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Hu Z, Guo X, Li Z, Meng Z, Huang S. The neoantigens derived from transposable elements - A hidden treasure for cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189126. [PMID: 38849060 DOI: 10.1016/j.bbcan.2024.189126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/26/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
Neoantigen-based therapy is a promising approach that selectively activates the immune system of the host to recognize and eradicate cancer cells. Preliminary clinical trials have validated the feasibility, safety, and immunogenicity of personalized neoantigen-directed vaccines, enhancing their effectiveness and broad applicability in immunotherapy. While many ongoing oncological trials concentrate on neoantigens derived from mutations, these targets do not consistently provoke an immune response in all patients harboring the mutations. Additionally, tumors like ovarian cancer, which have a low tumor mutational burden (TMB), may be less amenable to mutation-based neoantigen therapies. Recent advancements in next-generation sequencing and bioinformatics have uncovered a rich source of neoantigens from non-canonical RNAs associated with transposable elements (TEs). Considering the substantial presence of TEs in the human genome and the proven immunogenicity of TE-derived neoantigens in various tumor types, this review investigates the latest findings on TE-derived neoantigens, examining their clinical implications, challenges, and unique advantages in enhancing tumor immunotherapy.
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Affiliation(s)
- Zhixiang Hu
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinyi Guo
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ziteng Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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2
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Wang C, Liang C. CircCNNs, a convolutional neural network framework to better understand the biogenesis of exonic circRNAs. Sci Rep 2024; 14:18982. [PMID: 39152135 PMCID: PMC11329666 DOI: 10.1038/s41598-024-69262-1] [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: 03/03/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024] Open
Abstract
Circular RNAs (circRNAs) as biomarkers for cancer detection have been extensively explored, however, the biogenesis mechanism is still elusive. In contrast to linear splicing (LS) involved in linear transcript formation, the so-called back splicing (BS) process has been proposed to explain circRNA formation. To investigate the potential mechanism of BS via the machine learning approach, we curated a high-quality BS and LS exon pairs dataset with evidence-based stringent filtering. Two convolutional neural networks (CNN) base models with different structures for processing splicing junction sequences including motif extraction were created and compared after extensive hyperparameter tuning. In contrast to the previous study, we are able to identify motifs corresponding to well-established BS-associated genes such as MBNL1, QKI, and ESPR2. Importantly, despite prevalent high false positive rates in existing circRNA detection pipelines and databases, our base models demonstrated a notable high specificity (greater than 90%). To further improve the model performance, a novo fast numerical method was proposed and implemented to calculate the reverse complementary matches (RCMs) crossing two flanking regions and within each flanking region of exon pairs. Our CircCNNs framework that incorporated RCM information into the optimal base models further reduced the false positive rates leading to 88% prediction accuracy.
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Affiliation(s)
- Chao Wang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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3
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Dziulko AK, Allen H, Chuong EB. An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140. Hum Mol Genet 2024; 33:1454-1464. [PMID: 38751339 PMCID: PMC11305685 DOI: 10.1093/hmg/ddae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 07/26/2024] Open
Abstract
Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn's disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family and is regulated by oncogenic mitogen-activated protein kinase (MAPK) signaling. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.
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Affiliation(s)
- Adam K Dziulko
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Holly Allen
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
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4
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Shi Q, Li X, Liu Y, Chen Z, He X. FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues. Nucleic Acids Res 2024; 52:D124-D133. [PMID: 37697439 PMCID: PMC10767943 DOI: 10.1093/nar/gkad745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
Regulatory processes at the RNA transcript level play a crucial role in generating transcriptome diversity and proteome composition in human cells, impacting both physiological and pathological states. This study introduces FLIBase (www.FLIBase.org), a specialized database that focuses on annotating full-length isoforms using long-read sequencing techniques. We collected and integrated long-read (351 samples) and short-read (12 469 samples) RNA sequencing data from diverse normal and cancerous human tissues and cells. The current version of FLIBase comprises a total of 983 789 full-length spliced isoforms, identified through long-read sequences and verified using short-read exon-exon splice junctions. Of these, 188 248 isoforms have been annotated, while 795 541 isoforms remain unannotated. By overcoming the limitations of short-read RNA sequencing methods, FLIBase provides an accurate and comprehensive representation of full-length transcripts. These comprehensive annotations empower researchers to undertake various downstream analyses and investigations. Importantly, FLIBase exhibits a significant advantage in identifying a substantial number of previously unannotated isoforms and tumor-specific RNA transcripts. These tumor-specific RNA transcripts have the potential to serve as a source of immunogenic recurrent neoantigens. This remarkable discovery holds tremendous promise for advancing the development of tailored RNA-based diagnostic and therapeutic strategies for various types of human cancer.
