies on the potential of this sort of therapeutic strategy to recover aberrant splicing and increase enzyme activity in our diseases of interest: the LSDs. Special attention was paid to a particular subgroup of LSDs: the mucopolysaccharidoses (MPSs). By doing this, we hoped to unveil the unique therapeutic potential of the use of this sort of approach for LSDs as a whole.
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Qi W, Fu H, Luo X, Ren Y, Liu X, Dai H, Zheng Q, Liang F. Electroacupuncture at PC6 (Neiguan) Attenuates Angina Pectoris in Rats with Myocardial Ischemia-Reperfusion Injury Through Regulating the Alternative Splicing of the Major Inhibitory Neurotransmitter Receptor GABRG2. J Cardiovasc Transl Res 2022; 15:1176-1191. [PMID: 35377129 DOI: 10.1007/s12265-022-10245-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/25/2022] [Indexed: 11/27/2022]
Abstract
Angina pectoris is the most common manifestation of coronary heart disease, causing suffering in patients. Electroacupuncture at PC6 can effectively alleviate angina by regulating the expression of genes, whether the alternative splicing (AS) of genes is affected by acupuncture is still unknown. We established a rat model of myocardial ischemia-reperfusion by coronary artery ligation and confirmed electroacupuncture alleviated the abnormal discharge caused by angina pectoris measured in EMG electromyograms. Analysis of the GSE61840 dataset established that AS events were altered after I/R and regulated by electroacupuncture. I/R decreased the expression of splicing factor Nova1 while electroacupuncture rescued it. Further experiments in dorsal root ganglion cells showed Nova1 regulated the AS of the GABRG2, specifically on its exon 9 where an important phosphorylation site is present. In vivo, results also showed that electroacupuncture can restore AS of GABRG2. Our results proved that electroacupuncture alleviates angina results by regulating alternative splicing.
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Affiliation(s)
- Wenchuan Qi
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China
| | - Hongjuan Fu
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China
| | - Xinye Luo
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China
| | - Yanrong Ren
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China.,Shanxi University of Traditional Chinese Medicine, Jinzhong, 030002, Shanxi, China
| | - Xueying Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China.,Shanxi University of Traditional Chinese Medicine, Jinzhong, 030002, Shanxi, China
| | - Hongyuan Dai
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Qianhua Zheng
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China
| | - Fanrong Liang
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China.
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34
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Peymani F, Farzeen A, Prokisch H. RNA sequencing role and application in clinical diagnostic. Pediatr Investig 2022; 6:29-35. [PMID: 35382420 PMCID: PMC8960934 DOI: 10.1002/ped4.12314] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/18/2022] [Indexed: 12/31/2022] Open
Affiliation(s)
- Fatemeh Peymani
- School of Medicine, Institute of Human Genetics Technical University of Munich Munich Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre Munich Neuherberg Germany
| | - Aiman Farzeen
- School of Medicine, Institute of Human Genetics Technical University of Munich Munich Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre Munich Neuherberg Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics Technical University of Munich Munich Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre Munich Neuherberg Germany
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35
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Suay-Corredera C, Alegre-Cebollada J. The mechanics of the heart: zooming in on hypertrophic cardiomyopathy and cMyBP-C. FEBS Lett 2022; 596:703-746. [PMID: 35224729 DOI: 10.1002/1873-3468.14301] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/10/2022]
Abstract
Hypertrophic cardiomyopathy (HCM), a disease characterized by cardiac muscle hypertrophy and hypercontractility, is the most frequently inherited disorder of the heart. HCM is mainly caused by variants in genes encoding proteins of the sarcomere, the basic contractile unit of cardiomyocytes. The most frequently mutated among them is MYBPC3, which encodes cardiac myosin-binding protein C (cMyBP-C), a key regulator of sarcomere contraction. In this review, we summarize clinical and genetic aspects of HCM and provide updated information on the function of the healthy and HCM sarcomere, as well as on emerging therapeutic options targeting sarcomere mechanical activity. Building on what is known about cMyBP-C activity, we examine different pathogenicity drivers by which MYBPC3 variants can cause disease, focussing on protein haploinsufficiency as a common pathomechanism also in nontruncating variants. Finally, we discuss recent evidence correlating altered cMyBP-C mechanical properties with HCM development.
