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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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Advani R, Luzzi S, Scott E, Dalgliesh C, Weischenfeldt J, Munkley J, Elliott DJ. Epithelial specific splicing regulator proteins as emerging oncogenes in aggressive prostate cancer. Oncogene 2023; 42:3161-3168. [PMID: 37752235 PMCID: PMC10589096 DOI: 10.1038/s41388-023-02838-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
Prostate cancer progression is connected to the activity of conventional oncogenes and tumour suppressors and driven by circulating steroid hormones. A key issue has been how to identify and care for aggressively developing prostate tumours. Here we discuss how expression of the splicing regulators ESRP1 and ESRP2, and how their role as "masterminds" of epithelial splicing patterns, have been identified as markers of aggressively proliferating prostate primary tumours. We suggest that the origin of prostate cancer within epithelial cells, and the subsequent association of ESRP1 and ESRP2 expression with more aggressive disease progression, identify ESRP1 and ESRP2 as lineage survival oncogenes. To move this field on in the future it will be important to identify the gene expression targets controlled by ESRP1/2 that regulate prostate cancer proliferation. Potential future therapies could be designed to target ESRP1 and ESRP2 protein activity or their regulated splice isoforms in aggressive prostate tumours. Design of these therapies is potentially complicated by the risk of producing a more mesenchymal splicing environment that might promote tumour metastasis.
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Affiliation(s)
- Rahul Advani
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Sara Luzzi
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Emma Scott
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Caroline Dalgliesh
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer Munkley
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - David J Elliott
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom.
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3
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Belluti S, Imbriano C, Casarini L. Nuclear Estrogen Receptors in Prostate Cancer: From Genes to Function. Cancers (Basel) 2023; 15:4653. [PMID: 37760622 PMCID: PMC10526871 DOI: 10.3390/cancers15184653] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Estrogens are almost ubiquitous steroid hormones that are essential for development, metabolism, and reproduction. They exert both genomic and non-genomic action through two nuclear receptors (ERα and ERβ), which are transcription factors with disregulated functions and/or expression in pathological processes. In the 1990s, the discovery of an additional membrane estrogen G-protein-coupled receptor augmented the complexity of this picture. Increasing evidence elucidating the specific molecular mechanisms of action and opposing effects of ERα and Erβ was reported in the context of prostate cancer treatment, where these issues are increasingly investigated. Although new approaches improved the efficacy of clinical therapies thanks to the development of new molecules targeting specifically estrogen receptors and used in combination with immunotherapy, more efforts are needed to overcome the main drawbacks, and resistance events will be a challenge in the coming years. This review summarizes the state-of-the-art on ERα and ERβ mechanisms of action in prostate cancer and promising future therapies.
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Affiliation(s)
- Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (C.I.)
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (C.I.)
| | - Livio Casarini
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Ospedale di Baggiovara, 41126 Modena, Italy
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Biernacka KM, Barker R, Sewell A, Bahl A, Perks CM. A role for androgen receptor variant 7 in sensitivity to therapy: Involvement of IGFBP-2 and FOXA1. Transl Oncol 2023; 34:101698. [PMID: 37307644 PMCID: PMC10276180 DOI: 10.1016/j.tranon.2023.101698] [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: 03/29/2023] [Revised: 05/10/2023] [Accepted: 05/21/2023] [Indexed: 06/14/2023] Open
Abstract
Prostate cancer (PCa) is one of the leading causes of cancer-related deaths in men. Localised PCa can be treated effectively, but most patients relapse/progress to more aggressive disease. One possible mechanism underlying this progression is alternative splicing of the androgen receptor, with AR variant 7(ARV7) considered to play a major role. Using viability assays, we confirmed that ARV7-positive PCa cells were less sensitive to treatment with cabazitaxel and an anti-androgen-enzalutamide. Also, using live-holographic imaging, we showed that PCa cells with ARV7 exhibited an increased rate of cell division, proliferation, and motility, which could potentially contribute to a more aggressive phenotype. Furthermore, protein analysis demonstrated that ARV7 knock-down was associated with a decrease in insulin-like growth factor-2 (IGFBP-2) and forkhead box protein A1(FOXA1). This correlation was confirmed in-vivo using PCa tissue samples. Spearman rank correlation analysis showed significant positive associations between ARV7 and IGFBP-2 or FOXA1 in tissue from patients with PCa. This association was not present with the AR. These data suggest an interplay of FOXA1 and IGFBP-2 with ARV7-mediated acquisition of an aggressive prostate cancer phenotype.
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Affiliation(s)
- K M Biernacka
- Cancer Endocrinology Group, Translational Health Sciences, University of Bristol Southmead Hospital, BS10 5NB, Bristol, UK
| | - R Barker
- Cancer Endocrinology Group, Translational Health Sciences, University of Bristol Southmead Hospital, BS10 5NB, Bristol, UK
| | - A Sewell
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - A Bahl
- Bristol Haematology and Oncology Centre, Department of Clinical Oncology, University Hospitals Bristol, Bristol BS2 8ED, UK
| | - C M Perks
- Cancer Endocrinology Group, Translational Health Sciences, University of Bristol Southmead Hospital, BS10 5NB, Bristol, UK.
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Sun Y, Bae YE, Zhu J, Zhang Z, Zhong H, Cheng C, Deng Y, Wu C, Wu L. A Splicing Transcriptome-Wide Association Study Identifies Candidate Altered Splicing for Prostate Cancer Risk. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:372-380. [PMID: 37486714 DOI: 10.1089/omi.2023.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Prostate cancer (PCa) represents a huge public health burden among men. Many susceptibility genetic factors for PCa still remain unknown. In this study, we performed a large splicing transcriptome-wide association study (spTWAS) using three modeling strategies to develop alternative splicing genetic prediction models for identifying novel susceptibility loci and splicing introns for PCa risk by assessing 79,194 cases and 61,112 controls of European ancestry in the PRACTICAL, CRUK, CAPS, BPC3, and PEGASUS consortia. We identified 120 splicing introns of 97 genes showing an association with PCa risk at false discovery rate (FDR)-corrected threshold (FDR <0.05). Of them, 33 genes were enriched in PCa-related diseases and function categories. Fine-mapping analysis suggested that 21 splicing introns of 19 genes were likely causally associated with PCa risk. Thirty-five splicing introns of 34 novel genes were identified to be related to PCa susceptibility for the first time, and 11 of the genes were enriched in a cancer-related network. Our study identified novel loci and splicing introns associated with PCa risk, which can improve our understanding of the etiology of this common malignancy.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Longyan University, Longyan, P.R. China
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, P.R. China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, P.R. China
| | - Ye Eun Bae
- Department of Statistics, Florida State University, Tallahassee, Florida, USA
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Zichen Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Chunmei Cheng
- College of Life Science, Longyan University, Longyan, P.R. China
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
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Horn T, Gosliga A, Li C, Enculescu M, Legewie S. Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing. NPJ Syst Biol Appl 2023; 9:1. [PMID: 36653378 PMCID: PMC9849329 DOI: 10.1038/s41540-022-00264-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/08/2022] [Indexed: 01/19/2023] Open
Abstract
Alternative splicing is an important step in eukaryotic mRNA pre-processing which increases the complexity of gene expression programs, but is frequently altered in disease. Previous work on the regulation of alternative splicing has demonstrated that splicing is controlled by RNA-binding proteins (RBPs) and by epigenetic DNA/histone modifications which affect splicing by changing the speed of polymerase-mediated pre-mRNA transcription. The interplay of these different layers of splicing regulation is poorly understood. In this paper, we derived mathematical models describing how splicing decisions in a three-exon gene are made by combinatorial spliceosome binding to splice sites during ongoing transcription. We additionally take into account the effect of a regulatory RBP and find that the RBP binding position within the sequence is a key determinant of how RNA polymerase velocity affects splicing. Based on these results, we explain paradoxical observations in the experimental literature and further derive rules explaining why the same RBP can act as inhibitor or activator of cassette exon inclusion depending on its binding position. Finally, we derive a stochastic description of co-transcriptional splicing regulation at the single-cell level and show that splicing outcomes show little noise and follow a binomial distribution despite complex regulation by a multitude of factors. Taken together, our simulations demonstrate the robustness of splicing outcomes and reveal that quantitative insights into kinetic competition of co-transcriptional events are required to fully understand this important mechanism of gene expression diversity.
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Affiliation(s)
- Timur Horn
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Alison Gosliga
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany ,grid.5719.a0000 0004 1936 9713University of Stuttgart, Department of Systems Biology and Stuttgart Research Center Systems Biology (SRCSB), Allmandring 31, 70569 Stuttgart, Germany
| | - Congxin Li
- grid.5719.a0000 0004 1936 9713University of Stuttgart, Department of Systems Biology and Stuttgart Research Center Systems Biology (SRCSB), Allmandring 31, 70569 Stuttgart, Germany
| | - Mihaela Enculescu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany. .,University of Stuttgart, Department of Systems Biology and Stuttgart Research Center Systems Biology (SRCSB), Allmandring 31, 70569, Stuttgart, Germany.
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Alternatively Spliced Isoforms of MUC4 and ADAM12 as Biomarkers for Colorectal Cancer Metastasis. J Pers Med 2023; 13:jpm13010135. [PMID: 36675796 PMCID: PMC9861497 DOI: 10.3390/jpm13010135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/13/2023] Open
Abstract
There is a pertinent need to develop prognostic biomarkers for practicing predictive, preventive and personalized medicine (PPPM) in colorectal cancer metastasis. The analysis of isoform expression data governed by alternative splicing provides a high-resolution picture of mRNAs in a defined condition. This information would not be available by studying gene expression changes alone. Hence, we utilized our prior data from an exon microarray and found ADAM12 and MUC4 to be strong biomarker candidates based on their alternative splicing scores and pattern. In this study, we characterized their isoform expression in a cell line model of metastatic colorectal cancer (SW480 & SW620). These two genes were found to be good prognostic indicators in two cohorts from The Cancer Genome Atlas database. We studied their exon structure using sequence information in the NCBI and ENSEMBL genome databases to amplify and validate six isoforms each for the ADAM12 and MUC4 genes. The differential expression of these isoforms was observed between normal, primary and metastatic colorectal cancer cell lines. RNA-Seq analysis further proved the differential expression of the gene isoforms. The isoforms of MUC4 and ADAM12 were found to change expression levels in response to 5-Fluorouracil (5-FU) treatment in a dose-, time- and cell line-dependent manner. Furthermore, we successfully detected the protein isoforms of ADAM12 and MUC4 in cell lysates, reflecting the differential expression at the protein level. The change in the mRNA and protein expression of MUC4 and ADAM12 in primary and metastatic cells and in response to 5-FU qualifies them to be studied as potential biomarkers. This comprehensive study underscores the importance of studying alternatively spliced isoforms and their potential use as prognostic and/or predictive biomarkers in the PPPM approach towards cancer.
