1
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Peng T, Liu Z, Zhang Y, Liu X, Zhao L, Ma Y, Fan J, Song X, Wang L. The systematic identification of survival-related alternative splicing events and splicing factors in glioblastoma. Ann Hum Genet 2024; 88:320-335. [PMID: 38369937 DOI: 10.1111/ahg.12550] [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: 07/28/2023] [Revised: 09/21/2023] [Accepted: 12/30/2023] [Indexed: 02/20/2024]
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor, making it one of the most life-threatening human cancers. Nevertheless, research on the mechanism of action between alternative splicing (AS) and splicing factor (SF) or biomarkers in GBM is limited. AS is a crucial post-transcriptional regulatory mechanism. More than 95% of human genes undergo AS events. AS can diversify the expression patterns of genes, thereby increasing the diversity of proteins and playing a significant role in the occurrence and development of tumors. In this study, we downloaded 599 clinical data and 169 transcriptome analysis data from The Cancer Genome Atlas (TCGA) database. Besides, we collected AS data about GBM from TCGA-SpliceSeq. The overall survival (OS) related AS events in GBM were determined through least absolute shrinkage and selection operator (Lasso) and Cox analysis. Subsequently, the association of these 1825 OS-related AS events with patient survival was validated using the Kaplan-Meier survival analysis, receiver operating characteristic curve, risk curve analysis, and independent prognostic analysis. Finally, we depicted the AS-SF regulatory network, illustrating the interactions between splicing factors and various AS events in GBM. Additionally, we identified three splicing factors (RNU4-1, SEC31B, and CLK1) associated with patient survival. In conclusion, based on AS occurrences, we developed a predictive risk model and constructed an interaction network between GBM-related AS events and SFs, aiming to shed light on the underlying mechanisms of GBM pathogenesis and progression.
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Affiliation(s)
- Tao Peng
- College of Medicine, Xinyang Normal University, Xinyang, China
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Zhe Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Yu Zhang
- College of Medicine, Xinyang Normal University, Xinyang, China
- School of medical, Southeast University, Nanjing, China
| | - Xudong Liu
- School of Medicine, Chongqing University, Chongqing, China
| | - Lijun Zhao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Ying Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jinke Fan
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Xinqiang Song
- College of Medicine, Xinyang Normal University, Xinyang, China
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Lei Wang
- College of Medicine, Xinyang Normal University, Xinyang, China
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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2
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Lv J, Zhou F, Wei Q, Long X, Tian W, Zhai J, Wang J, Zhang Q, Wan D. An alternative 3' splice site of PeuHKT1;3 improves the response to salt stress through enhancing affinity to K + in Populus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108776. [PMID: 38843683 DOI: 10.1016/j.plaphy.2024.108776] [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: 01/29/2024] [Revised: 04/30/2024] [Accepted: 05/25/2024] [Indexed: 06/17/2024]
Abstract
Alternative splicing (AS) serves as a crucial post-transcriptional regulator in plants that contributes to the resistance to salt stress. However, the underlying mechanism is largely unknown. In this research, we identified an important AS transcript in Populus euphratica, PeuHKT1:3a, generated by alternative 3' splice site splicing mode that resulted in the removal of 252 bases at the 5' end of the first exon in PeuHKT1:3. Protein sequence comparison showed that the site of AS occurred in PeuHKT1:3 is located at a crucial Ser residue within the first pore-loop domain, which leads to inefficient K+ transport in HKT I-type transporters. Expressing PeuHKT1;3a in an axt3 mutant yeast strain can effectively compensate for the lack of intracellular K+, whereas the expression of PeuHKT1;3 cannot yield the effect. Furthermore, in transgenic Arabidopsis and poplar plants, it was observed that lines expressing PeuHKT1;3a exhibited greater salt tolerance compared to those expressing the PeuHKT1;3 strain. Analysis of ion content and flux demonstrated that the transgenic PeuHKT1;3a line exhibited significantly higher K+ content compared to the PeuHKT1;3 line, while there was no significant difference in Na+ content. In conclusion, our findings revealed that AS can give rise to novel variants of HKT I-type proteins in P. euphratica with modified K+ selectivity to keep a higher K+/Na+ ratio to enhanced salt tolerance.
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Affiliation(s)
- Jiaojiao Lv
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Fangfang Zhou
- College of Life and Health, Zhengzhou Technical College, Zhengzhou 450121, China.
| | - Qianqian Wei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Xiaoqin Long
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Wenjing Tian
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Jiajia Zhai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Junjie Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Qi Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Dongshi Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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3
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Zhuravskaya A, Yap K, Hamid F, Makeyev EV. Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons. Genome Biol 2024; 25:162. [PMID: 38902825 PMCID: PMC11188260 DOI: 10.1186/s13059-024-03305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identified several examples of such a regulation in developing neurons. However, the systems-level effects of AS-NMD in this context are poorly understood. RESULTS We developed an R package, factR2, which offers a comprehensive suite of AS-NMD analysis functions. Using this tool, we conducted a longitudinal analysis of gene expression in pluripotent stem cells undergoing induced neuronal differentiation. Our analysis uncovers hundreds of AS-NMD events with significant potential to regulate gene expression. Notably, this regulation is significantly overrepresented in specific functional groups of developmentally downregulated genes. Particularly strong association with gene downregulation is detected for alternative cassette exons stimulating NMD upon their inclusion into mature mRNA. By combining bioinformatic analyses with CRISPR/Cas9 genome editing and other experimental approaches we show that NMD-stimulating cassette exons regulated by the RNA-binding protein PTBP1 dampen the expression of their genes in developing neurons. We also provided evidence that the inclusion of NMD-stimulating cassette exons into mature mRNAs is temporally coordinated with NMD-independent gene repression mechanisms. CONCLUSIONS Our study provides an accessible workflow for the discovery and prioritization of AS-NMD targets. It further argues that the AS-NMD pathway plays a widespread role in developing neurons by facilitating the downregulation of functionally related non-neuronal genes.
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Affiliation(s)
- Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Karen Yap
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
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4
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Huang AC, Su JY, Hung YJ, Chiang HL, Chen YT, Huang YT, Yu CHA, Lin HN, Lin CL. SpliceAPP: an interactive web server to predict splicing errors arising from human mutations. BMC Genomics 2024; 25:600. [PMID: 38877417 PMCID: PMC11179192 DOI: 10.1186/s12864-024-10512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Splicing variants are a major class of pathogenic mutations, with their severity equivalent to nonsense mutations. However, redundant and degenerate splicing signals hinder functional assessments of sequence variations within introns, particularly at branch sites. We have established a massively parallel splicing assay to assess the impact on splicing of 11,191 disease-relevant variants. Based on the experimental results, we then applied regression-based methods to identify factors determining splicing decisions and their respective weights. RESULTS Our statistical modeling is highly sensitive, accurately annotating the splicing defects of near-exon intronic variants, outperforming state-of-the-art predictive tools. We have incorporated the algorithm and branchpoint information into a web-based tool, SpliceAPP, to provide an interactive application. This user-friendly website allows users to upload any genetic variants with genome coordinates (e.g., chr15 74,687,208 A G), and the tool will output predictions for splicing error scores and evaluate the impact on nearby splice sites. Additionally, users can query branch site information within the region of interest. CONCLUSIONS In summary, SpliceAPP represents a pioneering approach to screening pathogenic intronic variants, contributing to the development of precision medicine. It also facilitates the annotation of splicing motifs. SpliceAPP is freely accessible using the link https://bc.imb.sinica.edu.tw/SpliceAPP . Source code can be downloaded at https://github.com/hsinnan75/SpliceAPP .
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Affiliation(s)
- Ang-Chu Huang
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Jia-Ying Su
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Jen Hung
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Hung-Lun Chiang
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Yi-Ting Chen
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Chen-Hsin Albert Yu
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Hsin-Nan Lin
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan.
| | - Chien-Ling Lin
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan.
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan.
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan.
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Hwang H, Jeon H, Yeo N, Baek D. Big data and deep learning for RNA biology. Exp Mol Med 2024:10.1038/s12276-024-01243-w. [PMID: 38871816 DOI: 10.1038/s12276-024-01243-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
The exponential growth of big data in RNA biology (RB) has led to the development of deep learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL studies in other fields, the successful implementation of DL in RB depends heavily on the effective utilization of large-scale datasets from public databases. In achieving this goal, data encoding methods, learning algorithms, and techniques that align well with biological domain knowledge have played pivotal roles. In this review, we provide guiding principles for applying these DL concepts to various problems in RB by demonstrating successful examples and associated methodologies. We also discuss the remaining challenges in developing DL models for RB and suggest strategies to overcome these challenges. Overall, this review aims to illuminate the compelling potential of DL for RB and ways to apply this powerful technology to investigate the intriguing biology of RNA more effectively.
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Affiliation(s)
- Hyeonseo Hwang
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyeonseong Jeon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Genome4me Inc., Seoul, Republic of Korea
| | - Nagyeong Yeo
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- Genome4me Inc., Seoul, Republic of Korea.
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6
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Zhao P, Peng M, Zhang S, Dong Z, Liu M, Xing X, Shi Y, Li H, Chen L. Alternative splicing of the conserved drug-resistant orthologue FpNcb2 is associated with its nuclear accumulation of products and full virulence of Fusarium pseudograminearum. PEST MANAGEMENT SCIENCE 2024. [PMID: 38860488 DOI: 10.1002/ps.8219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/02/2024] [Accepted: 05/20/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Negative cofactor 2 NC2β (Ncb2 or Dr1) is the beta subunit of a conserved heterodimeric regulator of transcription negative cofactor 2 (NC2) complex that has been identified as key regulator of drug resistance in model fungi. However, its role in plant pathogens is still unclear. RESULTS We identified an NC2β orthologue, FpNcb2, in Fusarium pseudograminearum, which is not only a significant regulatory function in drug resistance, but also essential for growth, conidiation and penetration. Moreover, FpNcb2 undergoes alternative splicing which creates two mRNA isoforms. As a putative CCAAT binding protein, FpNcb2 concentrates in the nuclei, contributing to the expression of two spliced mRNA of FpNcb2 in hypha, conidiophores and conidia, with exception of FpNcb2ISOA in germlings. Expression of each spliced mRNA of FpNcb2 in Δfpncb2 mutant could full complement the defects on growth, conidiation and fungicides sensitivity to that of wild type. However, FpNcb2ISOA and FpNcb2ISOB have different effects on virulence. FpNcb2 acts as a regulator for the transcription of some genes encoding drug efflux and hydrolases. CONCLUSION Our analysis showed the existence of alternative mRNA splicing in the NC2β orthologue, which is associated with protein subcellular localization and fungal virulence. The further elucidation of the target genes of NC2β will provide insights into the potential regulation mechanisms in the antifungal resistance and pathogenesis of F. pseudograminearum. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Peiyi Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Mengya Peng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shiyu Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zaifang Dong
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Min Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xiaoping Xing
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Linlin Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
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7
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Riccardi F, Romano G, Licastro D, Pagani F. Age-dependent regulation of ELP1 exon 20 splicing in Familial Dysautonomia by RNA Polymerase II kinetics and chromatin structure. PLoS One 2024; 19:e0298965. [PMID: 38829854 PMCID: PMC11146744 DOI: 10.1371/journal.pone.0298965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/01/2024] [Indexed: 06/05/2024] Open
Abstract
Familial Dysautonomia (FD) is a rare disease caused by ELP1 exon 20 skipping. Here we clarify the role of RNA Polymerase II (RNAPII) and chromatin on this splicing event. A slow RNAPII mutant and chromatin-modifying chemicals that reduce the rate of RNAPII elongation induce exon skipping whereas chemicals that create a more relaxed chromatin exon inclusion. In the brain of a mouse transgenic for the human FD-ELP1 we observed on this gene an age-dependent decrease in the RNAPII density profile that was most pronounced on the alternative exon, a robust increase in the repressive marks H3K27me3 and H3K9me3 and a decrease of H3K27Ac, together with a progressive reduction in ELP1 exon 20 inclusion level. In HEK 293T cells, selective drug-induced demethylation of H3K27 increased RNAPII elongation on ELP1 and SMN2, promoted the inclusion of the corresponding alternative exons, and, by RNA-sequencing analysis, induced changes in several alternative splicing events. These data suggest a co-transcriptional model of splicing regulation in which age-dependent changes in H3K27me3/Ac modify the rate of RNAPII elongation and affect processing of ELP1 alternative exon 20.