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36
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Sergeeva OV, Shcherbinina EY, Shomron N, Zatsepin TS. Modulation of RNA Splicing by Oligonucleotides: Mechanisms of Action and Therapeutic Implications. Nucleic Acid Ther 2022; 32:123-138. [PMID: 35166605 DOI: 10.1089/nat.2021.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dysregulation of RNA splicing causes many diseases and disorders. Several therapeutic approaches have been developed to correct aberrant alternative splicing events for the treatment of cancers and hereditary diseases, including gene therapy and redirecting splicing, using small molecules or splice switching oligonucleotides (SSO). Significant advances in the chemistry and pharmacology of nucleic acid have led to the development of clinically approved SSO drugs for the treatment of spinal muscular dystrophy and Duchenne muscular dystrophy (DMD). In this review, we discuss the mechanisms of SSO action with emphasis on "less common" approaches to modulate alternative splicing, including bipartite and bifunctional SSO, oligonucleotide decoys for splice factors and SSO-mediated mRNA degradation via AS-NMD and NGD pathways. We briefly discuss the current progress and future perspectives of SSO therapy for rare and ultrarare diseases.
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Affiliation(s)
- Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry, Moscow State University, Moscow, Russia
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37
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Covello G, Ibrahim GH, Bacchi N, Casarosa S, Denti MA. Exon Skipping Through Chimeric Antisense U1 snRNAs to Correct Retinitis Pigmentosa GTPase-Regulator ( RPGR) Splice Defect. Nucleic Acid Ther 2022; 32:333-349. [PMID: 35166581 PMCID: PMC9416563 DOI: 10.1089/nat.2021.0053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal dystrophies are caused by mutations in more than 250 genes, each of them carrying several types of mutations that can lead to different clinical phenotypes. Mutations in Retinitis Pigmentosa GTPase-Regulator (RPGR) cause X-linked Retinitis pigmentosa (RP). A nucleotide substitution in intron 9 of RPGR causes the increase of an alternatively spliced isoform of the mature mRNA, bearing exon 9a (E9a). This introduces a stop codon, leading to truncation of the protein. Aiming at restoring impaired gene expression, we developed an antisense RNA-based therapeutic approach for the skipping of RPGR E9a. We designed a set of specific U1 antisense snRNAs (U1_asRNAs) and tested their efficacy in vitro, upon transient cotransfection with RPGR minigene reporter systems in HEK-293T, 661W, and PC-12 cell lines.
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Affiliation(s)
- Giuseppina Covello
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Gehan H Ibrahim
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Niccolò Bacchi
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Simona Casarosa
- Neural Development and Regeneration Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,Centre for Medical Science - CIS Med, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
| | - Michela Alessandra Denti
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
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38
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Using machine learning to detect the differential usage of novel gene isoforms. BMC Bioinformatics 2022; 23:45. [PMID: 35042461 PMCID: PMC8764765 DOI: 10.1186/s12859-022-04576-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
Background Differential isoform usage is an important driver of inter-individual phenotypic diversity and is linked to various diseases and traits. However, accurately detecting the differential usage of different gene transcripts between groups can be difficult, in particular in less well annotated genomes where the spectrum of transcript isoforms is largely unknown. Results We investigated whether machine learning approaches can detect differential isoform usage based purely on the distribution of reads across a gene region. We illustrate that gradient boosting and elastic net approaches can successfully identify large numbers of genes showing potential differential isoform usage between Europeans and Africans, that are enriched among relevant biological pathways and significantly overlap those identified by previous approaches. We demonstrate that diversity at the 3′ and 5′ ends of genes are primary drivers of these differences between populations. Conclusion Machine learning methods can effectively detect differential isoform usage from read fraction data, and can provide novel insights into the biological differences between groups. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04576-3.
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Kim BH, Woo TG, Kang SM, Park S, Park BJ. Splicing Variants, Protein-Protein Interactions, and Drug Targeting in Hutchinson-Gilford Progeria Syndrome and Small Cell Lung Cancer. Genes (Basel) 2022; 13:genes13020165. [PMID: 35205210 PMCID: PMC8871687 DOI: 10.3390/genes13020165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) is a biological operation that enables a messenger RNA to encode protein variants (isoforms) that give one gene several functions or properties. This process provides one of the major sources of use for understanding the proteomic diversity of multicellular organisms. In combination with post-translational modifications, it contributes to generating a variety of protein–protein interactions (PPIs) that are essential to cellular homeostasis or proteostasis. However, cells exposed to many kinds of stresses (aging, genetic changes, carcinogens, etc.) sometimes derive cancer or disease onset from aberrant PPIs caused by DNA mutations. In this review, we summarize how splicing variants may form a neomorphic protein complex and cause diseases such as Hutchinson-Gilford progeria syndrome (HGPS) and small cell lung cancer (SCLC), and we discuss how protein–protein interfaces obtained from the variants may represent efficient therapeutic target sites to treat HGPS and SCLC.