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8
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Lelong EIJ, Khelifi G, Adjibade P, Joncas FH, Grenier St-Sauveur V, Paquette V, Gris T, Zoubeidi A, Audet-Walsh E, Lambert JP, Toren P, Mazroui R, Hussein SMI. Prostate cancer resistance leads to a global deregulation of translation factors and unconventional translation. NAR Cancer 2022; 4:zcac034. [PMID: 36348939 PMCID: PMC9634437 DOI: 10.1093/narcan/zcac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Emerging evidence associates translation factors and regulators to tumorigenesis. However, our understanding of translational changes in cancer resistance is still limited. Here, we generated an enzalutamide-resistant prostate cancer (PCa) model, which recapitulated key features of clinical enzalutamide-resistant PCa. Using this model and poly(ribo)some profiling, we investigated global translation changes that occur during acquisition of PCa resistance. We found that enzalutamide-resistant cells exhibit an overall decrease in mRNA translation with a specific deregulation in the abundance of proteins involved in mitochondrial processes and in translational regulation. However, several mRNAs escape this translational downregulation and are nonetheless bound to heavy polysomes in enzalutamide-resistant cells suggesting active translation. Moreover, expressing these corresponding genes in enzalutamide-sensitive cells promotes resistance to enzalutamide treatment. We also found increased association of long non-coding RNAs (lncRNAs) with heavy polysomes in enzalutamide-resistant cells, suggesting that some lncRNAs are actively translated during enzalutamide resistance. Consistent with these findings, expressing the predicted coding sequences of known lncRNAs JPX, CRNDE and LINC00467 in enzalutamide-sensitive cells drove resistance to enzalutamide. Taken together, this suggests that aberrant translation of specific mRNAs and lncRNAs is a strong indicator of PCa enzalutamide resistance, which points towards novel therapeutic avenues that may target enzalutamide-resistant PCa.
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Affiliation(s)
- Emeline I J Lelong
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Gabriel Khelifi
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Pauline Adjibade
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - France-Hélène Joncas
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Valérie Grenier St-Sauveur
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Virginie Paquette
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Endocrinology and Nephrology Division , Quebec City, Québec G1V 4G2, Canada
| | - Typhaine Gris
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, Faculty of Medicine, University of British Columbia , Vancouver, British Columbia V6H 3Z6, Canada
| | - Etienne Audet-Walsh
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Endocrinology and Nephrology Division , Quebec City, Québec G1V 4G2, Canada
| | - Jean-Philippe Lambert
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Endocrinology and Nephrology Division , Quebec City, Québec G1V 4G2, Canada
| | - Paul Toren
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Rachid Mazroui
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
| | - Samer M I Hussein
- Cancer Research Center, Université Laval , Quebec City, Québec G1R 3S3, Canada
- CHU of Québec-Université Laval Research Center, Oncology Division , Quebec City, Québec G1R 3S3, Canada
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Forouzesh F, Kia FS, Nazemalhosseini-Mojarad E. BidSi6 and BidEL isoforms as a potential marker for predicting colorectal adenomatous polyps. BMC Med Genomics 2022; 15:129. [PMID: 35668495 PMCID: PMC9172139 DOI: 10.1186/s12920-022-01282-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 06/02/2022] [Indexed: 11/26/2022] Open
Abstract
Background As a well-known protein, Bid links the extrinsic and intrinsic apoptotic pathways and plays important roles in cell proliferation. In this study, we evaluated the expression of two isoforms of the Bid gene (BidSi6 and BidEL) in colorectal adenomatous polyps as a biomarker and investigated the relationship between their expression levels with clinicopathological factors. Methods The expression of BidSi6 and BidEL isoforms in 22 pairs of Adenomatous polyps and adjust non-polyp tissues was measured by qReal-Time PCR and compared with 10 normal colon tissues. ROC curve was performed to examine the diagnostic capacity. Also, sequencing was performed for molecular identification of BidSi6 isoform in adenomatous polyp. Results Our results showed that BidSi6 and BidEL isoforms were significantly overexpressed in Adenomatous polyps and non-polyp adjacent tissues from the same patients compared to that in normal colon tissues, but there was no significant expression between polyps and adjust non-polyp tissues. There were no significant correlations between the expression of two isoforms and other features of clinicopathology. The area under the curve of BidSi6 and BidEL isoforms indicated powerful diagnostic capability. The phylogenetic tree was constructed based on the sequence of idSi6 isoform, and the results showed that adenomatous polyp tissue and adjust non-polyp tissue were separated from healthy colorectal tissue and reference sequence (EU678292). Conclusions These findings suggest that BidSi6 and BidEL isoforms can be used as new potential biomarkers in adenomatous polyps. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01282-0.
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Affiliation(s)
- Flora Forouzesh
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, P.O. Box: 193951495, Tehran, Iran.
| | - Fatemeh Sadat Kia
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, P.O. Box: 193951495, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Department of Cancer, Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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10
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Mehterov N, Kazakova M, Sbirkov Y, Vladimirov B, Belev N, Yaneva G, Todorova K, Hayrabedyan S, Sarafian V. Alternative RNA Splicing-The Trojan Horse of Cancer Cells in Chemotherapy. Genes (Basel) 2021; 12:genes12071085. [PMID: 34356101 PMCID: PMC8306420 DOI: 10.3390/genes12071085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Almost all transcribed human genes undergo alternative RNA splicing, which increases the diversity of the coding and non-coding cellular landscape. The resultant gene products might have distinctly different and, in some cases, even opposite functions. Therefore, the abnormal regulation of alternative splicing plays a crucial role in malignant transformation, development, and progression, a fact supported by the distinct splicing profiles identified in both healthy and tumor cells. Drug resistance, resulting in treatment failure, still remains a major challenge for current cancer therapy. Furthermore, tumor cells often take advantage of aberrant RNA splicing to overcome the toxicity of the administered chemotherapeutic agents. Thus, deciphering the alternative RNA splicing variants in tumor cells would provide opportunities for designing novel therapeutics combating cancer more efficiently. In the present review, we provide a comprehensive outline of the recent findings in alternative splicing in the most common neoplasms, including lung, breast, prostate, head and neck, glioma, colon, and blood malignancies. Molecular mechanisms developed by cancer cells to promote oncogenesis as well as to evade anticancer drug treatment and the subsequent chemotherapy failure are also discussed. Taken together, these findings offer novel opportunities for future studies and the development of targeted therapy for cancer-specific splicing variants.
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Affiliation(s)
- Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Yordan Sbirkov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Nikolay Belev
- Medical Simulation and Training Center, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Galina Yaneva
- Department of Biology, Faculty of Pharmacy, Medical University of Varna, 9002 Varna, Bulgaria;
| | - Krassimira Todorova
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Soren Hayrabedyan
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +359-882-512-952
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The Function and Prognostic Value of RNA-Binding Proteins in Colorectal Adenocarcinoma Were Analyzed Based on Bioinformatics of Smart Medical Big Data. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:5536330. [PMID: 34188789 PMCID: PMC8192207 DOI: 10.1155/2021/5536330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/10/2021] [Indexed: 12/02/2022]
Abstract
Colon cancer is the third most frequent cancer in the world and is mainly adenocarcinoma in terms of pathological type. It has been confirmed that the dysregulation of RNA-binding proteins (RBPs) significantly participates in the occurrence and development of numerous malignant tumors. Therefore, we analyzed the RBPs associated with colon adenocarcinoma (COAD) to assess their possible biological effects and prognostic value. A total of 398 COAD tissue datasets and 39 normal tissue datasets were retrieved from the TCGA data resource and screened out the RBPs, which are differentially expressed between tumor tissues and nontumor tissues. Then, bioinformatics analyses based on smart medical big data were conducted on these RBPs. Overall, 181 differentially expressed RBPs were uncovered, consisting of 121 upregulated RBPs and 60 downregulated RBPs. Finally, we selected 7 prognostic-related RBPs with research prospects and constructed a prognostic model according to the median risk score. There were remarkable differences in OS between the high-risk and low-risk groups. In addition, the performance of the prognostic model was evaluated and verified with other COAD patient data in the TCGA database. The results showed that the area under the ROC curve (AUC) for the train group was 0.744 and the one for the test group was 0.661, confirming that the model assesses patients' prognosis to some extent. And based on 7 hub RBPs, we constructed a nomogram as a reference for evaluating the survival rate of COAD patients.
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12
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Identification of prognostic and metastasis-related alternative splicing signatures in hepatocellular carcinoma. Biosci Rep 2021; 40:225701. [PMID: 32627826 PMCID: PMC7364508 DOI: 10.1042/bsr20201001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/23/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
As the most common neoplasm in digestive system, hepatocellular carcinoma (HCC) is one of the most important leading cause of cancer deaths worldwide. Its high-frequency metastasis and relapse rate lead to the poor survival of HCC patients. However, the mechanism of HCC metastasis is still unclear. Alternative splicing events (ASEs) have a great effect in cancer development, progression and metastasis. We downloaded RNA sequencing and seven types of ASEs data of HCC samples, in order to explore the mechanism of ASEs underlying tumorigenesis and metastasis of HCC. The data were taken from the The Cancer Genome Atlas (TCGA) and TCGASpliceSeq databases. Univariate Cox regression analysis was used to determine a total of 3197 overall survival-related ASEs (OS-SEs). And based on five OS-SEs screened by Lasso regression, we constructed a prediction model with the Area Under Curve of 0.765. With a good reliability of the model, the risk score was also proved to be an independent predictor. Among identified 390 candidate SFs, Y-box protein 3 (YBX3) was significantly correlated with OS and metastasis. Among 177 ASEs, ATP-binding cassette subfamily A member 6 (ABCA6)-43162-AT and PLIN5-46808-AT were identified both associated with OS, bone metastasis and co-expressed with SFs. Then we identified primary bile acid biosynthesis as survival-related (KEGG) pathway by Gene Set Variation Analysis (GSVA) and univariate regression analysis, which was correlated with ABCA6-43162-AT and PLIN5-46808-AT. Finally, we proposed that ABCA6-43162-AT and PLIN5-46808-AT may contribute to HCC poor prognosis and metastasis under the regulation of aberrant YBX3 through the pathway of primary bile acid biosynthesis.