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Affiliation(s)
- Federico Riccardi
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Giulia Romano
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Danilo Licastro
- Laboratorio di Genomica ed Epigenomica, AREA Science Park, Padriciano, Trieste, Italy
| | - Franco Pagani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
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8
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Gao S, Tan S, Purcell SL, Whyte SK, Parrish K, Zhong L, Zheng S, Zhang Y, Zhu R, Jahangiri L, Li R, Fast MD, Cai W. A comparative analysis of alternative splicing patterns in Atlantic salmon (Salmo salar) in response to Moritella viscosa and sea lice (Lepeophtheirus salmonis) infection. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109606. [PMID: 38705547 DOI: 10.1016/j.fsi.2024.109606] [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: 01/06/2024] [Revised: 04/19/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Moritella viscosa (M. viscosa) and sea lice (Lepeophtheirus salmonis) are severe pathogens that primarily infect the skin of Atlantic salmon (Salmo salar), which cause significant economic losses in the farming industry. However, the pathogenesis and molecular mechanisms underlying the host's immune defence at the post-transcriptional level remain unclear. Alternative splicing (AS) is an evolutionarily conserved post-transcriptional mechanism that can greatly increase the richness of the transcriptome and proteome. In this study, transcriptomic data derived from skin tissues of Atlantic salmon after M. viscosa and sea lice infections were used to examine the AS profiles and their differential expression patterns. In total, we identified 33,044 AS events (involving 13,718 genes) in the control (CON) group, 35,147 AS events (involving 14,340 genes) in the M. viscosa infection (MV) group, and 30,364 AS events (involving 13,142 genes) in the sea lice infection (LC) group, respectively. Among the five types of AS identified in our study (i.e., SE, A5SS, A3SS, MXE, and RI), SE was the most prevalent type in all three groups (i.e., CON, MV, and LC groups). Decreased percent-spliced-in (PSI) levels were observed in SE events under both MV- and LC-infected conditions, suggesting that MV or LC infection elevated exon-skipping isoforms and promoted the selection of shorter transcripts in numerous DAS genes. In addition, most of the differential AS genes were found to be associated with pathways related to mRNA regulation, epithelial or muscle development, and immune response. These findings provide novel insights into the role of AS in host-pathogen interactions and represent the first comparative analysis of AS in response to bacterial and parasitic infections in fish.
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Affiliation(s)
- Shengnan Gao
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China; State Key Lab of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Suxu Tan
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Sara L Purcell
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, C1A 4P3, Canada
| | - Shona K Whyte
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, C1A 4P3, Canada
| | - Kathleen Parrish
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, C1A 4P3, Canada
| | - Liang Zhong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Shucheng Zheng
- State Key Lab of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Yuxuan Zhang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Ruoxi Zhu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Ladan Jahangiri
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, C1A 4P3, Canada
| | - Wenlong Cai
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China; Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, C1A 4P3, Canada; State Key Lab of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China.
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9
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Zhang Y, Yan H, Wei Z, Hong H, Huang D, Liu G, Qin Q, Rong R, Gao P, Meng J, Ying B. NanoMUD: Profiling of pseudouridine and N1-methylpseudouridine using Oxford Nanopore direct RNA sequencing. Int J Biol Macromol 2024; 270:132433. [PMID: 38759861 DOI: 10.1016/j.ijbiomac.2024.132433] [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: 02/27/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Nanopore direct RNA sequencing provided a promising solution for unraveling the landscapes of modifications on single RNA molecules. Here, we proposed NanoMUD, a computational framework for predicting the RNA pseudouridine modification (Ψ) and its methylated analog N1-methylpseudouridine (m1Ψ), which have critical application in mRNA vaccination, at single-base and single-molecule resolution from direct RNA sequencing data. Electric signal features were fed into a bidirectional LSTM neural network to achieve improved accuracy and predictive capabilities. Motif-specific models (NNUNN, N = A, C, U or G) were trained based on features extracted from designed dataset and achieved superior performance on molecule-level modification prediction (Ψ models: min AUC = 0.86, max AUC = 0.99; m1Ψ models: min AUC = 0.87, max AUC = 0.99). We then aggregated read-level predictions for site stoichiometry estimation. Given the observed sequence-dependent bias in model performance, we trained regression models based on the distribution of modification probabilities for sites with known stoichiometry. The distribution-based site stoichiometry estimation method allows unbiased comparison between different contexts. To demonstrate the feasibility of our work, three case studies on both in vitro and in vivo transcribed RNAs were presented. NanoMUD will make a powerful tool to facilitate the research on modified therapeutic IVT RNAs and provides useful insight to the landscape and stoichiometry of pseudouridine and N1-pseudouridine on in vivo transcribed RNA species.
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Affiliation(s)
- Yuxin Zhang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Huayuan Yan
- Suzhou Abogen Biosciences Co., Ltd., Suzhou 215123, China
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Haifeng Hong
- Suzhou Abogen Biosciences Co., Ltd., Suzhou 215123, China
| | - Daiyun Huang
- Wisdom Lake Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Guopeng Liu
- Suzhou Abogen Biosciences Co., Ltd., Suzhou 215123, China
| | - Qianshan Qin
- Suzhou Abogen Biosciences Co., Ltd., Suzhou 215123, China
| | - Rong Rong
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Peng Gao
- Suzhou Abogen Biosciences Co., Ltd., Suzhou 215123, China.
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom.
| | - Bo Ying
- Suzhou Abogen Biosciences Co., Ltd., Suzhou 215123, China.
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10
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Wang X, Guo S, Xiong L, Wu X, Bao P, Kang Y, Cao M, Ding Z, Liang C, Pei J, Guo X. Complete characterization of the yak testicular development using accurate full-length transcriptome sequencing. Int J Biol Macromol 2024; 271:132400. [PMID: 38759851 DOI: 10.1016/j.ijbiomac.2024.132400] [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: 02/21/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Alternative splicing is a prevalent phenomenon in testicular tissues. Due to the low assembly accuracy of short-read RNA sequencing technology in analyzing post-transcriptional regulatory events, full-length (FL) transcript sequencing is highly demanded to accurately determine FL splicing variants. In this study, we performed FL transcriptome sequencing of testicular tissues from 0.5, 1.5, 2.5, and 4-year-old yaks and 4-year-old cattle-yaks using Oxford Nanopore Technologies. The obtained sequencing data were predicted to have 47,185 open reading frames (ORFs), including 26,630 complete ORFs, detected 7645 fusion transcripts, 15,355 alternative splicing events, 25,798 simple sequence repeats, 7628 transcription factors, and 35,503 long non-coding RNAs. A total of 40,038 novel transcripts were obtained from the sequencing data, and the proportion was almost close to the number of known transcripts identified. Structural analysis and functional annotation of these novel transcripts resulted in the successful annotation of 9568 transcripts, with the highest and lowest annotation numbers in the Nr and KOG databases, respectively. Weighted gene co-expression network analysis revealed the key regulatory pathways and hub genes at various stages of yak testicular development. Our findings enhance our comprehension of transcriptome complexity, contribute to genome annotation refinement, and provide foundational data for further investigations into male sterility in cattle-yaks.
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Affiliation(s)
- Xingdong Wang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Lin Xiong
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Yandong Kang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Mengli Cao
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Ziqiang Ding
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Jie Pei
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China.
| | - Xian Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China.
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11
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Li C, Krishnan S, Zhang M, Hu D, Meng D, Riedelsberger J, Dougherty L, Xu K, Piñeros MA, Cheng L. Alternative Splicing Underpins the ALMT9 Transporter Function for Vacuolar Malic Acid Accumulation in Apple. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310159. [PMID: 38514904 PMCID: PMC11165477 DOI: 10.1002/advs.202310159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Vacuolar malic acid accumulation largely determines fruit acidity, a key trait for the taste and flavor of apple and other fleshy fruits. Aluminum-activated malate transporter 9 (ALMT9/Ma1) underlies a major genetic locus, Ma, for fruit acidity in apple, but how the protein transports malate across the tonoplast is unclear. Here, it is shown that overexpression of the coding sequence of Ma1 (Ma1α) drastically decreases fruit acidity in "Royal Gala" apple, leading to uncovering alternative splicing underpins Ma1's function. Alternative splicing generates two isoforms: Ma1β is 68 amino acids shorter with much lower expression than the full-length protein Ma1α. Ma1β does not transport malate itself but interacts with the functional Ma1α to form heterodimers, creating synergy with Ma1α for malate transport in a threshold manner (When Ma1β/Ma1α ≥ 1/8). Overexpression of Ma1α triggers feedback inhibition on the native Ma1 expression via transcription factor MYB73, decreasing the Ma1β level well below the threshold that leads to significant reductions in Ma1 function and malic acid accumulation in fruit. Overexpression of Ma1α and Ma1β or genomic Ma1 increases both isoforms proportionally and enhances fruit malic acid accumulation. These findings reveal an essential role of alternative splicing in ALMT9-mediated malate transport underlying apple fruit acidity.