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Affiliation(s)
- Bae-Hoon Kim
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
| | - Tae-Gyun Woo
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
| | - So-Mi Kang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
| | - Soyoung Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
| | - Bum-Joon Park
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
- Correspondence:
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40
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Francisco RD, Fernando V, Norma E, Madai ME, Marcelo B. Glial changes in schizophrenia: Genetic and epigenetic approach. Indian J Psychiatry 2022; 64:3-12. [PMID: 35400734 PMCID: PMC8992743 DOI: 10.4103/indianjpsychiatry.indianjpsychiatry_104_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 10/24/2021] [Accepted: 12/23/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Schizophrenia (SCZ) is a severe mental illness that affects one percent of the population, affecting how people think, feel, and behave. Evidence suggests glial cell alteration and some researchers have found genetic risk loci and epigenetic marks that may regulate glia-related genes implicated in SCZ. AIM The aim of this study is to identify genetic and epigenetic changes that have been reported in glial cells or glial-associated genes in SCZ. MATERIALS AND METHODS We searched the articles from PubMed, PubMed Central, Medline, Medscape, and Embase databases up to December 2020 to identify relevant peer-reviewed articles in English. The titles and abstracts were screened to eliminate irrelevant citations. RESULTS Twenty-four original articles were included in the review. Studies were categorized into the following four thematic via: (1) oligodendrocytes, (2) microglia, (3) astrocytes, and (4) perspectives. CONCLUSION This study is the first of its kind to review research on genetic variants and epigenetic modifications associated with glia-related genes implicated in SCZ. Epigenetic evidence is considerably less than genetic evidence in this field. Understanding the pathways of some risk genes and their genetic and epigenetic regulation allows us to understand and find potential targets for future interventions in this mental illness.
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Affiliation(s)
- Ramos Daniel Francisco
- Faculty of Chemical Sciences, Juarez University of the State of Durango, Durango, Mexico
| | - Vazquez Fernando
- Faculty of Chemical Sciences, Juarez University of the State of Durango, Durango, Mexico.,Research Unit, General Hospital 450, Durango, Mexico
| | - Estrada Norma
- Faculty of Chemical Sciences, Juarez University of the State of Durango, Durango, Mexico
| | - Méndez Edna Madai
- Scientific Research Institute, Juarez University of the State of Durango, Durango, Mexico
| | - Barraza Marcelo
- Faculty of Chemical Sciences, Juarez University of the State of Durango, Durango, Mexico
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41
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Titus MB, Chang AW, Olesnicky EC. Exploring the Diverse Functional and Regulatory Consequences of Alternative Splicing in Development and Disease. Front Genet 2021; 12:775395. [PMID: 34899861 PMCID: PMC8652244 DOI: 10.3389/fgene.2021.775395] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a fundamental mechanism of eukaryotic RNA regulation that increases the transcriptomic and proteomic complexity within an organism. Moreover, alternative splicing provides a framework for generating unique yet complex tissue- and cell type-specific gene expression profiles, despite using a limited number of genes. Recent efforts to understand the negative consequences of aberrant splicing have increased our understanding of developmental and neurodegenerative diseases such as spinal muscular atrophy, frontotemporal dementia and Parkinsonism linked to chromosome 17, myotonic dystrophy, and amyotrophic lateral sclerosis. Moreover, these studies have led to the development of innovative therapeutic treatments for diseases caused by aberrant splicing, also known as spliceopathies. Despite this, a paucity of information exists on the physiological roles and specific functions of distinct transcript spliceforms for a given gene. Here, we will highlight work that has specifically explored the distinct functions of protein-coding spliceforms during development. Moreover, we will discuss the use of alternative splicing of noncoding exons to regulate the stability and localization of RNA transcripts.