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13
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Yao J, Tang YC, Yi B, Yang J, Chai Y, Yin N, Zhang ZX, Wei YJ, Li DC, Zhou J. Signature of gene aberrant alternative splicing events in pancreatic adenocarcinoma prognosis. J Cancer 2021; 12:3164-3179. [PMID: 33976726 PMCID: PMC8100795 DOI: 10.7150/jca.48661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS), as an effective and universal mechanism of transcriptional regulation, is involved in the development and progression of cancer. Therefore, systematic analysis of alternative splicing in pancreatic adenocarcinoma (PAAD) is warranted. The corresponding clinical information of the RNA-Seq data and PAAD cohort was downloaded from the TCGA data portal. Then, a java application, SpliceSeq, was used to evaluate the RNA splicing pattern and calculate the splicing percentage index (PSI). Differentially expressed AS events (DEAS) were identified based on PSI values between PAAD cancer samples and normal samples of adjacent tissues. Kaplan-Meier and Cox regression analyses were used to assess the association between DEAS and patient clinical characteristics. Unsupervised cluster analysis used to reveal four clusters with different survival patterns. At the same time, GEO and TCGA combined with GTEx to verify the differential expression of AS gene and splicing factor. After rigorous filtering, a total of 45,313 AS events were identified, 1,546 of which were differentially expressed AS events. Nineteen DEAS were found to be associated with OS with a five-year overall survival rate of 0.946. And the subtype clusters results indicate that there are differences in the nature of individual AS that affect clinical outcomes. Results also identified 15 splicing factors associated with the prognosis of PAAD. And the splicing factors ESRP1 and RBM5 played an important role in the PAAD-associated AS events. The PAAD-associated AS events, splicing networks, and clusters identified in this study are valuable for deciphering the underlying mechanisms of AS in PAAD and may facilitate the establishment of therapeutic goals for further validation.
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Affiliation(s)
- Jun Yao
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yu-Chen Tang
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Bin Yi
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Jian Yang
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yun Chai
- Department of Plastic Surgery, Suzhou Municipal Hospital, Suzhou, Jiangsu, 215006, China
| | - Ni Yin
- Department of Oncology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Zi-Xiang Zhang
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yi-Jun Wei
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - De-Chun Li
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Jian Zhou
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
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14
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Yuan P, Ling L, Gao X, Sun T, Miao J, Yuan X, Liu J, Wang Z, Liu B. Identification of RNA-binding protein SNRPA1 for prognosis in prostate cancer. Aging (Albany NY) 2021; 13:2895-2911. [PMID: 33460399 PMCID: PMC7880319 DOI: 10.18632/aging.202387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023]
Abstract
Prostate cancer is one of the deadliest cancers in men. RNA-binding proteins play a critical role in human cancers; however, whether they have a significant effect on the prognosis of prostate cancer has yet to be elucidated. In the present study, we performed a comprehensive analysis of RNA sequencing and clinical data from the Cancer Genome Atlas dataset and obtained differentially expressed RNA-binding proteins between prostate cancer and benign tissues. We constructed a protein-protein interaction network and Cox regression analyses were conducted to identify prognostic hub RNA-binding proteins. SNRPA1 was associated with the highest risk of poor prognosis and was therefore selected for further analysis. SNRPA1 expression was positively correlated with Gleason score and pathological TNM stage in prostate cancer patients. Furthermore, the expression profile of SNRPA1 was validated using the Oncomine, Human Protein Atlas, and Cancer Cell Line Encyclopedia databases. Meanwhile, the prognostic profile of SNRPA1 was successfully verified in GSE70769. Additionally, the results of molecular experiments revealed the proliferative role of SNRPA1 in prostate cancer cells. In summary, our findings evidenced a relationship between RNA-binding proteins and prostate cancer and indicated the prognostic significance of SNRPA1 in prostate cancer.
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Affiliation(s)
- Penghui Yuan
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Le Ling
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xintao Gao
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Taotao Sun
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Jianping Miao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Jihong Liu
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Zhihua Wang
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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15
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Androgen receptor and its splice variant, AR-V7, differentially induce mRNA splicing in prostate cancer cells. Sci Rep 2021; 11:1393. [PMID: 33446905 PMCID: PMC7809134 DOI: 10.1038/s41598-021-81164-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer (PCa) is dependent on the androgen receptor (AR). Advanced PCa is treated with an androgen deprivation therapy-based regimen; tumors develop resistance, although they typically remain AR-dependent. Expression of constitutively active AR variants lacking the ligand-binding domain including the variant AR-V7 contributes to this resistance. AR and AR-V7, as transcription factors, regulate many of the same genes, but also have unique activities. In this study, the capacity of the two AR isoforms to regulate splicing was examined. RNA-seq data from models that endogenously express AR and express AR-V7 in response to doxycycline were used. Both AR isoforms induced multiple changes in splicing and many changes were isoform-specific. Analyses of two endogenous genes, PGAP2 and TPD52, were performed to examine differential splicing. A novel exon that appears to be a novel transcription start site was preferentially induced by AR-V7 in PGAP2 although it is induced to a lesser extent by AR. The previously described AR induced promoter 2 usage that results in a novel protein derived from TPD52 (PrLZ) was not induced by AR-V7. AR, but not AR-V7, bound to a site proximal to promoter 2, and induction was found to depend on FOXA1.
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16
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Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
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17
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Králíčková M, Vetvicka V, Laganà AS. Endometrial cancer-is our knowledge changing? Transl Cancer Res 2020; 9:7734-7745. [PMID: 35117376 PMCID: PMC8798081 DOI: 10.21037/tcr-20-1720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 04/29/2020] [Indexed: 11/27/2022]
Abstract
In developed countries, endometrial cancer (EC) is the most frequent gynecologic malignancy in postmenopausal women. At the same time, EC has become one of the most common cancers in numerous developing countries, probably influenced by global epidemic of obesity. The majority of patients have low-grade endometrioid cancer with a high 5-year survival rate, but with high-risk EC, the survival rates are still rather low. However, despite intensive research in last decades, our knowledge of the mechanisms, risk factors, diagnosis and treatment have not significantly improved. The standard treatment of all types of EC is still a traditional combination of surgery, irradiation and/or chemotherapy, despite the fact that each of these options is not without having some negative side effects. Despite the fact that on the molecular level, EC is relatively well-studied, but the efforts to transform these findings into either diagnosis or therapies of EC remain elusive. In addition, some research into risk factors involved in the development or progression of EC seems to be more a fishing expedition than a well thought-out approach. The purpose of this review is to summarize the most recent developments in the search for biomarkers and prognostic markers and to discuss the progress in EC treatment.
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Affiliation(s)
- Milena Králíčková
- Department of Histology and Embryology, Faculty of Medicine, Charles University, Karlovarska 48, Plzen, Czech Republic.,Department of Obstetrics and Gynecology, University Hospital, Faculty of Medicine, Charles University, Alej Svobody 80, Plzen, Czech Republic.,Biomedical Centre, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic
| | - Vaclav Vetvicka
- Department of Pathology, University of Louisville, Louisville, KY, USA
| | - Antonio Simone Laganà
- Department of Obstetrics and Gynecology, "Filippo Del Ponte" Hospital, University of Insubria, Piazza Biroldi 1, Varese, Italy
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18
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Oh J, Liu Y, Choi N, Ha J, Pradella D, Ghigna C, Zheng X, Shen H. Opposite Roles of Tra2β and SRSF9 in the v10 Exon Splicing of CD44. Cancers (Basel) 2020; 12:cancers12113195. [PMID: 33143085 PMCID: PMC7692347 DOI: 10.3390/cancers12113195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023] Open
Abstract
CD44 is a transmembrane glycoprotein involved in cell-cell and cell-matrix interactions. Several CD44 protein isoforms are generated in human through alternative splicing regulation of nine variable exons encoding for the extracellular juxta-membrane region. While the CD44 splicing variants have been described to be involved in cancer progression and development, the regulatory mechanism(s) underlying their production remain unclear. Here, we identify Tra2β and SRSF9 as proteins with opposite roles in regulating CD44 exon v10 splicing. While Tra2β promotes v10 inclusion, SRSF9 inhibits its inclusion. Mechanistically, we found that both proteins are able to target v10 exon, with GAAGAAG sequence being the binding site for Tra2β and AAGAC that for SRSF9. Collectively, our data add a novel layer of complexity to the sequential series of events involved in the regulation of CD44 splicing.
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Affiliation(s)
- Jagyeong Oh
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.L.); (N.C.); (J.H.)
| | - Yongchao Liu
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.L.); (N.C.); (J.H.)
| | - Namjeong Choi
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.L.); (N.C.); (J.H.)
| | - Jiyeon Ha
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.L.); (N.C.); (J.H.)
| | - Davide Pradella
- Istituto di Genetica Molecolare Luigi Luca Cavalli Sforza-Consiglio Nazionale delle Ricerche Via Abbiategrasso 207, 27100 Pavia, Italy; (D.P.); (C.G.)
| | - Claudia Ghigna
- Istituto di Genetica Molecolare Luigi Luca Cavalli Sforza-Consiglio Nazionale delle Ricerche Via Abbiategrasso 207, 27100 Pavia, Italy; (D.P.); (C.G.)
| | - Xuexiu Zheng
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.L.); (N.C.); (J.H.)
- Correspondence: (X.Z.); (H.S.); Tel.: +82-62-715-2520 (X.Z.); +82-62-715-2507 (H.S.); Fax: +82-62-715-2484 (X.Z.); +82-62-715-2484 (H.S.)
| | - Haihong Shen
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.L.); (N.C.); (J.H.)
- Correspondence: (X.Z.); (H.S.); Tel.: +82-62-715-2520 (X.Z.); +82-62-715-2507 (H.S.); Fax: +82-62-715-2484 (X.Z.); +82-62-715-2484 (H.S.)