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Affiliation(s)
- Qili Shi
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xinrong Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yizhe Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
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5
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Quesnel-Vallières M, Jewell S, Lynch KW, Thomas-Tikhonenko A, Barash Y. MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer. Nucleic Acids Res 2024; 52:D213-D221. [PMID: 37953365 PMCID: PMC10767883 DOI: 10.1093/nar/gkad1043] [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: 08/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023] Open
Abstract
Quantification of RNA splicing variations based on RNA-Sequencing can reveal tissue- and disease-specific splicing patterns. To study such splicing variations, we introduce MAJIQlopedia, an encyclopedia of splicing variations that encompasses 86 human tissues and 41 cancer datasets. MAJIQlopedia reports annotated and unannotated splicing events for a total of 486 175 alternative splice junctions in normal tissues and 338 317 alternative splice junctions in cancer. This database, available at https://majiq.biociphers.org/majiqlopedia/, includes a user-friendly interface that provides graphical representations of junction usage quantification for each junction across all tissue or cancer types. To demonstrate case usage of MAJIQlopedia, we review splicing variations in genes WT1, MAPT and BIN1, which all have known tissue or cancer-specific splicing variations. We also use MAJIQlopedia to highlight novel splicing variations in FDX1 and MEGF9 in normal tissues, and we uncover a novel exon inclusion event in RPS6KA6 that only occurs in two cancer types. Users can download the database, request the addition of data to the webtool, or install a MAJIQlopedia server to integrate proprietary data. MAJIQlopedia can serve as a reference database for researchers seeking to understand what splicing variations exist in genes of interest, and those looking to understand tissue- or cancer-specific splice isoform usage.
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Affiliation(s)
- Mathieu Quesnel-Vallières
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - San Jewell
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
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6
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Wu Y, Chen S, Shao Y, Su Y, Li Q, Wu J, Zhu J, Wen H, Huang Y, Zheng Z, Chen X, Ju X, Huang S, Wu X, Hu Z. KLF5 Promotes Tumor Progression and Parp Inhibitor Resistance in Ovarian Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304638. [PMID: 37702443 PMCID: PMC10625120 DOI: 10.1002/advs.202304638] [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: 07/10/2023] [Revised: 08/16/2023] [Indexed: 09/14/2023]
Abstract
One major characteristic of tumor cells is the aberrant activation of epigenetic regulatory elements, which remodel the tumor transcriptome and ultimately promote cancer progression and drug resistance. However, the oncogenic functions and mechanisms of ovarian cancer (OC) remain elusive. Here, super-enhancer (SE) regulatory elements that are aberrantly activated in OC are identified and it is found that SEs drive the relative specific expression of the transcription factor KLF5 in OC patients and poly(ADP-ribose) polymerase inhibitor (PARPi)-resistant patients. KLF5 expression is associated with poor outcomes in OC patients and can drive tumor progression in vitro and in vivo. Mechanistically, KLF5 forms a transcriptional complex with EHF and ELF3 and binds to the promoter region of RAD51 to enhance its transcription, strengthening the homologous recombination repair (HRR) pathway. Notably, the combination of suberoylanilide hydroxamic acid (SAHA) and olaparib significantly inhibits tumor growth and metastasis of PARPi-resistant OC cells with high KLF5. In conclusion, it is discovered that SEs-driven KLF5 is a key regulatory factor in OC progression and PARPi resistance; and potential therapeutic strategies for OC patients with PARPi resistance and high KLF5 are identified.