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Affiliation(s)
- M Brandon Titus
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Adeline W Chang
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Eugenia C Olesnicky
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
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42
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Liu W, Sun Y, Qiu X, Meng C, Song C, Tan L, Liao Y, Liu X, Ding C. Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken. Viruses 2021; 13:v13122409. [PMID: 34960678 PMCID: PMC8703359 DOI: 10.3390/v13122409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host-virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.
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Affiliation(s)
- Weiwei Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Yingjie Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Xusheng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Chunchun Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Cuiping Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Lei Tan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Xiufan Liu
- School of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-21-3429-3441
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43
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Xu Z, Platig J, Lee S, Boueiz A, Chase R, Jain D, Gregory A, Suryadevara R, Berman S, Bowler R, Hersh CP, Laederach A, Castaldi PJ. Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation. Genomics 2021; 113:4184-4195. [PMID: 34763026 PMCID: PMC8722433 DOI: 10.1016/j.ygeno.2021.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/22/2021] [Accepted: 11/03/2021] [Indexed: 11/24/2022]
Abstract
Cigarette smoking induces a profound transcriptomic and systemic inflammatory response. Previous studies have focused on gene level differential expression of smoking, but the genome-wide effects of smoking on alternative isoform regulation have not yet been described. We conducted RNA sequencing in whole-blood samples of 454 current and 767 former smokers in the COPDGene Study, and we analyzed the effects of smoking on differential usage of isoforms and exons. At 10% FDR, we detected 3167 differentially expressed genes, 945 differentially used isoforms and 160 differentially used exons. Isoform switch analysis revealed widespread 3' UTR lengthening associated with cigarette smoking. The lengthening of these 3' UTRs was consistent with alternative usage of distal polyadenylation sites, and these extended 3' UTR regions were significantly enriched with functional sequence elements including microRNA and RNA-protein binding sites. These findings warrant further studies on alternative polyadenylation events as potential biomarkers and novel therapeutic targets for smoking-related diseases.
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Affiliation(s)
- Zhonghui Xu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John Platig
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sool Lee
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Adel Boueiz
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rob Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dhawal Jain
- Pulmonary Drug Discovery Laboratory, Bayer US LLC. Pharmaceuticals, Research & Development, Boston, MA, USA
| | - Andrew Gregory
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Seth Berman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Northeastern University, Boston, MA, USA
| | - Russell Bowler
- Division of Pulmonary and Critical Care Medicine, National Jewish Health, Denver, CO, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA.
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44
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Liu L, Amorín R, Moriel P, DiLorenzo N, Lancaster PA, Peñagaricano F. Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle. BMC Genomics 2021; 22:780. [PMID: 34717556 PMCID: PMC8557564 DOI: 10.1186/s12864-021-08065-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/28/2021] [Indexed: 01/18/2023] Open
Abstract
Background The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively. Results Alternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons. Conclusions Overall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08065-4.
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Affiliation(s)
- Lihe Liu
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr, Madison, WI, 53706, USA
| | - Rocío Amorín
- University of Florida Genetics Institute, University of Florida, 32611, Gainesville, FL, USA
| | - Philipe Moriel
- Range Cattle Research and Education Center, University of Florida, 33865, Ona, FL, USA
| | - Nicolás DiLorenzo
- North Florida Research and Education Center, University of Florida, 32351, Marianna, FL, USA
| | - Phillip A Lancaster
- Department of Clinical Sciences, Kansas State University, 66506, Manhattan, KS, USA
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr, Madison, WI, 53706, USA.
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Hümmer S, Borao S, Guerra-Moreno A, Cozzuto L, Hidalgo E, Ayté J. Cross talk between the upstream exon-intron junction and Prp2 facilitates splicing of non-consensus introns. Cell Rep 2021; 37:109893. [PMID: 34706246 DOI: 10.1016/j.celrep.2021.109893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 04/27/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022] Open
Abstract
Splicing of mRNA precursors is essential in the regulation of gene expression. U2AF65 recognizes the poly-pyrimidine tract and helps in the recognition of the branch point. Inactivation of fission yeast U2AF65 (Prp2) blocks splicing of most, but not all, pre-mRNAs, for reasons that are not understood. Here, we have determined genome-wide the splicing efficiency of fission yeast cells as they progress into synchronous meiosis in the presence or absence of functional Prp2. Our data indicate that in addition to the splicing elements at the 3' end of any intron, the nucleotides immediately upstream the intron will determine whether Prp2 is required or dispensable for splicing. By changing those nucleotides in any given intron, we regulate its Prp2 dependency. Our results suggest a model in which Prp2 is required for the coordinated recognition of both intronic ends, placing Prp2 as a key regulatory element in the determination of the exon-intron boundaries.