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Affiliation(s)
- Chunlong Li
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan430070China
| | | | - Mengxia Zhang
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dagang Hu
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dong Meng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Janin Riedelsberger
- Center for Bioinformatics, Simulation and Modeling, Department of Bioinformatics, Faculty of EngineeringUniversity of TalcaTalca3460000Chile
| | - Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Miguel A. Piñeros
- Plant Biology Section, School of Integrative Plant Science and Robert W. Holley Center for Agriculture and HealthUSDA‐ARS Cornell UniversityIthacaNY14853USA
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
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12
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Frew E, Sainty R, Chappell-Maor L, Bone C, Daskeviciute D, Russell S, Buhigas C, Iglesias-Platas I, Lartey J, Monk D. Differential expression of PPP1R12A transcripts, including those harbouring alternatively spliced micro-exons, in placentae from complicated pregnancies. Placenta 2024; 151:1-9. [PMID: 38615553 DOI: 10.1016/j.placenta.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/04/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
INTRODUCTION Placenta-associated pregnancy complications, including pre-eclampsia (PE) and intrauterine growth restriction (IUGR) are conditions postulated to originate from initial failure of placentation, leading to clinical sequelae indicative of endothelial dysfunction. Vascular smooth muscle aberrations have also been implicated in the pathogenesis of both disorders via smooth muscle contractility and relaxation mediated by Myosin Light Chain Phosphatase (MLCP) and the oppositional contractile action of Myosin Light Chain Kinase. PPP1R12A is a constituent part of the MLCP complex responsible for dephosphorylation of myosin fibrils. We hypothesize that alternative splicing of micro-exons result in isoforms lacking the functional leucine zipper (LZ) domain which may give those cells expressing these alternative transcripts a tendency towards contraction and vasoconstriction. METHODS Expression was determined by qRT-PCR. Epigenetic profiling consisted of bisulphite-based DNA methylation analysis and ChIP for underlying histone modifications. RESULTS We identified several novel transcripts with alternative micro-exon inclusion that would produce LZ- PPP1R12A protein. qRT-PCR revealed some isoforms, including the PPP1R12A canonical transcript, are differentially expressed in placenta biopsies from PE and IUGR samples compared to uncomplicated pregnancies. DISCUSSION We propose that upregulation of PPP1R12A expression in complicated pregnancies may be due to enhanced promoter activity leading to increased transcription as a response to physiological stress in the placenta, which we show is independent of promoter DNA methylation.
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Affiliation(s)
- Edward Frew
- Department of Obstetrics and Gynaecology, Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, UK
| | - Rebecca Sainty
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Louise Chappell-Maor
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Caitlin Bone
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Dagne Daskeviciute
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sarah Russell
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Claudia Buhigas
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Isabel Iglesias-Platas
- Neonatal Unit, Institut de Recerca, Sant Joan de Déu, Barcelona, Spain; Neonatal Research, Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, UK
| | - Jon Lartey
- Department of Obstetrics and Gynaecology, Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, UK; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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13
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Kwak JS, Song JT, Seo HS. E3 SUMO ligase SIZ1 splicing variants localize and function according to external conditions. PLANT PHYSIOLOGY 2024; 195:1601-1623. [PMID: 38497423 PMCID: PMC11142376 DOI: 10.1093/plphys/kiae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024]
Abstract
SIZ1 (SAP and MIZ1) is a member of the Siz/PIAS-type RING family of E3 SUMO (small ubiquitin-related modifier) ligases that play key roles in growth, development, and stress responses in plant and animal systems. Nevertheless, splicing variants of SIZ1 have not yet been characterized. Here, we identified four splicing variants of Arabidopsis (Arabidopsis thaliana) SIZ1, which encode three different protein isoforms. The SIZ1 gene encodes an 873-amino acid (aa) protein. Among the four SIZ1 splicing variants (SSVs), SSV1 and SSV4 encode identical 885 aa proteins; SSV2 encodes an 832 aa protein; and SSV3 encodes an 884 aa protein. SSV2 mainly localized to the plasma membrane, whereas SIZ1, SSV1/SSV4, and SSV3 localized to the nucleus. Interestingly, SIZ1 and all SSVs exhibited similar E3 SUMO ligase activities and preferred SUMO1 and SUMO2 for their E3 ligase activity. Transcript levels of SSV2 were substantially increased by heat treatment, while those of SSV1, SSV3, and SSV4 transcripts were unaffected by various abiotic stresses. SSV2 directly interacted with and sumoylated cyclic nucleotide-gated ion channel 6 (CNGC6), a positive thermotolerance regulator, enhancing the stability of CNGC6. Notably, transgenic siz1-2 mutants expressing SSV2 exhibited greater heat stress tolerance than wild-type plants, whereas those expressing SIZ1 were sensitive to heat stress. Furthermore, transgenic cngc6 plants overaccumulating a mutated mCNGC6 protein (K347R, a mutation at the sumoylation site) were sensitive to heat stress, similar to the cngc6 mutants, while transgenic cngc6 plants overaccumulating CNGC6 exhibited restored heat tolerance. Together, we propose that alternative splicing is an important mechanism that regulates the function of SSVs during development or under adverse conditions, including heat stress.
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Affiliation(s)
- Jun Soo Kwak
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong Tae Song
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
| | - Hak Soo Seo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Bio-MAX Institute, Seoul National University, Seoul 08826, Korea
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14
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Liu H, Huang M, Xin D, Wang H, Yu H, Pu W. Natural products with anti-tumorigenesis potential targeting macrophage. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 131:155794. [PMID: 38875811 DOI: 10.1016/j.phymed.2024.155794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/06/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Inflammation is a risk factor for tumorigenesis. Macrophage, a subset of immune cells with high plasticity, plays a multifaceted role in this process. Natural products, which are bioactive compounds derived from traditional herbs or foods, have exhibited diverse effects on macrophages and tumorigenesis making them a valuable resource of drug discovery or optimization in tumor prevention. PURPOSE Provide a comprehensive overview of the various roles of macrophages in tumorigenesis, as well as the effects of natural products on tumorigenesis by modulating macrophage function. METHODS A thorough literature search spanning the past two decades was carried out using PubMed, Web of Science, Elsevier, and CNKI following the PRISMA guidelines. The search terms employed included "macrophage and tumorigenesis", "natural products, macrophages and tumorigenesis", "traditional Chinese medicine and tumorigenesis", "natural products and macrophage polarization", "macrophage and tumor related microenvironment", "macrophage and tumor signal pathway", "toxicity of natural products" and combinations thereof. Furthermore, certain articles are identified through the tracking of citations from other publications or by accessing the websites of relevant journals. Studies that meet the following criteria are excluded: (1) Articles not written in English or Chinese; (2) Full texts were not available; (3) Duplicate articles and irrelevant studies. The data collected was organized and summarized based on molecular mechanisms or compound structure. RESULTS This review elucidates the multifaceted effect of macrophages on tumorigenesis, encompassing process such as inflammation, angiogenesis, and tumor cell invasion by regulating metabolism, non-coding RNA, signal transduction and intercellular crosstalk. Natural products, including vitexin, ovatodiolide, ligustilide, and emodin, as well as herbal remedies, have demonstrated efficacy in modulating macrophage function, thereby attenuating tumorigenesis. These interventions mainly focus on mitigating the initial inflammatory response or modifying the inflammatory environment within the precancerous niche. CONCLUSIONS These mechanistic insights of macrophages in tumorigenesis offer valuable ideas for researchers. The identified natural products facilitate the selection of promising candidates for future cancer drug development.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Manru Huang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Dandan Xin
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Hong Wang
- School of Medical Technology, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China.
| | - Haiyang Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China.
| | - Weiling Pu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China.
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15
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Lang F, Sorn P, Suchan M, Henrich A, Albrecht C, Köhl N, Beicht A, Riesgo-Ferreiro P, Holtsträter C, Schrörs B, Weber D, Löwer M, Sahin U, Ibn-Salem J. Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates. BIOINFORMATICS ADVANCES 2024; 4:vbae080. [PMID: 38863673 PMCID: PMC11165244 DOI: 10.1093/bioadv/vbae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/26/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
Abstract
Motivation Neoantigens are promising targets for cancer immunotherapies and might arise from alternative splicing. However, detecting tumor-specific splicing is challenging because many non-canonical splice junctions identified in tumors also appear in healthy tissues. To increase tumor-specificity, we focused on splicing caused by somatic mutations as a source for neoantigen candidates in individual patients. Results We developed the tool splice2neo with multiple functionalities to integrate predicted splice effects from somatic mutations with splice junctions detected in tumor RNA-seq and to annotate the resulting transcript and peptide sequences. Additionally, we provide the tool EasyQuant for targeted RNA-seq read mapping to candidate splice junctions. Using a stringent detection rule, we predicted 1.7 splice junctions per patient as splice targets with a false discovery rate below 5% in a melanoma cohort. We confirmed tumor-specificity using independent, healthy tissue samples. Furthermore, using tumor-derived RNA, we confirmed individual exon-skipping events experimentally. Most target splice junctions encoded neoepitope candidates with predicted major histocompatibility complex (MHC)-I or MHC-II binding. Compared to neoepitope candidates from non-synonymous point mutations, the splicing-derived MHC-I neoepitope candidates had lower self-similarity to corresponding wild-type peptides. In conclusion, we demonstrate that identifying mutation-derived, tumor-specific splice junctions can lead to additional neoantigen candidates to expand the target repertoire for cancer immunotherapies. Availability and implementation The R package splice2neo and the python package EasyQuant are available at https://github.com/TRON-Bioinformatics/splice2neo and https://github.com/TRON-Bioinformatics/easyquant, respectively.
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Affiliation(s)
- Franziska Lang
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
- Faculty of Biology, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Patrick Sorn
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Martin Suchan
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Alina Henrich
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Christian Albrecht
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Nina Köhl
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Aline Beicht
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Pablo Riesgo-Ferreiro
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Christoph Holtsträter
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Barbara Schrörs
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - David Weber
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Martin Löwer
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Ugur Sahin
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
- BioNTech SE, Mainz 55131, Germany
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz 55131, Germany
| | - Jonas Ibn-Salem
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
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16
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Inamo J, Suzuki A, Ueda MT, Yamaguchi K, Nishida H, Suzuki K, Kaneko Y, Takeuchi T, Hatano H, Ishigaki K, Ishihama Y, Yamamoto K, Kochi Y. Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms. Nat Commun 2024; 15:4285. [PMID: 38806455 PMCID: PMC11133395 DOI: 10.1038/s41467-024-48615-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Alternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read sequencing. Here, we generate a full-length isoform annotation of human immune cells from an individual by long-read sequencing for 29 cell subsets. This contains a number of unannotated transcripts and isoforms such as a read-through transcript of TOMM40-APOE in the Alzheimer's disease locus. We profile characteristics of isoforms and show that repetitive elements significantly explain the diversity of unannotated isoforms, providing insight into the human genome evolution. In addition, some of the isoforms are expressed in a cell-type specific manner, whose alternative 3'-UTRs usage contributes to their specificity. Further, we identify disease-associated isoforms by isoform switch analysis and by integration of several quantitative trait loci analyses with genome-wide association study data. Our findings will promote the elucidation of the mechanism of complex diseases via alternative splicing.
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Affiliation(s)
- Jun Inamo
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Biomedical Engineering Research Innovation Center, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Hiroshi Nishida
- Department of Molecular Systems Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Katsuya Suzuki
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yuko Kaneko
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
- Saitama Medical University, 38 Morohongo, Moroyama, Iruma, Saitama, 350-0495, Japan
| | - Hiroaki Hatano
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yasushi Ishihama
- Department of Molecular Systems Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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17
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Pan D, Long L, Li C, Zhou Y, Liu Q, Zhao Z, Zhao H, Lin W, Zheng Z, Peng L, Li E, Xu L. Splicing factor hnRNPA1 regulates alternative splicing of LOXL2 to enhance production of LOXL2Δ13. J Biol Chem 2024:107414. [PMID: 38810697 DOI: 10.1016/j.jbc.2024.107414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) is a member of the lysyl oxidase family and has the ability to catalyze the cross-linking of extracellular matrix collagen and elastin. High expression of LOXL2 is related to tumor cell proliferation, invasion and metastasis. LOXL2 contains 14 exons. Previous studies have found that LOXL2 has abnormal alternative splicing and exon skipping in a variety of tissues and cells, resulting in a new alternatively-spliced isoform denoted LOXL2Δ13. LOXL2Δ13 lacks LOXL2WT exon 13, but its encoded protein has greater ability to induce tumor cell proliferation, invasion and metastasis. However, the molecular events that produce LOXL2Δ13 are still unclear. In this study, we found that overexpression of the splicing factor hnRNPA1 in cells can regulate the alternative splicing of LOXL2 and increase the expression of LOXL2Δ13. The exonic splicing silencer (ESS) exists at the 3' splice site (3' SS) and 5' splice site (5' SS) of LOXL2 exon 13. HnRNPA1 can bind to the ESS and inhibit the inclusion of exon 13. The RRM domain of hnRNPA1 and phosphorylation of hnRNPA1 at S91 and S95 are important for the regulation of LOXL2 alternative splicing. These results show that hnRNPA1 is a splicing factor that enhances the production of LOXL2Δ13.