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19
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Sciarrillo R, Wojtuszkiewicz A, Assaraf YG, Jansen G, Kaspers GJL, Giovannetti E, Cloos J. The role of alternative splicing in cancer: From oncogenesis to drug resistance. Drug Resist Updat 2020; 53:100728. [PMID: 33070093 DOI: 10.1016/j.drup.2020.100728] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022]
Abstract
Alternative splicing is a tightly regulated process whereby non-coding sequences of pre-mRNA are removed and protein-coding segments are assembled in diverse combinations, ultimately giving rise to proteins with distinct or even opposing functions. In the past decade, whole genome/transcriptome sequencing studies revealed the high complexity of splicing regulation, which occurs co-transcriptionally and is influenced by chromatin status and mRNA modifications. Consequently, splicing profiles of both healthy and malignant cells display high diversity and alternative splicing was shown to be widely deregulated in multiple cancer types. In particular, mutations in pre-mRNA regulatory sequences, splicing regulators and chromatin modifiers, as well as differential expression of splicing factors are important contributors to cancer pathogenesis. It has become clear that these aberrations contribute to many facets of cancer, including oncogenic transformation, cancer progression, response to anticancer drug treatment as well as resistance to therapy. In this respect, alternative splicing was shown to perturb the expression a broad spectrum of relevant genes involved in drug uptake/metabolism (i.e. SLC29A1, dCK, FPGS, and TP), activation of nuclear receptor pathways (i.e. GR, AR), regulation of apoptosis (i.e. MCL1, BCL-X, and FAS) and modulation of response to immunotherapy (CD19). Furthermore, aberrant splicing constitutes an important source of novel cancer biomarkers and the spliceosome machinery represents an attractive target for a novel and rapidly expanding class of therapeutic agents. Small molecule inhibitors targeting SF3B1 or splice factor kinases were highly cytotoxic against a wide range of cancer models, including drug-resistant cells. Importantly, these effects are enhanced in specific cancer subsets, such as splicing factor-mutated and c-MYC-driven tumors. Furthermore, pre-clinical studies report synergistic effects of spliceosome modulators in combination with conventional antitumor agents. These strategies based on the use of low dose splicing modulators could shift the therapeutic window towards decreased toxicity in healthy tissues. Here we provide an extensive overview of the latest findings in the field of regulation of splicing in cancer, including molecular mechanisms by which cancer cells harness alternative splicing to drive oncogenesis and evade anticancer drug treatment as well as splicing-based vulnerabilities that can provide novel treatment opportunities. Furthermore, we discuss current challenges arising from genome-wide detection and prediction methods of aberrant splicing, as well as unravelling functional relevance of the plethora of cancer-related splicing alterations.
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Affiliation(s)
- Rocco Sciarrillo
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Anna Wojtuszkiewicz
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Gerrit Jansen
- Amsterdam Immunology and Rheumatology Center, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Gertjan J L Kaspers
- Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Fondazione Pisana per la Scienza, Pisa, Italy
| | - Jacqueline Cloos
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands.
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20
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Jing L, Feng L, Zhou Z, Shi S, Deng R, Wang Z, Zhang Y, Ren Z, Liu Y. TNNT2 as a potential biomarker for the progression and prognosis of colorectal cancer. Oncol Rep 2020; 44:628-636. [PMID: 32627044 PMCID: PMC7336514 DOI: 10.3892/or.2020.7637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. At present, there are limited effective biomarkers of CRC. The present study aimed to identify potential signatures associated with the tumorigenesis and prognosis of CRC using publicly available databases, and further validate the identified biomarkers in CRC cell lines. Identification of differentially expressed mRNAs between CRC and paracancerous samples was conducted based on data from The Cancer Genome Atlas (TCGA; 471 tumor samples and 41 normal samples). Survival analysis was performed to explore the prognostic value of troponin 2 (TNNT2) in the TCGA training set, which was further validated in an external dataset, GSE17531. Functional enrichment analysis was conducted to determine the possible biological functions using GSEA 3.0. Reverse transcription-quantitative PCR (RT-qPCR) and western blotting were utilized to detect the mRNA and protein expression levels of TNNT2 between CRC and normal colorectal cells. Immunohistochemistry was performed to detect the protein expression of TNNT2 in CRC and normal tissues. TNNT2 was significantly upregulated in CRC samples compared with adjacent normal samples in the TCGA dataset. Increased expression of TNNT2 was associated with inferior prognosis in the TCGA training dataset and GSE17531 validation dataset. Functional enrichment analysis revealed that the ErbB signaling pathway and glycerophospholipid metabolism pathway were significantly activated in the TNNT2 high expression group. Overexpression of TNNT2 mRNA and TNNT2 protein in CRC tumor cells was confirmed by RT-qPCR and western blotting, respectively. Immunohistochemistry indicated increased protein expression levels of TNNT2 in CRC tissues in comparison with normal tissues. TNNT2 was associated with the tumorigenesis and prognosis of CRC, which may be useful for novel biomarker identification and targeted therapeutic strategy development.
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Affiliation(s)
- Li Jing
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Li Feng
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhiguo Zhou
- Department of Radiotherapy, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Shuai Shi
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Ruoying Deng
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhicong Wang
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Yi Zhang
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhixue Ren
- The Seven People's Hospital of Hebei Province, Dingzhou, Hebei 073000, P.R. China
| | - Yibing Liu
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
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21
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Ardura JA, Álvarez-Carrión L, Gutiérrez-Rojas I, Alonso V. Role of Calcium Signaling in Prostate Cancer Progression: Effects on Cancer Hallmarks and Bone Metastatic Mechanisms. Cancers (Basel) 2020; 12:E1071. [PMID: 32344908 PMCID: PMC7281772 DOI: 10.3390/cancers12051071] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022] Open
Abstract
Advanced prostate cancers that progress to tumor metastases are often considered incurable or difficult to treat. The etiology of prostate cancers is multi-factorial. Among other factors, de-regulation of calcium signals in prostate tumor cells mediates several pathological dysfunctions associated with tumor progression. Calcium plays a relevant role on tumor cell death, proliferation, motility-invasion and tumor metastasis. Calcium controls molecular factors and signaling pathways involved in the development of prostate cancer and its progression. Such factors and pathways include calcium channels and calcium-binding proteins. Nevertheless, the involvement of calcium signaling on prostate cancer predisposition for bone tropism has been relatively unexplored. In this regard, a diversity of mechanisms triggers transient accumulation of intracellular calcium in prostate cancer cells, potentially favoring bone metastases development. New therapies for the treatment of prostate cancer include compounds characterized by potent and specific actions that target calcium channels/transporters or pumps. These novel drugs for prostate cancer treatment encompass calcium-ATPase inhibitors, voltage-gated calcium channel inhibitors, transient receptor potential (TRP) channel regulators or Orai inhibitors. This review details the latest results that have evaluated the relationship between calcium signaling and progression of prostate cancer, as well as potential therapies aiming to modulate calcium signaling in prostate tumor progression.
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Affiliation(s)
- Juan A. Ardura
- Bone Physiopathology laboratory, Applied Molecular Medicine Institute (IMMA), Universidad San Pablo-CEU, CEU Universities, Campus Monteprincipe, 28925 Alcorcón, Madrid, Spain; (J.A.A.); (L.Á.-C.); (I.G.-R.)
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Campus Monteprincipe, 28925 Alcorcón, Madrid, Spain
| | - Luis Álvarez-Carrión
- Bone Physiopathology laboratory, Applied Molecular Medicine Institute (IMMA), Universidad San Pablo-CEU, CEU Universities, Campus Monteprincipe, 28925 Alcorcón, Madrid, Spain; (J.A.A.); (L.Á.-C.); (I.G.-R.)
| | - Irene Gutiérrez-Rojas
- Bone Physiopathology laboratory, Applied Molecular Medicine Institute (IMMA), Universidad San Pablo-CEU, CEU Universities, Campus Monteprincipe, 28925 Alcorcón, Madrid, Spain; (J.A.A.); (L.Á.-C.); (I.G.-R.)
| | - Verónica Alonso
- Bone Physiopathology laboratory, Applied Molecular Medicine Institute (IMMA), Universidad San Pablo-CEU, CEU Universities, Campus Monteprincipe, 28925 Alcorcón, Madrid, Spain; (J.A.A.); (L.Á.-C.); (I.G.-R.)
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Campus Monteprincipe, 28925 Alcorcón, Madrid, Spain
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22
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Caggiano C, Pieraccioli M, Panzeri V, Sette C, Bielli P. c-MYC empowers transcription and productive splicing of the oncogenic splicing factor Sam68 in cancer. Nucleic Acids Res 2020; 47:6160-6171. [PMID: 31066450 PMCID: PMC6614821 DOI: 10.1093/nar/gkz344] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified the promoter region of the Sam68 gene (KHDRBS1) and the proto-oncogenic transcription factor c-MYC as a key regulator of Sam68 expression. Upregulation of Sam68 and c-MYC correlate in PCa patients. c-MYC directly binds to and activates the Sam68 promoter. Furthermore, c-MYC affects productive splicing of the nascent Sam68 transcript by modulating the transcriptional elongation rate within the gene. Importantly, c-MYC-dependent expression of Sam68 is under the tight control of external cues, such as androgens and/or mitogens. These findings uncover an unexpected coordination of transcription and splicing of Sam68 by c-MYC, which may represent a key step in PCa tumorigenesis.