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Affiliation(s)
- Stefan Hümmer
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
| | - Sonia Borao
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Angel Guerra-Moreno
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Luca Cozzuto
- CRG Bioinformatics Core, Centre de Regulació Genòmica (CRG), 08003 Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
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46
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Liao KC, Garcia-Blanco MA. Role of Alternative Splicing in Regulating Host Response to Viral Infection. Cells 2021; 10:cells10071720. [PMID: 34359890 PMCID: PMC8306335 DOI: 10.3390/cells10071720] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/26/2023] Open
Abstract
The importance of transcriptional regulation of host genes in innate immunity against viral infection has been widely recognized. More recently, post-transcriptional regulatory mechanisms have gained appreciation as an additional and important layer of regulation to fine-tune host immune responses. Here, we review the functional significance of alternative splicing in innate immune responses to viral infection. We describe how several central components of the Type I and III interferon pathways encode spliced isoforms to regulate IFN activation and function. Additionally, the functional roles of splicing factors and modulators in antiviral immunity are discussed. Lastly, we discuss how cell death pathways are regulated by alternative splicing as well as the potential role of this regulation on host immunity and viral infection. Altogether, these studies highlight the importance of RNA splicing in regulating host–virus interactions and suggest a role in downregulating antiviral innate immunity; this may be critical to prevent pathological inflammation.
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Affiliation(s)
- Kuo-Chieh Liao
- Genome Institute of Singapore, A*STAR, Singapore 138672, Singapore
- Correspondence: (K.-C.L.); (M.A.G.-B.)
| | - Mariano A. Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77550, USA
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Correspondence: (K.-C.L.); (M.A.G.-B.)
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Li Q, Wang Y, Pan Y, Wang J, Yu W, Wang X. Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families. BMC Med Genomics 2021; 14:152. [PMID: 34107977 PMCID: PMC8188693 DOI: 10.1186/s12920-021-01008-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
Background Variants identified through parent–child trio-WES yield up to 28–55% positive diagnostic rate across a variety of Mendelian disorders, there remain numerous patients who do not receive a genetic diagnosis. Studies showed that some aberrant splicing variants, which are either not readily detectable by WES or could be miss-interpreted by regular detecting pipelines, are highly relevant to human diseases. Methods We retrospectively investigated the negative molecular diagnostics through trio-WES for 15 genetically undiagnosed patients whose clinical manifestations were highly suspected to be genetic disorders with well-established genotype–phenotype relationships. We scrutinized the synonymous variants from WES data and Sanger sequenced the suspected intronic region for deep intronic variants. The functional consequences of variants were analyzed by in vitro minigene experiments. Results Here, we report two abnormal splicing events, one of which caused exon truncating due to the activation of cryptic splicing site by a synonymous variant; the other caused partial intron retention due to the generation of splicing sites by a deep intronic variant. Conclusions We suggest that, despite initial negative genetic test results in clinically highly suspected genetic diseases, the combination of predictive bioinformatics and functional analysis should be considered to unveil the genetic etiology of undiagnosed rare diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01008-8.
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Affiliation(s)
- Qiang Li
- Guiyang Maternal and Child Health Care Hospital, Guiyang, 550002, China.