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Affiliation(s)
- Deyuan Pan
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Lin Long
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Chengyu Li
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Yingxin Zhou
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Qing Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, China
| | - Ziting Zhao
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Hui Zhao
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Wan Lin
- Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Zhenyuan Zheng
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Liu Peng
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Enmin Li
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China.
| | - Liyan Xu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong Province, China.
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18
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Barutcu AR, Black MB, Samuel R, Slattery S, McMullen PD, Nong A. Integrating gene expression and splicing dynamics across dose-response oxidative modulators. Front Genet 2024; 15:1389095. [PMID: 38846964 PMCID: PMC11155298 DOI: 10.3389/fgene.2024.1389095] [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: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
Toxicological risk assessment increasingly utilizes transcriptomics to derive point of departure (POD) and modes of action (MOA) for chemicals. One essential biological process that allows a single gene to generate several different RNA isoforms is called alternative splicing. To comprehensively assess the role of splicing dysregulation in toxicological evaluation and elucidate its potential as a complementary endpoint, we performed RNA-seq on A549 cells treated with five oxidative stress modulators across a wide dose range. Differential gene expression (DGE) showed limited pathway enrichment except at high concentrations. However, alternative splicing analysis revealed variable intron retention events affecting diverse pathways for all chemicals in the absence of significant expression changes. For instance, diazinon elicited negligible gene expression changes but progressive increase in the number of intron retention events, suggesting splicing alterations precede expression responses. Benchmark dose modeling of intron retention data highlighted relevant pathways overlooked by expression analysis. Systematic integration of splicing datasets should be a useful addition to the toxicogenomic toolkit. Combining both modalities paint a more complete picture of transcriptomic dose-responses. Overall, evaluating intron retention dynamics afforded by toxicogenomics may provide biomarkers that can enhance chemical risk assessment and regulatory decision making. This work highlights splicing-aware toxicogenomics as a possible additional tool for examining cellular responses.
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19
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Merens HE, Choquet K, Baxter-Koenigs AR, Churchman LS. Timing is everything: advances in quantifying splicing kinetics. Trends Cell Biol 2024:S0962-8924(24)00070-9. [PMID: 38777664 DOI: 10.1016/j.tcb.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 05/25/2024]
Abstract
Splicing is a highly regulated process critical for proper pre-mRNA maturation and the maintenance of a healthy cellular environment. Splicing events are impacted by ongoing transcription, neighboring splicing events, and cis and trans regulatory factors on the respective pre-mRNA transcript. Within this complex regulatory environment, splicing kinetics have the potential to influence splicing outcomes but have historically been challenging to study in vivo. In this review, we highlight recent technological advancements that have enabled measurements of global splicing kinetics and of the variability of splicing kinetics at single introns. We demonstrate how identifying features that are correlated with splicing kinetics has increased our ability to form potential models for how splicing kinetics may be regulated in vivo.
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Affiliation(s)
- Hope E Merens
- Harvard University, Department of Genetics, Boston, MA, USA
| | - Karine Choquet
- University of Sherbrooke, Department of Biochemistry and Functional Genomics, Sherbrooke, Québec, Canada
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20
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Li F, Karimi N, Wang S, Pan T, Dong J, Wang X, Ma S, Shan Q, Liu C, Zhang Y, Li W, Feng G. mRNA isoform switches during mouse zygotic genome activation. Cell Prolif 2024:e13655. [PMID: 38764347 DOI: 10.1111/cpr.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Affiliation(s)
- Fan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Najmeh Karimi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Tianshi Pan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Jingxi Dong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Sinan Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Qingtong Shan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
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21
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Hou Z, Li X, Xu M, Meng S, Xu H, Li M, Cai H. Comparative Genome-Wide Alternative Splicing Analysis between Preadipocytes and Adipocytes. Genes (Basel) 2024; 15:640. [PMID: 38790269 PMCID: PMC11121090 DOI: 10.3390/genes15050640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Alternative splicing is a ubiquitous regulatory mechanism in gene expression that allows a single gene to generate multiple messenger RNAs (mRNAs). Adipocyte development is regulated by many processes, and recent studies have found that splicing factors also play an important role in adipogenic development. In the present study, we further investigated the differences in selective shearing during different periods of adipocyte differentiation. We identified five alternative splicing types including skipped exon, mutually exclusive exon, Alternative 5' splice site, Alternative 3' splice site, and Retained intron, with skipped exons being the most abundant type of selective shearing. In total, 641 differentially expressed selective shearing genes were obtained, enriched in 279 pathways, from which we selected and verified the accuracy of the sequencing results. Overall, RNA-seq revealed changes in the splicing and expression levels of these new candidate genes between precursor adipocytes and adipocytes, suggesting that they may be involved in adipocyte generation and differentiation.
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Affiliation(s)
- Zhongyi Hou
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Maosheng Xu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Shengbo Meng
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou 450046, China
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22
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Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Gajos M, Ng AH, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A. Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol 2024:10.1038/s44320-024-00039-4. [PMID: 38755290 DOI: 10.1038/s44320-024-00039-4] [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: 10/20/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct differentiation stages. RNA isoforms mainly arise from exon skipping and the alternative usage of transcription start and polyadenylation sites during human neurogenesis. The transcript isoform changes can remodel the identity and functions of protein isoforms. Finally, our study identifies a set of RNA binding proteins as a potential determinant of differentiation stage-specific global isoform changes. This work supports the view of regulated isoform changes that underlie state-transitions during neurogenesis.
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Affiliation(s)
- Jelena Ulicevic
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Zhihao Shao
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Alex Hm Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Siddharth Annaldasula
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Volker Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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23
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Su Y, Yu Z, Jin S, Ai Z, Yuan R, Chen X, Xue Z, Guo Y, Chen D, Liang H, Liu Z, Liu W. Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data. Nat Commun 2024; 15:3972. [PMID: 38730241 PMCID: PMC11087464 DOI: 10.1038/s41467-024-48117-3] [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: 10/18/2022] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.
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Affiliation(s)
- Yaqi Su
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Zhejian Yu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Siqian Jin
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Zhipeng Ai
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Ruihong Yuan
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Xinyi Chen
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Ziwei Xue
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Yixin Guo
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Di Chen
- Center for Reproductive Medicine of the Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Zuozhu Liu
- Zhejiang University-Angel Align Inc. R&D Center for Intelligent Healthcare, Zhejiang University-University of Illinois at Urbana-Champaign Institute (ZJU-UIUC Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Wanlu Liu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China.
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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24
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Wan L, Kral AJ, Voss D, Schäfer B, Sudheendran K, Danielsen M, Caruthers MH, Krainer AR. Screening Splice-Switching Antisense Oligonucleotides in Pancreas-Cancer Organoids. Nucleic Acid Ther 2024. [PMID: 38716830 DOI: 10.1089/nat.2023.0070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024] Open
Abstract
Aberrant alternative splicing is emerging as a cancer hallmark and a potential therapeutic target. It is the result of dysregulated or mutated splicing factors, or genetic alterations in splicing-regulatory cis-elements. Targeting individual altered splicing events associated with cancer-cell dependencies is a potential therapeutic strategy, but several technical limitations need to be addressed. Patient-derived organoids are a promising platform to recapitulate key aspects of disease states, and to facilitate drug development for precision medicine. Here, we report an efficient antisense-oligonucleotide (ASO) lipofection method to systematically evaluate and screen individual splicing events as therapeutic targets in pancreatic ductal adenocarcinoma organoids. This optimized delivery method allows fast and efficient screening of ASOs, e.g., those that reverse oncogenic alternative splicing. In combination with advances in chemical modifications of oligonucleotides and ASO-delivery strategies, this method has the potential to accelerate the discovery of antitumor ASO drugs that target pathological alternative splicing.
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Affiliation(s)
- Ledong Wan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Stony Brook University, Stony Brook, New York, USA
| | - Alexander J Kral
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Stony Brook University, Stony Brook, New York, USA
| | - Dillon Voss
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Stony Brook University, Stony Brook, New York, USA
| | - Balázs Schäfer
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
| | | | - Mathias Danielsen
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Marvin H Caruthers
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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25
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Khalenkow D, Brandsma CA, Timens W, Choy DF, Grimbaldeston MA, Rosenberger CM, Slebos DJ, Kerstjens HAM, Faiz A, Koppelman GH, Nawijn MC, van den Berge M, Guryev V. Alternative Splicing Is a Major Factor Shaping Transcriptome Diversity in Mild and Severe Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2024; 70:414-423. [PMID: 38315810 DOI: 10.1165/rcmb.2023-0296oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
The role of alternative splicing in chronic obstructive pulmonary disease (COPD) is still largely unknown. We aimed to investigate the differences in alternatively splicing events between patients with mild-to-moderate and severe COPD compared with non-COPD control subjects and to identify splicing factors associated with aberrant alternative splicing in COPD. For this purpose, we performed genome-wide RNA-sequencing analysis of bronchial brushings from 23 patients with mild-to-moderate COPD, 121 with severe COPD, and 23 non-COPD control subjects. We found a significant difference in the frequency of alternative splicing events in patients with mild-to-moderate and severe COPD compared with non-COPD control subjects. There were from two to eight times (depending on event type) more differential alternative splicing events in the severe than in the mild-to-moderate stage. The severe COPD samples showed less intron retention and more exon skipping. It is interesting that the transcript levels of the top 10 differentially expressed splicing factors were significantly correlated with the percentage of many alternatively spliced transcripts in severe COPD. The aberrant alternative splicing in severe COPD was predicted to increase the overall protein-coding capacity of gene products. In conclusion, we observed large and significant differences in alternative splicing between bronchial samples of patients with COPD and control subjects, with more events observed in severe than in mild-to-moderate COPD. The changes in the expression of several splicing factors correlated with prevalence of alternative splicing in severe COPD. Alternative splicing can indirectly impact gene expression by changing the relative abundance of protein-coding isoforms potentially influencing pathophysiological changes. The results provide a better understanding of COPD-related alternative splicing changes.