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Affiliation(s)
- Cinzia Caggiano
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Marco Pieraccioli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Valentina Panzeri
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Science medical/chirurgic and translational medicine, University of Rome Sapienza,00189 Rome, Italy
| | - Claudio Sette
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy
| | - Pamela Bielli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
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23
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Wu F, Chen Q, Liu C, Duan X, Hu J, Liu J, Cao H, Li W, Li H. Profiles of prognostic alternative splicing signature in hepatocellular carcinoma. Cancer Med 2020; 9:2171-2180. [PMID: 31975560 PMCID: PMC7064038 DOI: 10.1002/cam4.2875] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/16/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Previous studies have demonstrated the role of abnormal alternative splicing (AS) in tumor progression. This study examines the prognostic index (PI) of alternative splices (ASs) in patients with hepatocellular carcinoma (HCC). The clinical features and splicing events of patients with HCC were downloaded from The Cancer Genome Atlas (TCGA). Differentially expressed AS (DEAS) were compared between HCC and adjacent normal samples. Univariate Cox regression analysis was used to determine changes in DEAS associated with overall survival (OS). A PI was generated from OS‐associated DEASs using Kaplan‐Meier curves, receiver operating characteristic (ROC) curves, multivariate Cox regression, and cluster analysis. Then, the correlation between DEASs and splicing factors was assessed, followed by functional and pathway enrichment analysis. We identified 34 163 ASs of 8985 genes in HCC, and 153 OS‐ASs were identified using univariate Cox regression analysis. Low‐ and high‐PI groups were determined based on the median “PI‐ALL” value according to significantly different survival (P = 2.2e − 16). The ROC curve of all PI (PI‐ALL) had an area under the curve (AUC) of 0.993 for survival status in patients with HCC. A potential regulatory network associated with prognosis of patients with HCC was established. Enrichment analysis also resulted in the identification of several pathways potentially associated with carcinogenesis and progression of HCC. Four clusters were identified that were associated with clinical features and prognosis. Our study generated comprehensive profiles of ASs in HCC. The interaction network and functional connections were used to elucidate the underlying mechanisms of AS in HCC.
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Affiliation(s)
- Fangming Wu
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Comprehensive Intervention, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Qifeng Chen
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chaojun Liu
- Biotherapy Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoran Duan
- Biotherapy Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinlong Hu
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Jian Liu
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Comprehensive Intervention, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Huicun Cao
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Comprehensive Intervention, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Wang Li
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hui Li
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Comprehensive Intervention, Zhengzhou University People's Hospital, Zhengzhou, China
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24
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Liu C, Guo T, Sakai A, Ren S, Fukusumi T, Ando M, Sadat S, Saito Y, Califano JA. A novel splice variant of LOXL2 promotes progression of human papillomavirus-negative head and neck squamous cell carcinoma. Cancer 2019; 126:737-748. [PMID: 31721164 DOI: 10.1002/cncr.32610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is one of the most frequently diagnosed cancers worldwide. LOXL2 demonstrates alternative splicing events in patients with human papillomavirus (HPV)-negative HNSCC. The current study explored the role of a dominant LOXL2 variant in HPV-negative HNSCC. METHODS Expression of the LOXL2 variant was analyzed using The Cancer Genome Atlas cohorts and validated using quantitative reverse transcriptase-polymerase chain reaction in a separate primary tumor set. The authors defined the effect of LOXL2 splice variants in assays for cell proliferation using a cell viability assay and colony formation assay. Cell migration and invasion were examined using a cell scratch assay and transwell cell migration and invasion assay in LOXL2 splice variant gain and loss of expression cells. Western blot analysis and gene set enrichment analysis were used to explore the potential mechanism of the LOXL2 splice variant in HPV-negative HNSCC. RESULTS Expression of a novel LOXL2 variant was found to be upregulated in The Cancer Genome Atlas HPV-negative HNSCC, and confirmed in the separate primary tumor validation set. Analyses of loss and gain of function demonstrated that this LOXL2 variant enhanced proliferation, migration, and invasion in HPV-negative HNSCC cells and activated the FAK/AKT pathway. A total of 837 upregulated and 820 downregulated genes and 526 upregulated and 124 downregulated pathways associated with LOXL2 variant expression were identified using gene set enrichment analysis, which helped in developing a better understanding of the networks activated by this LOXL2 variant in patients with HPV-negative HNSCC. CONCLUSIONS The novel LOXL2 variant can promote the progression of HPV-negative HNSCC, in part through FAK/AKT pathway activation, which may provide a new potential therapeutic target among patients with HPV-negative HNSCC.
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Affiliation(s)
- Chao Liu
- Moores Cancer Center, University of California at San Diego, San Diego, California.,Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Akihiro Sakai
- Moores Cancer Center, University of California at San Diego, San Diego, California
| | - Shuling Ren
- Moores Cancer Center, University of California at San Diego, San Diego, California.,Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Takahito Fukusumi
- Moores Cancer Center, University of California at San Diego, San Diego, California
| | - Mizuo Ando
- Moores Cancer Center, University of California at San Diego, San Diego, California
| | - Sayed Sadat
- Moores Cancer Center, University of California at San Diego, San Diego, California
| | - Yuki Saito
- Moores Cancer Center, University of California at San Diego, San Diego, California
| | - Joseph A Califano
- Moores Cancer Center, University of California at San Diego, San Diego, California.,Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California at San Diego, San Diego, California
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25
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Katsogiannou M, Boyer JB, Valdeolivas A, Remy E, Calzone L, Audebert S, Rocchi P, Camoin L, Baudot A. Integrative proteomic and phosphoproteomic profiling of prostate cell lines. PLoS One 2019; 14:e0224148. [PMID: 31675377 PMCID: PMC6824562 DOI: 10.1371/journal.pone.0224148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/06/2019] [Indexed: 12/15/2022] Open
Abstract
Background Prostate cancer is a major public health issue, mainly because patients relapse after androgen deprivation therapy. Proteomic strategies, aiming to reflect the functional activity of cells, are nowadays among the leading approaches to tackle the challenges not only of better diagnosis, but also of unraveling mechanistic details related to disease etiology and progression. Methods We conducted here a large SILAC-based Mass Spectrometry experiment to map the proteomes and phosphoproteomes of four widely used prostate cell lines, namely PNT1A, LNCaP, DU145 and PC3, representative of different cancerous and hormonal status. Results We identified more than 3000 proteins and phosphosites, from which we quantified more than 1000 proteins and 500 phosphosites after stringent filtering. Extensive exploration of this proteomics and phosphoproteomics dataset allowed characterizing housekeeping as well as cell-line specific proteins, phosphosites and functional features of each cell line. In addition, by comparing the sensitive and resistant cell lines, we identified protein and phosphosites differentially expressed in the resistance context. Further data integration in a molecular network highlighted the differentially expressed pathways, in particular migration and invasion, RNA splicing, DNA damage repair response and transcription regulation. Conclusions Overall, this study proposes a valuable resource toward the characterization of proteome and phosphoproteome of four widely used prostate cell lines and reveals candidates to be involved in prostate cancer progression for further experimental validation.
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Affiliation(s)
- Maria Katsogiannou
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- Obstetrics and Gynecology department, Hôpital Saint Joseph, Marseille, France
| | - Jean-Baptiste Boyer
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Alberto Valdeolivas
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- ProGeLife, Marseille, France
| | - Elisabeth Remy
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Laurence Calzone
- Mines Paris Tech, Institut Curie, PSL Research University, Paris, France
| | - Stéphane Audebert
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Palma Rocchi
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail: (PR); (LC); (AB)
| | - Luc Camoin
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail: (PR); (LC); (AB)
| | - Anaïs Baudot
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- * E-mail: (PR); (LC); (AB)
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26
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Luo J, Ye H, Hao L, Sun Y, Li R, Li Y, Yang Z. SRSFs mediate the function of AR in the ovarian granulosa cells of patients with PCOS. Genes Dis 2019; 8:94-109. [PMID: 33569518 PMCID: PMC7859457 DOI: 10.1016/j.gendis.2019.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/26/2019] [Accepted: 09/04/2019] [Indexed: 12/04/2022] Open
Abstract
Ovarian hyperandrogenism is one of the characteristics of polycystic ovary syndrome (PCOS) and androgen receptor (AR) in ovarian granulosa cells (GCs) functions as an important element to the accumulation of androgens. This study verified the existence of alternative splicing variant of AR (AR-SVs) in the GCs of PCOS patients and found that the function of AR decreased significantly in the presence of AR-SVs. And compared to the normal individuals, the expression of Serine/arginine-rich splicing factor 2(SRSF2) was higher and the expression of SRSF3 was lower in the GCs of patients with AR-SVs. More importantly, we found that the expression of SRSF2 was inhibited and that the expression of AR was decreased after the successful upregulation of miRNA-183, and testostrone (T) concentrations in the culture medium were increased. The results also showed that the expression of SRSF3 decreased when miRNA-124 was successfully upregulated, while the expression of AR significantly increased; however, the function of AR was also inhibited when T concentration in the culture medium was increased. This study has proved that SRSFs are regulated by corresponding miRNAs, and the altered expression of SRSFs interferenced the alternative splicing process of AR and ultimately decreased the function of AR, leading to the accumulation of androgens in the ovary.
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Affiliation(s)
- Jing Luo
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Hong Ye
- Gynecologic Endocrinology of Chongqing Health Center for Women and Children, Chongqing, PR China
| | - Lijuan Hao
- Gynecologic Endocrinology of Chongqing Health Center for Women and Children, Chongqing, PR China
| | - Yixuan Sun
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Ruohan Li
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Yanxi Li
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Zhu Yang
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
- Corresponding author.
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27
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Liang Y, Song J, He D, Xia Y, Wu Y, Yin X, Liu J. Systematic analysis of survival-associated alternative splicing signatures uncovers prognostic predictors for head and neck cancer. J Cell Physiol 2019; 234:15836-15846. [PMID: 30740675 PMCID: PMC6618130 DOI: 10.1002/jcp.28241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/10/2019] [Accepted: 01/16/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Previous studies have shown that alternative splicing (AS) plays a key role in carcinogenesis and prognosis of cancer. However, systematic profiles of AS signatures in head and neck cancer (HNC) have not yet been reported. METHODS In this study, AS data, RNA-Seq data, and corresponding clinicopathological information of 489 HNC patients were downloaded from The Cancer Genome Atlas. Univariate and multivariate Cox regression analyses were performed to screen for survival-associated AS events. Functional and pathway enrichment analysis was also performed. The prognostic models and splicing networks were constructed using integrated bioinformatics analysis tools. RESULTS Among the 42,849 alternating splicing events identified in 10,121 genes, 5,165 survival-associated AS events in 2,419 genes were observed in univariate Cox regression analysis. Among the seven types, alternate terminator events were the most powerful prognostic factors. Multivariate Cox analysis was then used to screen for the AS genes with prognostic value. Four candidate genes (TPM1, CLASRP, PRRC1, and DNASE1L1) were found to be independent prognostic factors for HNC patients. A prognostic prediction model was built based on the four genes. The area under the receiver operating characteristic risk score curve for predicting the survival status of HNC patients was 0.704. In addition, splicing interaction network indicated that the splicing factors have significant functions in HNC. CONCLUSION A comprehensive analysis of AS events in HNC was performed. A powerful prognostic predictor for HNC patients was established based on AS events could.