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Affiliation(s)
- Yong Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Siyu Chen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yang Shao
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Ying Su
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qin Li
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Jiangchun Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Jun Zhu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Hao Wen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Yan Huang
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Zhong Zheng
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xiaojun Chen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xingzhu Ju
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Shenglin Huang
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Xiaohua Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhixiang Hu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
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7
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Yadav P, Pandey A, Kakani P, Mutnuru SA, Samaiya A, Mishra J, Shukla S. Hypoxia-induced loss of SRSF2-dependent DNA methylation promotes CTCF-mediated alternative splicing of VEGFA in breast cancer. iScience 2023; 26:106804. [PMID: 37235058 PMCID: PMC10206493 DOI: 10.1016/j.isci.2023.106804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/21/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Alternative splicing of vascular endothelial growth factor A (VEGFA) generates numerous isoforms with unique roles in tumor angiogenesis, and investigating the underlying mechanism during hypoxia necessitates diligent pursuance. Our research systematically demonstrated that the splicing factor SRSF2 causes the inclusion of exon-8b, leading to the formation of the anti-angiogenic VEGFA-165b isoform under normoxic conditions. Additionally, SRSF2 interacts with DNMT3A and maintains methylation on exon-8a, inhibiting CCCTC-binding factor (CTCF) recruitment and RNA polymerase II (pol II) occupancy, causing exon-8a exclusion and decreased expression of pro-angiogenic VEGFA-165a. Conversely, SRSF2 is downregulated by HIF1α-induced miR-222-3p under hypoxic conditions, which prevents exon-8b inclusion and reduces VEGFA-165b expression. Furthermore, reduced SRSF2 under hypoxia promotes hydroxymethylation on exon-8a, increasing CTCF recruitment, pol II occupancy, exon-8a inclusion, and VEGFA-165a expression. Overall, our findings unveil a specialized dual mechanism of VEGFA-165 alternative splicing, instrumented by the cross-talk between SRSF2 and CTCF, which promotes angiogenesis under hypoxic conditions.
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Affiliation(s)
- Pooja Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Anchala Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Parik Kakani
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Srinivas Abhishek Mutnuru
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Atul Samaiya
- Department of Surgical Oncology, BH, Bhopal, Madhya Pradesh 462016, India
| | - Jharna Mishra
- Department of Pathology, Bansal Hospital (BH), Bhopal, Madhya Pradesh 462016, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
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8
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Levacher C, Viennot M, Drouet A, Beaussire L, Coutant S, Théry JC, Baert-Desurmont S, Laé M, Ruminy P, Houdayer C. Disequilibrium between BRCA1 and BRCA2 Circular and Messenger RNAs Plays a Role in Breast Cancer. Cancers (Basel) 2023; 15:2176. [PMID: 37046838 PMCID: PMC10093293 DOI: 10.3390/cancers15072176] [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: 03/16/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Breast cancer is a frequent disease for which the discovery of markers that enable early detection or prognostic assessment remains challenging. Circular RNAs (circRNAs) are single-stranded structures in closed loops that are produced by backsplicing. CircRNA and messenger RNA (mRNA) are generated co-transcriptionally, and backsplicing and linear splicing compete against each other. As mRNAs are key players in tumorigenesis, we hypothesize that a disruption of the balance between circRNAs and mRNAs could promote breast cancer. Hence, we developed an assay for a simultaneous study of circRNAs and mRNAs, which we have called splice and expression analyses by exon ligation and high-throughput sequencing (SEALigHTS). Following SEALigHTS validation for BRCA1 and BRCA2, our hypothesis was tested using an independent research set of 95 pairs from tumor and adjacent normal breast tissues. In this research set, ratios of BRCA1 and BRCA2 circRNAs/mRNAs were significantly lower in the tumor breast tissue compared to normal tissue (p = 1.6 × 10-9 and p = 4.4 × 10-5 for BRCA1 and BRCA2, respectively). Overall, we developed an innovative method to study linear splicing and backsplicing, described the repertoire of BRCA1 and BRCA2 circRNAs, including 15 novel ones, and showed for the first time that a disequilibrium between BRCA1 and BRCA2 circRNAs and mRNAs plays a role in breast cancer.