| | | | - Yijun Pan
- Guiyang Maternal and Child Health Care Hospital, Guiyang, 550002, China
| | - Jia Wang
- Cipher Gene, Ltd., Beijing, 100080, China
| | - Weishi Yu
- Cipher Gene, Ltd., Beijing, 100080, China
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48
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Denti L, Pirola Y, Previtali M, Ceccato T, Della Vedova G, Rizzi R, Bonizzoni P. Shark: fishing relevant reads in an RNA-Seq sample. Bioinformatics 2021; 37:464-472. [PMID: 32926128 PMCID: PMC8088329 DOI: 10.1093/bioinformatics/btaa779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/17/2020] [Accepted: 09/02/2020] [Indexed: 11/19/2022] Open
Abstract
Motivation Recent advances in high-throughput RNA-Seq technologies allow to produce massive datasets. When a study focuses only on a handful of genes, most reads are not relevant and degrade the performance of the tools used to analyze the data. Removing irrelevant reads from the input dataset leads to improved efficiency without compromising the results of the study. Results We introduce a novel computational problem, called gene assignment and we propose an efficient alignment-free approach to solve it. Given an RNA-Seq sample and a panel of genes, a gene assignment consists in extracting from the sample, the reads that most probably were sequenced from those genes. The problem becomes more complicated when the sample exhibits evidence of novel alternative splicing events. We implemented our approach in a tool called Shark and assessed its effectiveness in speeding up differential splicing analysis pipelines. This evaluation shows that Shark is able to significantly improve the performance of RNA-Seq analysis tools without having any impact on the final results. Availability and implementation The tool is distributed as a stand-alone module and the software is freely available at https://github.com/AlgoLab/shark. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luca Denti
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano 20126, Italy
| | - Yuri Pirola
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano 20126, Italy
| | - Marco Previtali
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano 20126, Italy
| | - Tamara Ceccato
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano 20126, Italy
| | - Gianluca Della Vedova
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano 20126, Italy
| | - Raffaella Rizzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano 20126, Italy
| | - Paola Bonizzoni
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano 20126, Italy
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49
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Schlieben LD, Prokisch H, Yépez VA. How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data. Front Mol Biosci 2021; 8:647277. [PMID: 34141720 PMCID: PMC8204083 DOI: 10.3389/fmolb.2021.647277] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Rare diseases, although individually rare, collectively affect approximately 350 million people worldwide. Currently, nearly 6,000 distinct rare disorders with a known molecular basis have been described, yet establishing a specific diagnosis based on the clinical phenotype is challenging. Increasing integration of whole exome sequencing into routine diagnostics of rare diseases is improving diagnostic rates. Nevertheless, about half of the patients do not receive a genetic diagnosis due to the challenges of variant detection and interpretation. During the last years, RNA sequencing is increasingly used as a complementary diagnostic tool providing functional data. Initially, arbitrary thresholds have been applied to call aberrant expression, aberrant splicing, and mono-allelic expression. With the application of RNA sequencing to search for the molecular diagnosis, the implementation of robust statistical models on normalized read counts allowed for the detection of significant outliers corrected for multiple testing. More recently, machine learning methods have been developed to improve the normalization of RNA sequencing read count data by taking confounders into account. Together the methods have increased the power and sensitivity of detection and interpretation of pathogenic variants, leading to diagnostic rates of 10-35% in rare diseases. In this review, we provide an overview of the methods used for RNA sequencing and illustrate how these can improve the diagnostic yield of rare diseases.
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Affiliation(s)
- Lea D. Schlieben
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Vicente A. Yépez
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Munich, Germany
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50
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Li D, McIntosh CS, Mastaglia FL, Wilton SD, Aung-Htut MT. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl Neurodegener 2021; 10:16. [PMID: 34016162 PMCID: PMC8136212 DOI: 10.1186/s40035-021-00240-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is a fundamental step in eukaryotic gene expression that systematically removes non-coding regions (introns) and ligates coding regions (exons) into a continuous message (mature mRNA). This process is highly regulated and can be highly flexible through a process known as alternative splicing, which allows for several transcripts to arise from a single gene, thereby greatly increasing genetic plasticity and the diversity of proteome. Alternative splicing is particularly prevalent in neuronal cells, where the splicing patterns are continuously changing to maintain cellular homeostasis and promote neurogenesis, migration and synaptic function. The continuous changes in splicing patterns and a high demand on many cis- and trans-splicing factors contribute to the susceptibility of neuronal tissues to splicing defects. The resultant neurodegenerative diseases are a large group of disorders defined by a gradual loss of neurons and a progressive impairment in neuronal function. Several of the most common neurodegenerative diseases involve some form of splicing defect(s), such as Alzheimer's disease, Parkinson's disease and spinal muscular atrophy. Our growing understanding of RNA splicing has led to the explosion of research in the field of splice-switching antisense oligonucleotide therapeutics. Here we review our current understanding of the effects alternative splicing has on neuronal differentiation, neuronal migration, synaptic maturation and regulation, as well as the impact on neurodegenerative diseases. We will also review the current landscape of splice-switching antisense oligonucleotides as a therapeutic strategy for a number of common neurodegenerative disorders.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Craig Stewart McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Frank Louis Mastaglia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Steve Donald Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia. .,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia.
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