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Affiliation(s)
- Ying Liang
- Department of Orthodontics, Guiyang Hospital of Stomatology, Medical CollegeGuiyangChina,Guiyang Stomatological Hospital Affiliated to Zunyi Medical UniversityGuizhouChina
| | - Jukun Song
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's HospitalGuizhouChina
| | - Dengqi He
- Department of Stomatology, First Hospital of Lanzhou UniversityLanzhouChina
| | - Yu Xia
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's HospitalGuizhouChina
| | - Yadong Wu
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's HospitalGuizhouChina
| | - Xinhai Yin
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's HospitalGuizhouChina
| | - Jianguo Liu
- Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical UniversityGuizhouChina
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28
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Chen QF, Li W, Wu P, Shen L, Huang ZL. Alternative splicing events are prognostic in hepatocellular carcinoma. Aging (Albany NY) 2019; 11:4720-4735. [PMID: 31301224 PMCID: PMC6660027 DOI: 10.18632/aging.102085] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
Alternative splicing events (ASEs) play a role in cancer development and progression. We investigated whether ASEs are prognostic for overall survival (OS) in hepatocellular carcinoma (HCC). RNA sequencing data was obtained for 343 patients included in The Cancer Genome Atlas. Matched splicing event data for these patients was then obtained from the TCGASpliceSeq database, which includes data for seven types of ASEs. Univariate and multivariate Cox regression analysis demonstrated that 3,814 OS-associated splicing events (OS-SEs) were correlated with OS. Prognostic indices were developed based on the most significant OS-SEs. The prognostic index based on all seven types of ASEs (PI-ALL) demonstrated superior efficacy in predicting OS of HCC patients at 2,000 days compared to those based on single ASE types. Patients were stratified into two risk groups (high and low) based on the median prognostic index. Kaplan-Meier survival analysis demonstrated that PI-ALL had the greatest capacity to distinguish between patients with favorable vs. poor outcomes. Finally, univariate Cox regression analysis demonstrated that the expression of 23 splicing factors was correlated with OS-SEs in the HCC cohort. Our data indicate that a prognostic index based on ASEs is prognostic for OS in HCC.
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Affiliation(s)
- Qi-Feng Chen
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
- State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510060, P.R. China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong 510060, P.R. China
| | - Wang Li
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Peihong Wu
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Lujun Shen
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
- State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510060, P.R. China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong 510060, P.R. China
| | - Zi-Lin Huang
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
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29
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Expression of TRA2B in endometrial carcinoma and its regulatory roles in endometrial carcinoma cells. Oncol Lett 2019; 18:2455-2463. [PMID: 31452736 PMCID: PMC6676653 DOI: 10.3892/ol.2019.10553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/16/2019] [Indexed: 12/24/2022] Open
Abstract
Expression levels of Transformer 2 protein homolog beta (TRA2B) in patients with endometrial carcinoma were assessed to investigate the impact of TRA2B on endometrial carcinoma cells. Furthermore, we analyzed the expression of several genes in the tissue samples from patients with endometrial cancer (EC) to identify whether cancer related genes we chose are differently expressed between the endometrial carcinoma tissues and adjacent normal tissues. The results of RT-qPCR analysis, western blot technology and immunofluorescence method consistently manifested that the expression of several genes in endometrial carcinoma tissue was significantly dysregulated between the two groups. Among the dysregulated genes, the strongly upregulated TRA2B in the tissues and serum from patients with EC was selected for further analysis. Endometrial carcinoma cells were transfected with chemically synthesized TRA2B plasmid, siRNA-TRA2B and their corresponding negative control respectively to assess the effects of TRA2B on the EC cells. Overexpression of TRA2B increased both the cell viability and proliferation potency of EC cells. Whereas, the viability and the proliferation ability of EC cells were strongly decreased by siRNA-TRA2B treatment. Furthermore, the invasion of EC cells was promoted by transfection of TRA2B and overexpression of TRA2B decreased the apoptosis of EC cells. Moreover, siRNA-TRA2B transfection inhibited the invasion but accelerated apoptosis of EC cells. Our results demonstrated that TRA2B is closely related to the development of endometrial carcinoma, and inhibition of TRA2B can decrease viability, proliferation and invasion of endometrial carcinoma, suggesting TRA2B is associated with the pathogenesis of human EC. Knockdown of TRA2B may be used for treatment of endometrial carcinoma, furthermore, these findings suggest an experimental foundation to clinical prognostic role of TRA2B in patients with endometrial carcinoma.
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30
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Song J, Liu YD, Su J, Yuan D, Sun F, Zhu J. Systematic analysis of alternative splicing signature unveils prognostic predictor for kidney renal clear cell carcinoma. J Cell Physiol 2019; 234:22753-22764. [PMID: 31140607 PMCID: PMC6771988 DOI: 10.1002/jcp.28840] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 01/28/2023]
Abstract
There is growing evidence that alternative splicing (AS) plays an important role in cancer development. However, a comprehensive analysis of AS signatures in kidney renal clear cell carcinoma (KIRC) is lacking and urgently needed. It remains unclear whether AS acts as diagnostic biomarkers in predicting the prognosis of KIRC patients. In the work, gene expression and clinical data of KIRC were obtained from The Cancer Genome Atlas (TCGA), and profiles of AS events were downloaded from the SpliceSeq database. The RNA sequence/AS data and clinical information were integrated, and we conducted the Cox regression analysis to screen survival‐related AS events and messenger RNAs (mRNAs). Correlation between prognostic AS events and gene expression were analyzed using the Pearson correlation coefficient. Protein‐protein interaction analysis was conducted for the prognostic AS‐related genes, and a potential regulatory network was built using Cytoscape (version 3.6.1). Meanwhile, functional enrichment analysis was conducted. A prognostic risk score model is then established based on seven hub genes (KRT222, LENG8, APOB, SLC3A1, SCD5, AQP1, and ADRA1A) that have high performance in the risk classification of KIRC patients. A total 46,415 AS events including 10,601 genes in 537 patients with KIRC were identified. In univariate Cox regression analysis, 13,362 survival associated AS events and 8,694 survival‐specific mRNAs were detected. Common 3,105 genes were screen by overlapping 13,362 survival associated AS events and 8,694 survival‐specific mRNAs. The Pearson correlation analysis suggested that 13 genes were significantly correlated with AS events (Pearson correlation coefficient >0.8 or <−0.8). Then, We conducted multivariate Cox regression analyses to select the potential prognostic AS genes. Seven genes were identified to be significantly related to OS. A prognostic model based on seven genes was constructed. The area under the ROC curve was 0.767. In the current study, a robust prognostic prediction model was constructed for KIRC patients, and the findings revealed that the AS events could act as potential prognostic biomarkers for KIRC.
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Affiliation(s)
- Jukun Song
- School Of Medicine, Guizhou University, Guiyang, Guizhou, China.,Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Yong Da Liu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Jiaming Su
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Dongbo Yuan
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Fa Sun
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Jianguo Zhu
- School Of Medicine, Guizhou University, Guiyang, Guizhou, China.,Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
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Wang WY, Cao YX, Zhou X, Wei B, Zhan L, Sun SY. Stimulative role of ST6GALNAC1 in proliferation, migration and invasion of ovarian cancer stem cells via the Akt signaling pathway. Cancer Cell Int 2019; 19:86. [PMID: 30996686 PMCID: PMC6451308 DOI: 10.1186/s12935-019-0780-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
Background Ovarian cancer is known as one of the most common cancers in the world among women. ST6GALNAC1 is highly expressed in cancer stem cells (CSCs), which correlates to high tumor-initiating, self-renewal and differentiation abilities. This present study aims to investigate how ST6GALNAC1 affects ovarian cancer stem cells (OCSCs). Methods In order to identify the differentially expressed genes related to ovarian cancer, microarray-based gene expression profiling of ovarian cancer was used, and ST6GALANC1 was one of the identified targets. After that, levels of ST6GALNAC1 in OCSCs and ovarian cancer cells were examined. Subsequently, an Akt signaling pathway inhibitor LY294002 was introduced into the cluster of differentiation 90+ (CD90+) stem cells, and cell proliferation, migration and invasion, levels of CXCL16, EGFR, CD44, Nanog and Oct4, as well as tumorigenicity of OCSCs were examined. Results By using a comprehensive microarray analysis, it was determined that ST6GALNAC1 was highly expressed in ovarian cancer and it regulated the Akt signaling pathway. High levels of ST6GALNAC1 were observed in OCSCs and ovarian cancer cells. Silencing ST6GALNAC1 was shown to be able to reduce cell proliferation, migration, invasion, self-renewal ability, tumorigenicity of OCSCs. In accordance with these results, the effects of ST6GALNAC1 in OCSCs were dependent on the Akt signaling pathway. Conclusions When taken together, our findings defined the potential stimulative roles of ST6GALNAC1 in ovarian cancer and OCSCs, which relied on the Akt signaling pathway.