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Affiliation(s)
- Corentin Levacher
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France; (C.L.)
| | - Mathieu Viennot
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France (M.L.); (P.R.)
| | - Aurélie Drouet
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France; (C.L.)
| | - Ludivine Beaussire
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France; (C.L.)
- Department of Pathology, Centre Henri Becquerel, 1 Rue d’Amiens, 76038 Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France; (C.L.)
| | - Jean-Christophe Théry
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France; (C.L.)
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d’Amiens, 76038 Rouen, France
| | - Stéphanie Baert-Desurmont
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique and CHU Rouen, Department of Genetics, 76000 Rouen, France
| | - Marick Laé
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France (M.L.); (P.R.)
- Department of Pathology, Centre Henri Becquerel, 1 Rue d’Amiens, 76038 Rouen, France
| | - Philippe Ruminy
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France (M.L.); (P.R.)
| | - Claude Houdayer
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique and CHU Rouen, Department of Genetics, 76000 Rouen, France
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9
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Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas. Nat Commun 2023; 14:1028. [PMID: 36823172 PMCID: PMC9950149 DOI: 10.1038/s41467-023-36707-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
Diffuse midline glioma-H3K27M mutant (DMG) and glioblastoma (GBM) are the most lethal brain tumors that primarily occur in pediatric and adult patients, respectively. Both tumors exhibit significant heterogeneity, shaped by distinct genetic/epigenetic drivers, transcriptional programs including RNA splicing, and microenvironmental cues in glioma niches. However, the spatial organization of cellular states and niche-specific regulatory programs remain to be investigated. Here, we perform a spatial profiling of DMG and GBM combining short- and long-read spatial transcriptomics, and single-cell transcriptomic datasets. We identify clinically relevant transcriptional programs, RNA isoform diversity, and multi-cellular ecosystems across different glioma niches. We find that while the tumor core enriches for oligodendrocyte precursor-like cells, radial glial stem-like (RG-like) cells are enriched in the neuron-rich invasive niche in both DMG and GBM. Further, we identify niche-specific regulatory programs for RG-like cells, and functionally confirm that FAM20C mediates invasive growth of RG-like cells in a neuron-rich microenvironment in a human neural stem cell derived orthotopic DMG model. Together, our results provide a blueprint for understanding the spatial architecture and niche-specific vulnerabilities of DMG and GBM.
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10
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García-Ruiz S, Gustavsson EK, Zhang D, Reynolds RH, Chen Z, Fairbrother-Browne A, Gil-Martínez AL, Botia JA, Collado-Torres L, Ryten M. IntroVerse: a comprehensive database of introns across human tissues. Nucleic Acids Res 2023; 51:D167-D178. [PMID: 36399497 PMCID: PMC9825543 DOI: 10.1093/nar/gkac1056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Dysregulation of RNA splicing contributes to both rare and complex diseases. RNA-sequencing data from human tissues has shown that this process can be inaccurate, resulting in the presence of novel introns detected at low frequency across samples and within an individual. To enable the full spectrum of intron use to be explored, we have developed IntroVerse, which offers an extensive catalogue on the splicing of 332,571 annotated introns and a linked set of 4,679,474 novel junctions covering 32,669 different genes. This dataset has been generated through the analysis of 17,510 human control RNA samples from 54 tissues provided by the Genotype-Tissue Expression Consortium. IntroVerse has two unique features: (i) it provides a complete catalogue of novel junctions and (ii) each novel junction has been assigned to a specific annotated intron. This unique, hierarchical structure offers multiple uses, including the identification of novel transcripts from known genes and their tissue-specific usage, and the assessment of background splicing noise for introns thought to be mis-spliced in disease states. IntroVerse provides a user-friendly web interface and is freely available at https://rytenlab.com/browser/app/introverse.