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Affiliation(s)
- Dmitry Khalenkow
- European Research Institute for the Biology of Ageing
- Groningen Research Institute for Asthma and COPD
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital
| | - Corry-Anke Brandsma
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - David F Choy
- Genentech, Inc., South San Francisco, California; and
| | | | | | | | - Huib A M Kerstjens
- Department of Pulmonology and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alen Faiz
- Faculty of Science, Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Victor Guryev
- European Research Institute for the Biology of Ageing
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26
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Liu L, Hong Y, Ma C, Zhang F, Li Q, Li B, He H, Zhu J, Wang H, Chen L. Circular RNA Gtdc1 Protects Against Offspring Osteoarthritis Induced by Prenatal Prednisone Exposure by Regulating SRSF1-Fn1 Signaling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307442. [PMID: 38520084 PMCID: PMC11132075 DOI: 10.1002/advs.202307442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/21/2024] [Indexed: 03/25/2024]
Abstract
Chondrodysplasia is closely associated with low birth weight and increased susceptibility to osteoarthritis in adulthood. Prenatal prednisone exposure (PPE) can cause low birth weight; however, its effect on offspring cartilage development remains unexplored. Herein, rats are administered clinical doses of prednisone intragastrically on gestational days (GDs) 0-20 and underwent long-distance running during postnatal weeks (PWs) 24-28. Knee cartilage is assayed for quality and related index changes on GD20, PW12, and PW28. In vitro experiments are performed to elucidate the mechanism. PPE decreased cartilage proliferation and matrix synthesis, causing offspring chondrodysplasia. Following long-distance running, the PPE group exhibited more typical osteoarthritis-like changes. Molecular analysis revealed that PPE caused cartilage circRNomics imbalance in which circGtdc1 decreased most significantly and persisted postnatally. Mechanistically, prednisolone reduced circGtdc1 expression and binding with Srsf1 to promote degradation of Srsf1 via K48-linked polyubiquitination. This further inhibited the formation of EDA/B+Fn1 and activation of PI3K/AKT and TGFβ pathways, reducing chondrocyte proliferation and matrix synthesis. Finally, intra-articular injection of offspring with AAV-circGtdc1 ameliorated PPE-induced chondrodysplasia, but this effect is reversed by Srsf1 knockout. Altogether, this study confirms that PPE causes chondrodysplasia and susceptibility to osteoarthritis by altering the circGtdc1-Srsf1-Fn1 axis; in vivo, overexpression of circGtdc1 can represent an effective intervention target for ameliorating PPE-induced chondrodysplasia.
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Affiliation(s)
- Liang Liu
- Department of Orthopedic SurgeryJoint Disease Research Center of Wuhan UniversityZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Yuntian Hong
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Chi Ma
- Department of Orthopedic SurgeryJoint Disease Research Center of Wuhan UniversityZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Fan Zhang
- Department of Orthopedic SurgeryJoint Disease Research Center of Wuhan UniversityZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Qingxian Li
- Department of Orthopedic SurgeryJoint Disease Research Center of Wuhan UniversityZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Bin Li
- Department of Orthopedic SurgeryJoint Disease Research Center of Wuhan UniversityZhongnan Hospital of Wuhan UniversityWuhan430071China
- Hubei Provincial Key Laboratory of Developmentally Originated DiseaseWuhan430071China
| | - Hangyuan He
- Department of Orthopedic SurgeryJoint Disease Research Center of Wuhan UniversityZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Jiayong Zhu
- Department of Orthopedic SurgeryJoint Disease Research Center of Wuhan UniversityZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Hui Wang
- Hubei Provincial Key Laboratory of Developmentally Originated DiseaseWuhan430071China
- Department of PharmacologyWuhan University School of Basic Medical SciencesWuhan430071China
| | - Liaobin Chen
- Department of Orthopedic SurgeryJoint Disease Research Center of Wuhan UniversityZhongnan Hospital of Wuhan UniversityWuhan430071China
- Hubei Provincial Key Laboratory of Developmentally Originated DiseaseWuhan430071China
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27
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Wei Y, Chen Z, Li Y, Song K. The splicing factor WBP11 mediates MCM7 intron retention to promote the malignant progression of ovarian cancer. Oncogene 2024; 43:1565-1578. [PMID: 38561505 DOI: 10.1038/s41388-024-03015-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Accumulating studies suggest that splicing factors play important roles in many diseases including human cancers. Our study revealed that WBP11, a core splicing factor, is highly expressed in ovarian cancer (OC) tissues and associated with a poor prognosis. WBP11 inhibition significantly impaired the proliferation and mobility of ovarian cancer cells in vitro and in vivo. Furthermore, FOXM1 transcriptionally activated WBP11 expression by directly binding to its promoter in OC cells. Importantly, RNA-seq and alternative splicing event analysis revealed that WBP11 silencing decreased the expression of MCM7 by regulating intron 4 retention. MCM7 inhibition attenuated the increase in malignant behaviors of WBP11-overexpressing OC cells. Overall, WBP11 was identified as an oncogenic splicing factor that contributes to malignant progression by repressing intron 4 retention of MCM7 in OC cells. Thus, WBP11 is an oncogenic splicing factor with potential therapeutic and prognostic implications in OC.
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Affiliation(s)
- Yuan Wei
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Ji'nan, 250012, Shandong, China
| | - Zhongshao Chen
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Ji'nan, 250012, Shandong, China
| | - Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, Shandong, China.
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Ji'nan, 250012, Shandong, China.
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28
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Abudureyimu S, He C, Xie W, Chen Z, Airikenjiang H, Abulaiti D, Cao Y, Qiu H, Gao Y. FOXO3a functions as a transcriptional and co-transcriptional splicing regulator in vascular endothelial cell lines. Gene 2024; 904:148221. [PMID: 38286271 DOI: 10.1016/j.gene.2024.148221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
Recent studies have indicated a connection between Forkhead box O3a protein and coronary artery disease, yet the exact role of FOXO3a in the regulation of metabolic processes and apoptosis in vascular endothelial cells is still unknown. Therefore, we investigated the role of FOXO3a on target genes in a human vascular endothelial cell line. Through the utilization of high-throughput sequencing technology, we analyzed gene expression profiles and alternative splicing patterns in human vascular endothelial cells with FOXO3a over expression. This study identified 419 DEGs between FOXO3a-OE HUVEC model and control cells. KEGG analysis indicated that the upregulated genes were mainly enriched in inflammation-related signaling pathways, and the downregulated genes were enriched in lipid metabolism-related pathways.
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Affiliation(s)
- Shajidan Abudureyimu
- Department of Comprehensive Internal Medicine, The First Affiliated Hospital of Xinjiang Medical University, 830011 Urumqi, Xinjiang, China
| | - Chunhui He
- China Heart Failure Center, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, 100010 Beijing, China
| | - Wei Xie
- Department of Cardiology, Xinjiang Production and Construction Corps Hospital, 830011 Urumqi, Xinjiang, China
| | - Zhuo Chen
- The Second Clinical Medical College of Xinjiang Medical University, 830011 Urumqi, Xinjiang, China
| | - Halisha Airikenjiang
- Department of Comprehensive Internal Medicine, The First Affiliated Hospital of Xinjiang Medical University, 830011 Urumqi, Xinjiang, China
| | - Dilihumaer Abulaiti
- Department of Comprehensive Internal Medicine, The First Affiliated Hospital of Xinjiang Medical University, 830011 Urumqi, Xinjiang, China
| | - Yan Cao
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Cancer Hospital Xinjiang Medical University, 830000 Urumqi, Xinjiang, China
| | - Haitang Qiu
- Department of Comprehensive Internal Medicine, The First Affiliated Hospital of Xinjiang Medical University, 830011 Urumqi, Xinjiang, China
| | - Ying Gao
- Department of Comprehensive Internal Medicine, The First Affiliated Hospital of Xinjiang Medical University, 830011 Urumqi, Xinjiang, China.
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29
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Kato Y, Nitta JH, Perez CAG, Adhitama N, Religia P, Toyoda A, Iwasaki W, Watanabe H. Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Sci Rep 2024; 14:9407. [PMID: 38688940 PMCID: PMC11061156 DOI: 10.1038/s41598-024-59774-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
The cladoceran crustacean Daphnia exhibits phenotypic plasticity, a phenomenon that leads to diverse phenotypes from one genome. Alternative usage of gene isoforms has been considered a key gene regulation mechanism for controlling different phenotypes. However, to understand the phenotypic plasticity of Daphnia, gene isoforms have not been comprehensively analyzed. Here we identified 25,654 transcripts derived from the 9710 genes expressed during environmental sex determination of Daphnia magna using the long-read RNA-Seq with PacBio Iso-Seq. We found that 14,924 transcripts were previously unidentified and 5713 genes produced two or more isoforms. By a combination of Illumina short-read RNA-Seq, we detected 824 genes that implemented switching of the highest expressed isoform between females and males. Among the 824 genes, we found isoform switching of an ortholog of CREB-regulated transcription coactivator, a major regulator of carbohydrate metabolism in animals, and a correlation of this switching event with the sexually dimorphic expression of carbohydrate metabolic genes. These results suggest that a comprehensive catalog of isoforms may lead to understanding the molecular basis for environmental sex determination of Daphnia. We also infer the applicability of the full-length isoform analyses to the elucidation of phenotypic plasticity in Daphnia.
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Affiliation(s)
- Yasuhiko Kato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan.
| | - Joel H Nitta
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Nikko Adhitama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Pijar Religia
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
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30
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Hou Y, Wang S, Zhang Y, Huang X, Zhang X, He F, Tian C, Sun A. Proteomics Identifies LUC7L3 as a Prognostic Biomarker for Hepatocellular Carcinoma. Curr Issues Mol Biol 2024; 46:4004-4020. [PMID: 38785515 PMCID: PMC11120364 DOI: 10.3390/cimb46050247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Alternative splicing has been shown to participate in tumor progression, including hepatocellular carcinoma. The poor prognosis of patients with HCC calls for molecular classification and biomarker identification to facilitate precision medicine. We performed ssGSEA analysis to quantify the pathway activity of RNA splicing in three HCC cohorts. Kaplan-Meier and Cox methods were used for survival analysis. GO and GSEA were performed to analyze pathway enrichment. We confirmed that RNA splicing is significantly correlated with prognosis, and identified an alternative splicing-associated protein LUC7L3 as a potential HCC prognostic biomarker. Further bioinformatics analysis revealed that high LUC7L3 expression indicated a more progressive HCC subtype and worse clinical features. Cell proliferation-related pathways were enriched in HCC patients with high LUC7L3 expression. Consistently, we proved that LUC7L3 knockdown could significantly inhibit cell proliferation and suppress the activation of associated signaling pathways in vitro. In this research, the relevance between RNA splicing and HCC patient prognosis was outlined. Our newly identified biomarker LUC7L3 could provide stratification for patient survival and recurrence risk, facilitating early medical intervention before recurrence or disease progression.