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Affiliation(s)
- Wen-Yan Wang
- 1Department of Obstetrics and Gynecology, The Second Hospital of Anhui Medical University, Hefei, 230601 People's Republic of China.,2Teaching and Research Group of Obstetrics & Gynecology, Anhui Medical University, No. 81, Meishan Road, Hefei, 230032 Anhui People's Republic of China
| | - Yun-Xia Cao
- 2Teaching and Research Group of Obstetrics & Gynecology, Anhui Medical University, No. 81, Meishan Road, Hefei, 230032 Anhui People's Republic of China
| | - Xiao Zhou
- 3Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601 People's Republic of China
| | - Bing Wei
- 1Department of Obstetrics and Gynecology, The Second Hospital of Anhui Medical University, Hefei, 230601 People's Republic of China
| | - Lei Zhan
- 1Department of Obstetrics and Gynecology, The Second Hospital of Anhui Medical University, Hefei, 230601 People's Republic of China
| | - Shi-Ying Sun
- 1Department of Obstetrics and Gynecology, The Second Hospital of Anhui Medical University, Hefei, 230601 People's Republic of China
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32
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Meng L, Li Y, Ren J, Shi T, Men J, Chang C. Early Stage Biomarkers Screening of Prostate Cancer Based on Weighted Gene Coexpression Network Analysis. DNA Cell Biol 2019; 38:468-475. [PMID: 30835547 DOI: 10.1089/dna.2018.4406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Although the morbidity and mortality rates of prostate cancer (PCa) are considerably high, many PCas are characterized as indolent and slow growing, which do not require overtreatment. Overdiagnosis and overtreatment of early detected PCa are an emerging problem, owing to a lack of biomarkers that detect advanced disease at an earlier stage. In this study, RNA-Seq data of 57,045 genes for 495 PCa samples and 52 normal samples in the The Cancer Genome Atlas (TCGA) database were downloaded. Subsequently, we performed weighted gene coexpression network analysis to identify the Gleason score-related coexpression gene module, and further screened out oncogenes and tumor suppressors that were upregulated or downregulated in the early stage of PCa as well as those related to the clinical prognosis of PCa patients. Based on this study, some novel biomarkers were identified for the disease-free survival, which are helpful for fast diagnosis and prognosis.
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Affiliation(s)
- Lingyin Meng
- 1 Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yang Li
- 2 Precision Medicine Center, Tianjin Medical University General Hospital, Tianjin, China
| | - Jing Ren
- 2 Precision Medicine Center, Tianjin Medical University General Hospital, Tianjin, China
| | - Tao Shi
- 2 Precision Medicine Center, Tianjin Medical University General Hospital, Tianjin, China
| | - Jianlong Men
- 2 Precision Medicine Center, Tianjin Medical University General Hospital, Tianjin, China
| | - Chawnshang Chang
- 1 Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.,3 George Whipple Lab for Cancer Research, Departments of Urology, Pathology and the Cancer Center, University of Rochester, Rochester, New York
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33
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Olender J, Lee NH. Role of Alternative Splicing in Prostate Cancer Aggressiveness and Drug Resistance in African Americans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1164:119-139. [PMID: 31576545 PMCID: PMC6777849 DOI: 10.1007/978-3-030-22254-3_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alternative splicing, the process of removing introns and joining exons of pre-mRNA, is critical for growth, development, tissue homeostasis, and species diversity. Dysregulation of alternative splicing can initiate and drive disease. Aberrant alternative splicing has been shown to promote the "hallmarks of cancer" in both hematological and solid cancers. Of interest, recent work has focused on the role of alternative splicing in prostate cancer and prostate cancer health disparities. We will provide a review of prostate cancer health disparities involving the African American population, alternative RNA splicing, and alternative splicing in prostate cancer. Lastly, we will summarize our work on differential alternative splicing in prostate cancer disparities and its implications for disparate health outcomes and therapeutic targets.
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Affiliation(s)
- Jacqueline Olender
- Department of Pharmacology and Physiology, GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Norman H Lee
- Department of Pharmacology and Physiology, GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
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Huang ZG, He RQ, Mo ZN. Prognostic value and potential function of splicing events in prostate adenocarcinoma. Int J Oncol 2018; 53:2473-2487. [PMID: 30221674 PMCID: PMC6203144 DOI: 10.3892/ijo.2018.4563] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Prostate adenocarcinoma (PRAD) is one of the most common types of malignancy in males and at present, effective prognostic indicators are limited. The development of PRAD has been associated with abnormalities in alternative splicing (AS), a requisite biological process of gene expression in eukaryotic cells; however, the prognostic value of AS products and splicing events remains to be elucidated. In the present study, the data of splicing events and the clinical information of PRAD patients were obtained from The Cancer Genome Atlas (TCGA)SpliceSeq and TCGA databases, respectively. A prognostic index (PI) was generated from disease-free survival-associated splicing events (DFS-SEs), which were identified by univariate/multivariate Cox regression analysis. A total of 6,909 DFS-SEs were identified in PRAD. The corresponding genes for the DFS-SEs were significantly enriched in mitochondria and their associated pathways according to Gene Ontology annotation and in the pathways of fatty acid metabolism, oxidative phosphorylation and Huntington's disease according to a Kyoto Encyclopedia of Genes and Genomes pathway analysis. The PI for mutually exclusive exons had the greatest ability to predict the probability of five-year disease-free survival of patients with PRAD, with an area under the time-dependent receiver-operating characteristic curve of 0.7606. Patients with PRAD, when divided into a 'low' and a 'high' group based on their median PI for exon skip values, exhibited a marked difference in disease-free survival (low vs. high, 3,588.45±250.51 vs. 1,531.08±136.50 days; P=7.43×10−9). A correlation network between DFS-SEs of splicing factors and non-splicing factors was constructed to determine the potential mechanisms in PRAD, which included the potential regulatory interaction between the splicing event of splicing factor RNA binding motif protein 5-alternate terminator (AT)-64957 and the splicing event of non-splicing factor heterochromatin protein 1 binding protein 3-AT-939. In conclusion, the PIs derived from DFS-SEs are valuable prognostic factors for patients with PRAD, and the function of splicing events in PRAD deserves further exploration.
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Affiliation(s)
- Zhi-Guang Huang
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rong-Quan He
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Zeng-Nan Mo
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Munkley J, Maia TM, Ibarluzea N, Livermore KE, Vodak D, Ehrmann I, James K, Rajan P, Barbosa-Morais NL, Elliott DJ. Androgen-dependent alternative mRNA isoform expression in prostate cancer cells. F1000Res 2018; 7:1189. [PMID: 30271587 PMCID: PMC6143958 DOI: 10.12688/f1000research.15604.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
Background: Androgen steroid hormones are key drivers of prostate cancer. Previous work has shown that androgens can drive the expression of alternative mRNA isoforms as well as transcriptional changes in prostate cancer cells. Yet to what extent androgens control alternative mRNA isoforms and how these are expressed and differentially regulated in prostate tumours is unknown. Methods: Here we have used RNA-Seq data to globally identify alternative mRNA isoform expression under androgen control in prostate cancer cells, and profiled the expression of these mRNA isoforms in clinical tissue. Results: Our data indicate androgens primarily switch mRNA isoforms through alternative promoter selection. We detected 73 androgen regulated alternative transcription events, including utilisation of 56 androgen-dependent alternative promoters, 13 androgen-regulated alternative splicing events, and selection of 4 androgen-regulated alternative 3' mRNA ends. 64 of these events are novel to this study, and 26 involve previously unannotated isoforms. We validated androgen dependent regulation of 17 alternative isoforms by quantitative PCR in an independent sample set. Some of the identified mRNA isoforms are in genes already implicated in prostate cancer (including LIG4, FDFT1 and RELAXIN), or in genes important in other cancers (e.g. NUP93 and MAT2A). Importantly, analysis of transcriptome data from 497 tumour samples in the TGCA prostate adenocarcinoma (PRAD) cohort identified 13 mRNA isoforms (including TPD52, TACC2 and NDUFV3) that are differentially regulated in localised prostate cancer relative to normal tissue, and 3 ( OSBPL1A, CLK3 and TSC22D3) which change significantly with Gleason grade and tumour stage. Conclusions: Our findings dramatically increase the number of known androgen regulated isoforms in prostate cancer, and indicate a highly complex response to androgens in prostate cancer cells that could be clinically important.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Teresa M. Maia
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, 1649-028, Portugal
- VIB Proteomics Core, Albert Baertsoenkaai 3, Ghent, 9000, Belgium
| | - Nekane Ibarluzea
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
- Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, 48903, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Valencia, 46010, Spain
| | - Karen E. Livermore
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Daniel Vodak
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Ehrmann
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Katherine James
- Interdisciplinary Computing and Complex BioSystems Research Group, Newcastle University, Newcastle upon Tyne, NE4 5TG, UK
- Life and Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Prabhakar Rajan
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, EC1M 6BQ, UK
| | - Nuno L. Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, 1649-028, Portugal
| | - David J. Elliott
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
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A new metabolic gene signature in prostate cancer regulated by JMJD3 and EZH2. Oncotarget 2018; 9:23413-23425. [PMID: 29805743 PMCID: PMC5955128 DOI: 10.18632/oncotarget.25182] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
Histone methylation is essential for gene expression control. Trimethylated lysine 27 of histone 3 (H3K27me3) is controlled by the balance between the activities of JMJD3 demethylase and EZH2 methyltransferase. This epigenetic mark has been shown to be deregulated in prostate cancer, and evidence shows H3K27me3 enrichment on gene promoters in prostate cancer. To study the impact of this enrichment, a transcriptomic analysis with TaqMan Low Density Array (TLDA) of several genes was studied on prostate biopsies divided into three clinical grades: normal (n = 23) and two tumor groups that differed in their aggressiveness (Gleason score ≤ 7 (n = 20) and >7 (n = 19)). ANOVA demonstrated that expression of the gene set was upregulated in tumors and correlated with Gleason score, thus discriminating between the three clinical groups. Six genes involved in key cellular processes stood out: JMJD3, EZH2, MGMT, TRA2A, U2AF1 and RPS6KA2. Chromatin immunoprecipitation demonstrated collocation of EZH2 and JMJD3 on gene promoters that was dependent on disease stage. Gene set expression was also evaluated on prostate cancer cell lines (DU 145, PC-3 and LNCaP) treated with an inhibitor of JMJD3 (GSK-J4) or EZH2 (DZNeP) to study their involvement in gene regulation. Results showed a difference in GSK-J4 sensitivity under PTEN status of cell lines and an opposite gene expression profile according to androgen status of cells. In summary, our data describe the impacts of JMJD3 and EZH2 on a new gene signature involved in prostate cancer that may help identify diagnostic and therapeutic targets in prostate cancer.