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Affiliation(s)
- Sonia García-Ruiz
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Emil K Gustavsson
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - David Zhang
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Regina H Reynolds
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Zhongbo Chen
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Aine Fairbrother-Browne
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, WC2R 2LS, UK
| | - Ana Luisa Gil-Martínez
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- Department of Information and Communications Engineering Faculty of Informatics, Espinardo Campus, University of Murcia, Murcia, 30100, Spain
| | - Juan A Botia
- Department of Information and Communications Engineering Faculty of Informatics, Espinardo Campus, University of Murcia, Murcia, 30100, Spain
| | | | - Mina Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, WC1N 1EH, UK
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11
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [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: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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12
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Gallego-Paez LM, Mauer J. DJExpress: An Integrated Application for Differential Splicing Analysis and Visualization. FRONTIERS IN BIOINFORMATICS 2022; 2:786898. [PMID: 36304260 PMCID: PMC9580925 DOI: 10.3389/fbinf.2022.786898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/08/2022] [Indexed: 12/22/2022] Open
Abstract
RNA-seq analysis of alternative pre-mRNA splicing has facilitated an unprecedented understanding of transcriptome complexity in health and disease. However, despite the availability of countless bioinformatic pipelines for transcriptome-wide splicing analysis, the use of these tools is often limited to expert bioinformaticians. The need for high computational power, combined with computational outputs that are complicated to visualize and interpret present obstacles to the broader research community. Here we introduce DJExpress, an R package for differential expression analysis of transcriptomic features and expression-trait associations. To determine gene-level differential junction usage as well as associations between junction expression and molecular/clinical features, DJExpress uses raw splice junction counts as input data. Importantly, DJExpress runs on an average laptop computer and provides a set of interactive and intuitive visualization formats. In contrast to most existing pipelines, DJExpress can handle both annotated and de novo identified splice junctions, thereby allowing the quantification of novel splice events. Moreover, DJExpress offers a web-compatible graphical interface allowing the analysis of user-provided data as well as the visualization of splice events within our custom database of differential junction expression in cancer (DJEC DB). DJEC DB includes not only healthy and tumor tissue junction expression data from TCGA and GTEx repositories but also cancer cell line data from the DepMap project. The integration of DepMap functional genomics data sets allows association of junction expression with molecular features such as gene dependencies and drug response profiles. This facilitates identification of cancer cell models for specific splicing alterations that can then be used for functional characterization in the lab. Thus, DJExpress represents a powerful and user-friendly tool for exploration of alternative splicing alterations in RNA-seq data, including multi-level data integration of alternative splicing signatures in healthy tissue, tumors and cancer cell lines.
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Affiliation(s)
| | - Jan Mauer
- *Correspondence: Lina Marcela Gallego-Paez, ; Jan Mauer,
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13
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Zhang Y, Yao X, Zhou H, Wu X, Tian J, Zeng J, Yan L, Duan C, Liu H, Li H, Chen K, Hu Z, Ye Z, Xu H. OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. Nucleic Acids Res 2021; 50:D1340-D1347. [PMID: 34554251 PMCID: PMC8728274 DOI: 10.1093/nar/gkab851] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 11/24/2022] Open
Abstract
Alternative splicing (AS) represents a crucial method in mRNA level to regulate gene expression and contributes to the protein complexity. Abnormal splicing has been reported to play roles in several diseases, including cancers. We developed the OncoSplicing database for visualization of survival-associated and differential alternative splicing in 2019. Here, we provide an updated version of OncoSplicing for an integrative view of clinically relevant alternative splicing based on 122 423 AS events across 33 cancers in the TCGA SpliceSeq project and 238 558 AS events across 32 cancers in the TCGA SplAdder project. The new version of the database contains several useful features, such as annotation of alternative splicing-associated transcripts, survival analysis based on median and optimal cut-offs, differential analysis between TCGA tumour samples and adjacent normal samples or GTEx normal samples, pan-cancer views of alternative splicing, splicing differences and results of Cox’PH regression, identification of clinical indicator-relevant and cancer-specific splicing events, and downloadable splicing data in the SplAdder project. Overall, the substantially updated version of OncoSplicing (www.oncosplicing.com) is a user-friendly and registration-free database for browsing and searching clinically relevant alternative splicing in human cancers.
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Affiliation(s)
- Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Xiangyang Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Hui Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Xiaoliang Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jin Zeng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330000, China
| | - Libin Yan
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310000, China
| | - Chen Duan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Haoran Liu
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650000, China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Institute of Urology of Hubei Province, Wuhan 430030, China
| | - Hua Xu
- Institute of Urology of Hubei Province, Wuhan 430030, China.,Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Wuhan 430030, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430030, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430030, China
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