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Affiliation(s)
- Yushan Hou
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Siqi Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yiming Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaofen Huang
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Xiuyuan Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Chunyan Tian
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Aihua Sun
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- College of Life Sciences, Hebei University, Baoding 071002, China
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
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31
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Wang J, Zhang Y, Gao J, Feng G, Liu C, Li X, Li P, Liu Z, Lu F, Wang L, Li W, Zhou Q, Liu Y. Alternative splicing of CARM1 regulated by LincGET-guided paraspeckles biases the first cell fate in mammalian early embryos. Nat Struct Mol Biol 2024:10.1038/s41594-024-01292-9. [PMID: 38658621 DOI: 10.1038/s41594-024-01292-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
The heterogeneity of CARM1 controls first cell fate bias during early mouse development. However, how this heterogeneity is established is unknown. Here, we show that Carm1 mRNA is of a variety of specific exon-skipping splicing (ESS) isoforms in mouse two-cell to four-cell embryos that contribute to CARM1 heterogeneity. Disruption of paraspeckles promotes the ESS of Carm1 precursor mRNAs (pre-mRNAs). LincGET, but not Neat1, is required for paraspeckle assembly and inhibits the ESS of Carm1 pre-mRNAs in mouse two-cell to four-cell embryos. We further find that LincGET recruits paraspeckles to the Carm1 gene locus through HNRNPU. Interestingly, PCBP1 binds the Carm1 pre-mRNAs and promotes its ESS in the absence of LincGET. Finally, we find that the ESS seen in mouse two-cell to four-cell embryos decreases CARM1 protein levels and leads to trophectoderm fate bias. Our findings demonstrate that alternative splicing of CARM1 has an important role in first cell fate determination.
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Affiliation(s)
- Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
| | - Yiwei Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jiaze Gao
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xueke Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Pengcheng Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Yusheng Liu
- College of Life Science, Northeast Forestry University, Harbin, China.
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Jin J, Nguyen LTG, Wassef A, Sadek R, Schmitt TM, Guo GL, Rasmussen TP, Zhong XB. Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction. Noncoding RNA 2024; 10:28. [PMID: 38668386 PMCID: PMC11053763 DOI: 10.3390/ncrna10020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
The long non-coding RNA (lncRNA) hepatocyte nuclear factor-1 alpha (HNF1A) antisense RNA 1 (HNF1A-AS1) is an important lncRNA for liver growth, development, cell differentiation, and drug metabolism. Like many lncRNAs, HNF1A-AS1 has multiple annotated alternative transcripts in the human genome. Several fundamental biological questions are still not solved: (1) How many transcripts really exist in biological samples, such as liver samples and liver cell lines? (2) What are the expression patterns of different alternative HNF1A-AS1 transcripts at different conditions, including during cell growth and development, after exposure to xenobiotics (such as drugs), and in disease conditions, such as metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD) cirrhosis, and obesity? (3) Does the siRNA used in previous studies knock down one or multiple transcripts? (4) Do different transcripts have the same or different functions for gene regulation? The presented data confirm the existence of several annotated HNF1A-AS1 transcripts in liver samples and cell lines, but also identify some new transcripts, which are not annotated in the Ensembl genome database. Expression patterns of the identified HNF1A-AS1 transcripts are highly correlated with the cell differentiation of matured hepatocyte-like cells from human embryonic stem cells (hESC), growth and differentiation of HepaRG cells, in response to rifampicin induction, and in various liver disease conditions. The expression levels of the HNF1A-AS1 transcripts are also highly correlated to the expression of cytochrome P450 enzymes, such as CYP3A4, during HepaRG growth, differentiation, and in response to rifampicin induction.
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Affiliation(s)
- Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Le Tra Giang Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Andrew Wassef
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
- Center of Excellence for Pharmaceutical Translational Research and Education, Rutgers University, Piscataway, NJ 08901, USA
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Ragui Sadek
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Timothy M. Schmitt
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Grace L. Guo
- Department of Pharmacology and Toxicology, Ernst Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
| | - Theodore P. Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
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33
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Santos-Rebouças CB, Ferreira CDS, Nogueira JDS, Brustolini OJ, de Almeida LGP, Gerber AL, Guimarães APDC, Piergiorge RM, Struchiner CJ, Porto LC, de Vasconcelos ATR. Immune response stability to the SARS-CoV-2 mRNA vaccine booster is influenced by differential splicing of HLA genes. Sci Rep 2024; 14:8982. [PMID: 38637586 PMCID: PMC11026523 DOI: 10.1038/s41598-024-59259-1] [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: 09/12/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Many molecular mechanisms that lead to the host antibody response to COVID-19 vaccines remain largely unknown. In this study, we used serum antibody detection combined with whole blood RNA-based transcriptome analysis to investigate variability in vaccine response in healthy recipients of a booster (third) dose schedule of the mRNA BNT162b2 vaccine against COVID-19. The cohort was divided into two groups: (1) low-stable individuals, with antibody concentration anti-SARS-CoV IgG S1 below 0.4 percentile at 180 days after boosting vaccination; and (2) high-stable individuals, with antibody values greater than 0.6 percentile of the range in the same period (median 9525 [185-80,000] AU/mL). Differential gene expression, expressed single nucleotide variants and insertions/deletions, differential splicing events, and allelic imbalance were explored to broaden our understanding of the immune response sustenance. Our analysis revealed a differential expression of genes with immunological functions in individuals with low antibody titers, compared to those with higher antibody titers, underscoring the fundamental importance of the innate immune response for boosting immunity. Our findings also provide new insights into the determinants of the immune response variability to the SARS-CoV-2 mRNA vaccine booster, highlighting the significance of differential splicing regulatory mechanisms, mainly concerning HLA alleles, in delineating vaccine immunogenicity.
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Affiliation(s)
- Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Cristina Dos Santos Ferreira
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Jeane de Souza Nogueira
- Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Otávio José Brustolini
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Luiz Gonzaga Paula de Almeida
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Ana Paula de Campos Guimarães
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Cláudio José Struchiner
- School of Applied Mathematics, Getúlio Vargas Foundation, Rio de Janeiro, Brazil
- Social Medicine Institute Hesio Cordeiro, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil.
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34
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Carvalho S, Zea-Redondo L, Tang TCC, Stachel-Braum P, Miller D, Caldas P, Kukalev A, Diecke S, Grosswendt S, Grosso AR, Pombo A. SRRM2 splicing factor modulates cell fate in early development. Biol Open 2024; 13:bio060415. [PMID: 38656788 PMCID: PMC11070786 DOI: 10.1242/bio.060415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterised by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum-response transcription factor (SRF) and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 heterozygosity are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.
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Affiliation(s)
- Silvia Carvalho
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology (GABBA), ICBAS, University of Porto, 4050-313 Porto, Portugal
| | - Luna Zea-Redondo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
| | - Tsz Ching Chloe Tang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
| | - Philipp Stachel-Braum
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Exploratory Diagnostic Sciences (EDS) 10178 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), From Cell State to Function Group, 10115 Berlin, Germany
| | - Duncan Miller
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Pluripotent Stem Cells Platform, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Paulo Caldas
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alexander Kukalev
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Pluripotent Stem Cells Platform, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Stefanie Grosswendt
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Exploratory Diagnostic Sciences (EDS) 10178 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), From Cell State to Function Group, 10115 Berlin, Germany
| | - Ana Rita Grosso
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
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35
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Shah K, He S, Turner DJ, Corbo J, Rebbani K, Dominguez D, Bateman JM, Cheloufi S, Igreja C, Valkov E, Murn J. Regulation by the RNA-binding protein Unkempt at its effector interface. Nat Commun 2024; 15:3159. [PMID: 38605040 PMCID: PMC11009413 DOI: 10.1038/s41467-024-47449-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here, we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for the reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface.
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Affiliation(s)
- Kriti Shah
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
| | - Shiyang He
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
| | - David J Turner
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Joshua Corbo
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - Khadija Rebbani
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Road, SE5 9RX, London, UK
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, D-72076, Tübingen, Germany
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA.
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA.
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36
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González-Iglesias A, Arcas A, Domingo-Muelas A, Mancini E, Galcerán J, Valcárcel J, Fariñas I, Nieto MA. Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche. Nat Commun 2024; 15:2837. [PMID: 38565566 PMCID: PMC10987655 DOI: 10.1038/s41467-024-47092-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The adult mammalian brain retains some capacity to replenish neurons and glia, holding promise for brain regeneration. Thus, understanding the mechanisms controlling adult neural stem cell (NSC) differentiation is crucial. Paradoxically, adult NSCs in the subependymal zone transcribe genes associated with both multipotency maintenance and neural differentiation, but the mechanism that prevents conflicts in fate decisions due to these opposing transcriptional programmes is unknown. Here we describe intron detention as such control mechanism. In NSCs, while multiple mRNAs from stemness genes are spliced and exported to the cytoplasm, transcripts from differentiation genes remain unspliced and detained in the nucleus, and the opposite is true under neural differentiation conditions. We also show that m6A methylation is the mechanism that releases intron detention and triggers nuclear export, enabling rapid and synchronized responses. m6A RNA methylation operates as an on/off switch for transcripts with antagonistic functions, tightly controlling the timing of NSCs commitment to differentiation.
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Affiliation(s)
| | - Aida Arcas
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
| | - Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Carlos Simon Foundation, 46980, Paterna, Valencia, Spain
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Igenomix Foundation, 46980, Paterna, Valencia, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Joan Galcerán
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
| | - M Angela Nieto
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain.
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37
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Wang Y, Xie Z, Kutschera E, Adams JI, Kadash-Edmondson KE, Xing Y. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data. Nat Protoc 2024; 19:1083-1104. [PMID: 38396040 DOI: 10.1038/s41596-023-00944-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/02/2023] [Indexed: 02/25/2024]
Abstract
Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays a role in many biological processes, and dysregulated alternative splicing is a feature of many human diseases. Short-read RNA sequencing (RNA-seq) is now the standard approach for transcriptome-wide analysis of alternative splicing. Since 2011, our laboratory has developed and maintained Replicate Multivariate Analysis of Transcript Splicing (rMATS), a computational tool for discovering and quantifying alternative splicing events from RNA-seq data. Here we provide a protocol for the contemporary version of rMATS, rMATS-turbo, a fast and scalable re-implementation that maintains the statistical framework and user interface of the original rMATS software, while incorporating a revamped computational workflow with a substantial improvement in speed and data storage efficiency. The rMATS-turbo software scales up to massive RNA-seq datasets with tens of thousands of samples. To illustrate the utility of rMATS-turbo, we describe two representative application scenarios. First, we describe a broadly applicable two-group comparison to identify differential alternative splicing events between two sample groups, including both annotated and novel alternative splicing events. Second, we describe a quantitative analysis of alternative splicing in a large-scale RNA-seq dataset (~1,000 samples), including the discovery of alternative splicing events associated with distinct cell states. We detail the workflow and features of rMATS-turbo that enable efficient parallel processing and analysis of large-scale RNA-seq datasets on a compute cluster. We anticipate that this protocol will help the broad user base of rMATS-turbo make the best use of this software for studying alternative splicing in diverse biological systems.