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37
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Liu J, Li H, Shen S, Sun L, Yuan Y, Xing C. Alternative splicing events implicated in carcinogenesis and prognosis of colorectal cancer. J Cancer 2018; 9:1754-1764. [PMID: 29805701 PMCID: PMC5968763 DOI: 10.7150/jca.24569] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/03/2018] [Indexed: 12/15/2022] Open
Abstract
Background: Emerging evidence suggested that aberrant alternative splicing (AS) is pervasive event in development and progression of cancer. However, the information of aberrant splicing events involved in colorectal carcinogenesis and progression is still elusive. Materials and Methods: In this study, splicing data of 499 colon adenocarcinoma cases (COAD) and 176 rectum adenocarcinoma (READ) with clinicopathological information were obtained from The Cancer Genome Atlas (TCGA) to explore the changes of alternative splicing events in relation to the carcinogenesis and prognosis of colorectal cancer (CRC). Gene interaction network construction, functional and pathway enrichment analysis were performed by multiple bioinformatics tools. Results: Overall, most AS patterns were more active in CRC tissues than adjacent normal ones. We detected altogether 35391 AS events of 9084 genes in COAD and 34900 AS events of 9032 genes in READ, some of which were differentially spliced between cancer tissues and normal tissues including genes of SULT1A2, CALD1, DTNA, COL12A1 and TTLL12. Differentially spliced genes were enriched in biological process including muscle organ development, cytoskeleton organization, actin cytoskeleton organization, biological adhesion, and cell adhesion. The integrated predictor model of COAD showed an AUC of 0.805 (sensitivity: 0.734; specificity: 0.756) while READ predictor had an AUC of 0.738 (sensitivity: 0.614; specificity: 0.900). In addition, a number of prognosis-associated AS events were discovered, including genes of PSMD2, NOL8, ALDH4A1, SLC10A7 and PPAT. Conclusion: We draw comprehensive profiles of alternative splicing events in the carcinogenesis and prognosis of CRC. The interaction network and functional connections were constructed to elucidate the underlying mechanisms of alternative splicing in CRC.
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Affiliation(s)
- Jingwei Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Hao Li
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Shixuan Shen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Liping Sun
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Chengzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
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Lee AR, Che N, Lovnicki JM, Dong X. Development of Neuroendocrine Prostate Cancers by the Ser/Arg Repetitive Matrix 4-Mediated RNA Splicing Network. Front Oncol 2018; 8:93. [PMID: 29666783 PMCID: PMC5891588 DOI: 10.3389/fonc.2018.00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/16/2018] [Indexed: 12/19/2022] Open
Abstract
While the use of next-generation androgen receptor pathway inhibition (ARPI) therapy has significantly increased the survival of patients with metastatic prostate adenocarcinoma (AdPC), several groups have reported a treatment-resistant mechanism, whereby cancer cells can become androgen receptor (AR) indifferent and gain a neuroendocrine (NE)-like phenotype. This subtype of castration-resistant prostate cancer has been termed "treatment-induced castration-resistant neuroendocrine prostate cancer" (CRPC-NE). Recent reports indicate that the overall genomic landscapes of castration-resistant tumors with AdPC phenotypes and CRPC-NE are not significantly altered. However, CRPC-NE tumors have been found to contain a NE-specific pattern throughout their epigenome and splicing transcriptome, which are significantly modified. The molecular mechanisms by which CRPC-NE develops remain unclear, but several factors have been implicated in the progression of the disease. Recently, Ser/Arg repetitive matrix 4 (SRRM4), a neuronal-specific RNA splicing factor that is upregulated in CRPC-NE tumors, has been shown to establish a CRPC-NE-unique splicing transcriptome, to induce a NE-like morphology in AdPC cells, and, most importantly, to transform AdPC cells into CRPC-NE xenografts under ARPI. Moreover, the SRRM4-targeted splicing genes are highly enriched in various neuronal processes, suggesting their roles in facilitating a CRPC-NE program. This article will address the importance of SRRM4-mediated alternative RNA splicing in reprogramming translated proteins to facilitate NE differentiation, survival, and proliferation of cells to establish CRPC-NE tumors. In addition, we will discuss the potential roles of SRRM4 in conjunction with other known pathways and factors important for CRPC-NE development, such as the AR pathway, TP53 and RB1 genes, the FOXA family of proteins, and environmental factors. This study aims to explore the multifaceted functions of SRRM4 and SRRM4-mediated splicing in driving a CRPC-NE program as a coping mechanism for therapy resistance, as well as define future SRRM4-targeted therapeutic approaches for treating CRPC-NE or mitigating its development.
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Affiliation(s)
- Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Che
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jessica M Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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Patel R, Khalifa AO, Isali I, Shukla S. Prostate cancer susceptibility and growth linked to Y chromosome genes. Front Biosci (Elite Ed) 2018; 10:423-436. [PMID: 29293466 PMCID: PMC6152832 DOI: 10.2741/e830] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The role of Y chromosome in prostate cancer progression and incidence is not well known. Among the 46 chromosomes, Y chromosome determines the male gender. The Y chromosome is smaller than the X chromosome and contains only 458 genes compared to over 2000 genes found in the X chromosome. The Y chromosome is prone to high mutation rates, created exclusively in sperm cells due to the highly oxidative environment of the testis. Y chromosome harbors epigenetic information, which affects the expression of genes associated with the incidence and progression of prostate cancer. In this review, we focus on Y chromosome related genetic abnormalities, likely to be involved in the development and progression of prostate cancer.
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Affiliation(s)
- Riddhi Patel
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA
| | - Ahmad O Khalifa
- Urology Dept. Case Western Reserve University, Cleveland, Ohio and Menofia University, Shebin Al kom, Egpt
| | - Ilaha Isali
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA
| | - Sanjeev Shukla
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA,
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Coppin L, Leclerc J, Vincent A, Porchet N, Pigny P. Messenger RNA Life-Cycle in Cancer Cells: Emerging Role of Conventional and Non-Conventional RNA-Binding Proteins? Int J Mol Sci 2018; 19:ijms19030650. [PMID: 29495341 PMCID: PMC5877511 DOI: 10.3390/ijms19030650] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 02/06/2023] Open
Abstract
Functional specialization of cells and tissues in metazoans require specific gene expression patterns. Biological processes, thus, need precise temporal and spatial coordination of gene activity. Regulation of the fate of messenger RNA plays a crucial role in this context. In the present review, the current knowledge related to the role of RNA-binding proteins in the whole mRNA life-cycle is summarized. This field opens up a new angle for understanding the importance of the post-transcriptional control of gene expression in cancer cells. The emerging role of non-classic RNA-binding proteins is highlighted. The goal of this review is to encourage readers to view, through the mRNA life-cycle, novel aspects of the molecular basis of cancer and the potential to develop RNA-based therapies.
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Affiliation(s)
- Lucie Coppin
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Julie Leclerc
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Audrey Vincent
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Nicole Porchet
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Pascal Pigny
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
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SRSF10-mediated IL1RAP alternative splicing regulates cervical cancer oncogenesis via mIL1RAP-NF-κB-CD47 axis. Oncogene 2018; 37:2394-2409. [PMID: 29429992 PMCID: PMC5931977 DOI: 10.1038/s41388-017-0119-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/06/2017] [Accepted: 12/14/2017] [Indexed: 02/05/2023]
Abstract
High-risk human papillomavirus oncoproteins E6 and E7 are the major etiological factors of cervical cancer but are insufficient for malignant transformation of cervical cancer. Dysregulated alternative splicing, mainly ascribed to aberrant splicing factor levels and activities, contributes to most cancer hallmarks. However, do E6 and E7 regulate the expression of splicing factors? Does alternative splicing acts as an “accomplice” of E6E7 to promote cervical cancer progression? Here, we identified that the splicing factor SRSF10, which promotes tumorigenesis of cervix, was upregulated by E6E7 via E2F1 transcriptional activation. SRSF10 modulates the alternate terminator of interleukin-1 receptor accessory protein exon 13 to increase production of the membrane form of interleukin-1 receptor accessory protein. SRSF10-mediated mIL1RAP upregulates the expression of the “don’t eat me” signal CD47 to inhibit macrophage phagocytosis by promoting nuclear factor-κB activation, which is pivotal in inflammatory, immune, and tumorigenesis processes. Altogether, these data reveal a close relationship among HPV infection, alternative splicing and tumor immune evasion, and also suggests that the SRSF10-mIL1RAP-CD47 axis could be an attractive therapeutic target for the treatment of cervical cancer.
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Siegfried Z, Karni R. The role of alternative splicing in cancer drug resistance. Curr Opin Genet Dev 2018; 48:16-21. [DOI: 10.1016/j.gde.2017.10.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 09/14/2017] [Accepted: 10/02/2017] [Indexed: 12/27/2022]
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Xu Y, Gu S, Bi Y, Qi X, Yan Y, Lou M. Transcription factor PU.1 is involved in the progression of glioma. Oncol Lett 2018; 15:3753-3759. [PMID: 29467892 PMCID: PMC5795926 DOI: 10.3892/ol.2018.7766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/03/2018] [Indexed: 01/04/2023] Open
Abstract
Glioma is a severe disease of the central nervous system. Although previous studies have identified the important role of the immune response in association with tumor intervention, it is still unknown whether PU.1, a transcription factor known for its role in myeloid differentiation and immune responses, is involved in the progression of glioma. In the present study, we found a significant increase in SPI1, the gene that encodes PU.1, in samples from patients with glioma. Through genotype-phenotype association analysis several candidate factors that may mediate the role of PU.1 in glioma were identified. To further validate the association between PU.1 and glioma we found that the expression of BTK, a potential target of PU.1, was also upregulated in patients with glioma. We also demonstrated that various biological pathways could be involved in PU.1-associated glioma by analyzing these potential targets in the Reactome database. These results provide evidence that PU.1 could serve a role in the progress of glioma through its transcriptional targets in multiple signaling pathways. Therefore, in addition to its role in hematopoietic linage development and leukemia, PU.1 appears to be involved in the regulation of glioma and potentially in other malignant cancers.
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Affiliation(s)
- Yuanzhi Xu
- Department of Neurosurgery, Shanghai First People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, P.R. China
| | - Song Gu
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yunke Bi
- Department of Neurosurgery, Shanghai First People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, P.R. China
| | - Xiangqian Qi
- Department of Neurosurgery, Shanghai First People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, P.R. China
| | - Yujin Yan
- Department of Neurosurgery, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang 315020, P.R. China
| | - Meiqing Lou
- Department of Neurosurgery, Shanghai First People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, P.R. China
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Wang W, Gao D, Wang X. Can single-cell RNA sequencing crack the mystery of cells? Cell Biol Toxicol 2017; 34:1-6. [DOI: 10.1007/s10565-017-9404-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/28/2017] [Indexed: 12/15/2022]
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