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Affiliation(s)
- Yuanyuan Wang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zhijie Xie
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jenea I Adams
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn E Kadash-Edmondson
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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38
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Liu X, Zhang J, Wang Z, Yan M, Xu M, Li G, Shender V, Wei J, Li J, Shao C, Zhang S, Kong B, Song K, Liu Z. Splicing Factor PQBP1 Curtails BAX Expression to Promote Ovarian Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306229. [PMID: 38342602 PMCID: PMC11022708 DOI: 10.1002/advs.202306229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/27/2023] [Indexed: 02/13/2024]
Abstract
Splicing factor polyglutamine binding protein-1 (PQBP1) is abundantly expressed in the central nervous system during development, and mutations in the gene cause intellectual disability. However, the roles of PQBP1 in cancer progression remain largely unknown. Here, it is shown that PQBP1 overexpression promotes tumor progression and indicates worse prognosis in ovarian cancer. Integrative analysis of spyCLIP-seq and RNA-seq data reveals that PQBP1 preferentially binds to exon regions and modulates exon skipping. Mechanistically, it is shown that PQBP1 regulates the splicing of genes related to the apoptotic signaling pathway, including BAX. PQBP1 promotes BAX exon 2 skipping to generate a truncated isoform that undergoes degradation by nonsense-mediated mRNA decay, thus making cancer cells resistant to apoptosis. In contrast, PQBP1 depletion or splice-switching antisense oligonucleotides promote exon 2 inclusion and thus increase BAX expression, leading to inhibition of tumor growth. Together, the results demonstrate an oncogenic role of PQBP1 in ovarian cancer and suggest that targeting the aberrant splicing mediated by PQBP1 has therapeutic potential in cancer treatment.
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Affiliation(s)
- Xihan Liu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
| | - Jiaojiao Zhang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Zixiang Wang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
| | - Mingyao Yan
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Meining Xu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Gaoyuan Li
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Victoria Shender
- Center for Precision Genome Editing and Genetic Technologies for BiomedicineFederal Research and Clinical Center of Physical‐Chemical Medicine of Federal Medical Biological AgencyMoscow119435Russia
| | - Jian‐jun Wei
- Department of PathologyNorthwestern University School of MedicineChicagoIL60611USA
| | - Jianqiao Li
- Department of OphthalmologyQilu HospitalShandong UniversityJinan250012China
| | - Changshun Shao
- Key Laboratory of Radiation Medicine and ProtectionInstitutes for Translational MedicineSoochow UniversitySuzhou215127China
| | - Shiqian Zhang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Beihua Kong
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Kun Song
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Zhaojian Liu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
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39
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Zhang H, Wang Y, Hu Z, Wu Y, Chen N, Zhu Y, Yu Y, Fan H, Wang H. Zygotic Splicing Activation of the Transcriptome is a Crucial Aspect of Maternal-to-Zygotic Transition and Required for the Conversion from Totipotency to Pluripotency. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308496. [PMID: 38308190 PMCID: PMC11005748 DOI: 10.1002/advs.202308496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/27/2023] [Indexed: 02/04/2024]
Abstract
During maternal-to-zygotic transition (MZT) in the embryo, mRNA undergoes complex post-transcriptional regulatory processes. However, it is unclear whether and how alternative splicing plays a functional role in MZT. By analyzing transcriptome changes in mouse and human early embryos, dynamic changes in alternative splicing during MZT are observed and a previously unnoticed process of zygotic splicing activation (ZSA) following embryonic transcriptional activation is described. As the underlying mechanism of RNA splicing, splicing factors undergo dramatic maternal-to-zygotic conversion. This conversion relies on the key maternal factors BTG4 and PABPN1L and is zygotic-transcription-dependent. CDK11-dependent phosphorylation of the key splicing factor, SF3B1, and its aggregation with SRSF2 in the subnuclear domains of 2-cell embryos are prerequisites for ZSA. Isoforms generated by erroneous splicing, such as full-length Dppa4, hinder normal embryonic development. Moreover, alternative splicing regulates the conversion of early embryonic blastomeres from totipotency to pluripotency, thereby affecting embryonic lineage differentiation. ZSA is an essential post-transcriptional process of MZT and has physiological significance in generating new life. In addition to transcriptional activation, appropriate expression of transcript isoforms is also necessary for preimplantation embryonic development.
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Affiliation(s)
- Hua Zhang
- MOA Key Laboratory of Animal VirologyCenter for Veterinary SciencesZhejiang UniversityHangzhou310058China
- Department of Veterinary MedicineCollege of Animal SciencesZhejiang UniversityHangzhou310058China
| | - Yang Wang
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhe‐Wei Hu
- MOA Key Laboratory of Animal VirologyCenter for Veterinary SciencesZhejiang UniversityHangzhou310058China
| | - Yun‐Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Nuo Chen
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Yi‐Min Zhu
- Department of Reproductive EndocrinologyWomen's HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310002China
| | - Yuan‐Song Yu
- Savaid Stomatology SchoolHangzhou Medical CollegeHangzhou310053China
| | - Heng‐Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
- Center for Biomedical ResearchShaoxing InstituteZhejiang UniversityShaoxing312000China
| | - Hua‐Nan Wang
- MOA Key Laboratory of Animal VirologyCenter for Veterinary SciencesZhejiang UniversityHangzhou310058China
- Department of Veterinary MedicineCollege of Animal SciencesZhejiang UniversityHangzhou310058China
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40
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Al'Khafaji AM, Smith JT, Garimella KV, Babadi M, Popic V, Sade-Feldman M, Gatzen M, Sarkizova S, Schwartz MA, Blaum EM, Day A, Costello M, Bowers T, Gabriel S, Banks E, Philippakis AA, Boland GM, Blainey PC, Hacohen N. High-throughput RNA isoform sequencing using programmed cDNA concatenation. Nat Biotechnol 2024; 42:582-586. [PMID: 37291427 DOI: 10.1038/s41587-023-01815-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/02/2023] [Indexed: 06/10/2023]
Abstract
Full-length RNA-sequencing methods using long-read technologies can capture complete transcript isoforms, but their throughput is limited. We introduce multiplexed arrays isoform sequencing (MAS-ISO-seq), a technique for programmably concatenating complementary DNAs (cDNAs) into molecules optimal for long-read sequencing, increasing the throughput >15-fold to nearly 40 million cDNA reads per run on the Sequel IIe sequencer. When applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq demonstrated a 12- to 32-fold increase in the discovery of differentially spliced genes.
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Affiliation(s)
| | | | | | | | | | - Moshe Sade-Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Marc A Schwartz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Emily M Blaum
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Allyson Day
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Tera Bowers
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Eric Banks
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Genevieve M Boland
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research at the Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA.
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41
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Fan C, Lyu M, Zeng B, He Q, Wang X, Lu MZ, Liu B, Liu J, Esteban E, Pasha A, Provart NJ, Wang H, Zhang J. Profiling of the gene expression and alternative splicing landscapes of Eucalyptus grandis. PLANT, CELL & ENVIRONMENT 2024; 47:1363-1378. [PMID: 38221855 DOI: 10.1111/pce.14814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/05/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
Abstract
Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain poorly understood. In this study, we performed a comprehensive analysis of the gene expression profile and the alternative splicing (AS) landscape of E. grandis using strand-specific RNA-Seq, which encompassed 201 libraries including different organs, developmental stages, and environmental stresses. We identified 10 416 genes (33.49%) that underwent AS, and numerous differentially expressed and/or differential AS genes involved in critical biological processes, such as primary-to-secondary growth transition of stems, adventitious root formation, aging and responses to phosphorus- or boron-deficiency. Co-expression analysis of AS events and gene expression patterns highlighted the potential upstream regulatory role of AS events in multiple processes. Additionally, we highlighted the lignin biosynthetic pathway to showcase the potential regulatory functions of AS events in the KNAT3 and IRL3 genes within this pathway. Our high-quality expression atlas and AS landscape serve as valuable resources for unravelling the genetic control of woody plant development, long-term adaptation, and understanding transcriptional diversity in Eucalyptus. Researchers can conveniently access these resources through the interactive ePlant browser (https://bar.utoronto.ca/eplant_eucalyptus).
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Affiliation(s)
- Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingjie Lyu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Bingshan Zeng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qiang He
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Bobin Liu
- Jiansu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Eddi Esteban
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
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42
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Shi W, Tang J, Xiang J. Therapeutic strategies for aberrant splicing in cancer and genetic disorders. Clin Genet 2024; 105:345-354. [PMID: 38165092 DOI: 10.1111/cge.14478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Accurate pre-mRNA splicing is essential for proper protein translation; however, aberrant splicing is commonly observed in the context of cancer and genetic disorders. Notably, in genetic diseases, these splicing abnormalities often play a pivotal role. Substantial challenges persist in accurately identifying and classifying disease-induced aberrant splicing, as well as in development of targeted therapeutic strategies. In this review, we examine prevalent forms of aberrant splicing and explore potential therapeutic approaches aimed at addressing these splicing-related diseases. This summary contributes to a deeper understanding of the complexities about aberrant splicing and provide a foundation for the development of effective therapeutic interventions in the field of genetic disorders and cancer.
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Affiliation(s)
- Wenhua Shi
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingqun Tang
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Juanjuan Xiang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
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43
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Takashima S, Sun W, Otten ABC, Cai P, Peng SI, Tong E, Bui J, Mai M, Amarbayar O, Cheng B, Odango RJ, Li Z, Qu K, Sun BK. Alternative mRNA splicing events and regulators in epidermal differentiation. Cell Rep 2024; 43:113814. [PMID: 38402585 DOI: 10.1016/j.celrep.2024.113814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/22/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024] Open
Abstract
Alternative splicing (AS) of messenger RNAs occurs in ∼95% of multi-exon human genes and generates diverse RNA and protein isoforms. We investigated AS events associated with human epidermal differentiation, a process crucial for skin function. We identified 6,413 AS events, primarily involving cassette exons. We also predicted 34 RNA-binding proteins (RBPs) regulating epidermal AS, including 19 previously undescribed candidate regulators. From these results, we identified FUS as an RBP that regulates the balance between keratinocyte proliferation and differentiation. Additionally, we characterized the function of a cassette exon AS event in MAP3K7, which encodes a kinase involved in cell signaling. We found that a switch from the short to long isoform of MAP3K7, triggered during differentiation, enforces the demarcation between proliferating basal progenitors and overlying differentiated strata. Our findings indicate that AS occurs extensively in the human epidermis and has critical roles in skin homeostasis.
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Affiliation(s)
- Shota Takashima
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - Wujianan Sun
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Auke B C Otten
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - Pengfei Cai
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Shaohong Isaac Peng
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - Elton Tong
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - Jolina Bui
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - McKenzie Mai
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - Oyumergen Amarbayar
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - Binbin Cheng
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - Rowen Jane Odango
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA
| | - Zongkai Li
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Bryan K Sun
- Department of Dermatology, University of California San Diego, La Jolla, CA 92109, USA.
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44
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Lu D, Mihoayi M, Ablikim Y, Arikin A. RNA splicing regulator EIF3D regulates the tumor microenvironment through immunogene-related alternative splicing in head and neck squamous cell carcinoma. Aging (Albany NY) 2024; 16:5929-5948. [PMID: 38535990 PMCID: PMC11042944 DOI: 10.18632/aging.205681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/27/2024] [Indexed: 04/23/2024]
Abstract
Study finds that eukaryotic translation initiation factor 3 subunit D (EIF3D) may play an important role in aberrant alternative splicing (AS) events in tumors. AS possesses a pivotal role in both tumour progression and the constitution of the tumour microenvironment (TME). Regrettably, our current understanding of AS remains circumscribed especially in the context of immunogene-related alternative splicing (IGAS) profiles within Head and Neck Squamous Cell Carcinoma (HNSC). In this study, we comprehensively analyzed the function and mechanism of action of EIF3D by bioinformatics analysis combined with in vitro cellular experiments, and found that high expression of EIF3D in HNSC was associated with poor prognosis of overall survival (OS) and progression-free survival (PFS). The EIF3D low expression group had a higher degree of immune infiltration and better efficacy against PD1 and CTLA4 immunotherapy compared to the EIF3D high expression group. TCGA SpliceSeq analysis illustrated that EIF3D influenced differentially spliced alternative splicing (DSAS) events involving 105 differentially expressed immunogenes (DEIGs). We observed an induction of apoptosis and a suppression of cell proliferation, migration, and invasion in EIF3D knock-down FaDu cells. RNA-seq analysis unveiled that 531 genes exhibited differential expression following EIF3D knockdown in FaDu cells. These include 52 DEIGs. Furthermore, EIF3D knockdown influenced the patterns of 1923 alternative splicing events (ASEs), encompassing 129 IGASs. This study identified an RNA splicing regulator and revealed its regulatory role in IGAS and the TME of HNSC, suggesting that EIF3D may be a potential target for predicting HNSC prognosis and immunotherapeutic response.
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Affiliation(s)
- Dandan Lu
- Otolaryngology Diagnosis and Treatment Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
- Department of Otolaryngology, Shaanxi Nuclear Industry 215 Hospital, Xianyang 712000, China
| | - Mijti Mihoayi
- Otolaryngology Diagnosis and Treatment Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
| | - Yimin Ablikim
- Otolaryngology Diagnosis and Treatment Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
| | - Abdeyrim Arikin
- Otolaryngology Diagnosis and Treatment Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
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Da Cunha D, Miro J, Van Goethem C, Notarnicola C, Hugon G, Carnac G, Cossée M, Koenig M, Tuffery-Giraud S. The exon junction complex is required for DMD gene splicing fidelity and myogenic differentiation. Cell Mol Life Sci 2024; 81:150. [PMID: 38512499 PMCID: PMC10957711 DOI: 10.1007/s00018-024-05188-1] [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: 09/10/2023] [Revised: 02/14/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Deposition of the exon junction complex (EJC) upstream of exon-exon junctions helps maintain transcriptome integrity by preventing spurious re-splicing events in already spliced mRNAs. Here we investigate the importance of EJC for the correct splicing of the 2.2-megabase-long human DMD pre-mRNA, which encodes dystrophin, an essential protein involved in cytoskeletal organization and cell signaling. Using targeted RNA-seq, we show that knock-down of the eIF4A3 and Y14 core components of EJC in a human muscle cell line causes an accumulation of mis-splicing events clustered towards the 3' end of the DMD transcript (Dp427m). This deregulation is conserved in the short Dp71 isoform expressed ubiquitously except in adult skeletal muscle and is rescued with wild-type eIF4A3 and Y14 proteins but not with an EJC assembly-defective mutant eIF4A3. MLN51 protein and EJC-associated ASAP/PSAP complexes independently modulate the inclusion of the regulated exons 71 and 78. Our data confirm the protective role of EJC in maintaining splicing fidelity, which in the DMD gene is necessary to preserve the function of the critical C-terminal protein-protein interaction domain of dystrophin present in all tissue-specific isoforms. Given the role of the EJC in maintaining the integrity of dystrophin, we asked whether the EJC could also be involved in the regulation of a mechanism as complex as skeletal muscle differentiation. We found that eIF4A3 knockdown impairs myogenic differentiation by blocking myotube formation. Collectively, our data provide new insights into the functional roles of EJC in human skeletal muscle.
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Affiliation(s)
- Dylan Da Cunha
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Julie Miro
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Charles Van Goethem
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
- Montpellier BioInformatique Pour Le Diagnostic Clinique (MOBIDIC), Plateau de Médecine Moléculaire Et Génomique (PMMG), CHU Montpellier, 34295, Montpellier, France
| | | | - Gérald Hugon
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Gilles Carnac
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Mireille Cossée
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
| | - Michel Koenig
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
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46
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Jones EF, Haldar A, Oza VH, Lasseigne BN. Quantifying transcriptome diversity: a review. Brief Funct Genomics 2024; 23:83-94. [PMID: 37225889 DOI: 10.1093/bfgp/elad019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/14/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Following the central dogma of molecular biology, gene expression heterogeneity can aid in predicting and explaining the wide variety of protein products, functions and, ultimately, heterogeneity in phenotypes. There is currently overlapping terminology used to describe the types of diversity in gene expression profiles, and overlooking these nuances can misrepresent important biological information. Here, we describe transcriptome diversity as a measure of the heterogeneity in (1) the expression of all genes within a sample or a single gene across samples in a population (gene-level diversity) or (2) the isoform-specific expression of a given gene (isoform-level diversity). We first overview modulators and quantification of transcriptome diversity at the gene level. Then, we discuss the role alternative splicing plays in driving transcript isoform-level diversity and how it can be quantified. Additionally, we overview computational resources for calculating gene-level and isoform-level diversity for high-throughput sequencing data. Finally, we discuss future applications of transcriptome diversity. This review provides a comprehensive overview of how gene expression diversity arises, and how measuring it determines a more complete picture of heterogeneity across proteins, cells, tissues, organisms and species.
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Affiliation(s)
- Emma F Jones
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anisha Haldar
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishal H Oza
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brittany N Lasseigne
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
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47
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Kim J, Taketomi T, Yamada A, Uematsu Y, Ueda K, Chiba T, Tsuruta F. USP4 regulates TUT1 ubiquitination status in concert with SART3. Biochem Biophys Res Commun 2024; 701:149557. [PMID: 38310689 DOI: 10.1016/j.bbrc.2024.149557] [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: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/06/2024]
Abstract
The ubiquitin system plays pivotal roles in diverse cellular processes, including signal transduction, transcription and translation, organelle quality control, and protein degradation. Recent investigations have revealed the regulatory influence of ubiquitin systems on RNA metabolism. Previously, we reported that the deubiquitinating enzyme, ubiquitin specific peptidase 15 (USP15), promotes deubiquitination of terminal uridylyl transferase 1 (TUT1), a key regulator within the U4/U6 spliceosome, thereby instigating significant alterations in global RNA splicing [1]. In this study, we report that ubiquitin specific peptidase 4 (USP4), a homologous protein to USP15, also exerts control over the ubiquitination status of TUT1. Analogous to USP15, the expression of USP4 results in a reduction of TUT1 ubiquitination. Furthermore, squamous cell carcinoma antigen recognized by T-cells 3 (SART3) collaborates in enhancing the deubiquitinating activity of USP4 towards TUT1. A crucial revelation is that USP4 orchestrates the subnuclear relocation of TUT1 from the nucleolus to the nucleoplasm and facilitates the stability of U6 small nuclear RNA (snRNA). Notably, USP4 has a more profound effect on TUT1 redistribution compared to USP15. Our findings suggest that USP4 intricately modulates the ubiquitination status of TUT1, thereby exerting pronounced effects on the spliceosome functions.
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Affiliation(s)
- Jaehyun Kim
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takumi Taketomi
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Atsuma Yamada
- College of Biological Sciences, School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yukino Uematsu
- Master's and Doctoral Program in Biology, Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kentaro Ueda
- College of Biological Sciences, School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Tomoki Chiba
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan; Ph.D. Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan; Master's and Doctoral Program in Biology, Institute of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Fuminori Tsuruta
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan; Master's and Doctoral Program in Neuroscience, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan; Ph.D. Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan; Master's and Doctoral Program in Biology, Institute of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
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48
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Chen W, Geng D, Chen J, Han X, Xie Q, Guo G, Chen X, Zhang W, Tang S, Zhong X. Roles and mechanisms of aberrant alternative splicing in melanoma - implications for targeted therapy and immunotherapy resistance. Cancer Cell Int 2024; 24:101. [PMID: 38462618 PMCID: PMC10926661 DOI: 10.1186/s12935-024-03280-x] [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: 10/29/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Despite advances in therapeutic strategies, resistance to immunotherapy and the off-target effects of targeted therapy have significantly weakened the benefits for patients with melanoma. MAIN BODY Alternative splicing plays a crucial role in transcriptional reprogramming during melanoma development. In particular, aberrant alternative splicing is involved in the efficacy of immunotherapy, targeted therapy, and melanoma metastasis. Abnormal expression of splicing factors and variants may serve as biomarkers or therapeutic targets for the diagnosis and prognosis of melanoma. Therefore, comprehensively integrating their roles and related mechanisms is essential. This review provides the first detailed summary of the splicing process in melanoma and the changes occurring in this pathway. CONCLUSION The focus of this review is to provide strategies for developing novel diagnostic biomarkers and summarize their potential to alter resistance to targeted therapies and immunotherapy.
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Affiliation(s)
- Wanxian Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Deyi Geng
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Jiasheng Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaosha Han
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Qihu Xie
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Genghong Guo
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xuefen Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Wancong Zhang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Shijie Tang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaoping Zhong
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China.
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China.
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49
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Xiang X, He Y, Zhang Z, Yang X. Interrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance. Nat Commun 2024; 15:2164. [PMID: 38461306 PMCID: PMC10925056 DOI: 10.1038/s41467-024-46480-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 02/28/2024] [Indexed: 03/11/2024] Open
Abstract
RNA splicing shapes the gene regulatory programs that underlie various physiological and disease processes. Here, we present the SCASL (single-cell clustering based on alternative splicing landscapes) method for interrogating the heterogeneity of RNA splicing with single-cell RNA-seq data. SCASL resolves the issue of biased and sparse data coverage on single-cell RNA splicing and provides a new scheme for classifications of cell identities. With previously published datasets as examples, SCASL identifies new cell clusters indicating potentially precancerous and early-tumor stages in triple-negative breast cancer, illustrates cell lineages of embryonic liver development, and provides fine clusters of highly heterogeneous tumor-associated CD4 and CD8 T cells with functional and physiological relevance. Most of these findings are not readily available via conventional cell clustering based on single-cell gene expression data. Our study shows the potential of SCASL in revealing the intrinsic RNA splicing heterogeneity and generating biological insights into the dynamic and functional cell landscapes in complex tissues.
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Affiliation(s)
- Xianke Xiang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Yao He
- Biomedical Pioneering Innovation Center and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- Cancer Research Institute, Shenzhen Bay Lab, Shenzhen, 518132, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.
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50
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Role of Post-Transcriptional Regulation in Learning and Memory in Mammals. Genes (Basel) 2024; 15:337. [PMID: 38540396 PMCID: PMC10970538 DOI: 10.3390/genes15030337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024] Open
Abstract
After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is of the most importance in the brain, where all the steps of mRNA maturation, transport to different regions of the cells and actual expression, in response to specific signals, constitute the molecular basis for neuronal plasticity and, as a consequence, for structural stabilization/modification of synapses; notably, these latter events are fundamental for the highest brain functions, such as learning and memory, and are characterized by long-term potentiation (LTP) of specific synapses. Here, we will discuss the molecular bases of these fundamental events by considering both the role of RNA-binding proteins (RBPs) and the effects of non-coding RNAs involved in controlling splicing, editing, stability and translation of mRNAs. Importantly, it has also been found that dysregulation of mRNA metabolism/localization is involved in many pathological conditions, arising either during brain development or in the adult nervous system.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
- Neurology and Multiple Sclerosis Center, Unità Operativa Complessa (UOC), Foundation Institute “G. Giglio”, 90015 Cefalù, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
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