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Wang X, Lin Y, Li Z, Li Y, Chen M. Alternative Polyadenylation Regulatory Factors Signature for Survival Prediction in Kidney Renal Cell Carcinoma. Cancer Inform 2024; 23:11769351231180789. [PMID: 38617569 PMCID: PMC11015750 DOI: 10.1177/11769351231180789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 04/16/2024] Open
Abstract
Background Alternative polyadenylation (APA) plays a vital regulatory role in various diseases. It is widely accepted that APA is regulated by APA regulatory factors. Objective Whether APA regulatory factors affect the prognosis of renal cell carcinoma remains unclear, and this is the main topic of this study. Methods We downloaded the transcriptome and clinical data from The Cancer Genome Atlas (TCGA) database. We used the Lasso regression system to construct an APA model for analyzing the relationship between common APA regulatory factors and renal cell carcinoma. We also validated our APA model using independent GEO datasets (GSE29609, GSE76207). Results It was found that the expression levels of 5 APA regulatory factors (CPSF1, CPSF2, CSTF2, PABPC1, and PABPC4) were significantly associated with tumor gene mutation burden (TMB) score in renal clear cell carcinoma, and the risk score constructed using the expression level of 5 key APA regulatory factors could be used to predict the outcome of renal clear cell carcinoma. The TMB score is associated with the remodeling of the immune microenvironment. Conclusions By identifying key APA regulatory factors in renal cell carcinoma and constructing risk scores for key APA regulatory factors, we showed that key APA regulators affect prognosis of renal clear cell carcinoma patients. In addition, the risk score level is associated with TMB, indicating that APA may affect the efficacy of immunotherapy through immune microenvironment-related genes. This helps us better understand the mRNA processing mechanism of renal clear cell carcinoma.
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Affiliation(s)
- Xiaoyu Wang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yao Lin
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Zheng Li
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yueqi Li
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Mingcong Chen
- Department of Orthopedics and Traumatology, Shenzhen University General Hospital, Shenzhen, China
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Xiong M, Liu C, Li W, Jiang H, Long W, Zhou M, Yang C, Kazobinka G, Sun Y, Zhao J, Hou T. PABPN1 promotes clear cell renal cell carcinoma progression by suppressing the alternative polyadenylation of SGPL1 and CREG1. Carcinogenesis 2023; 44:576-586. [PMID: 37452741 DOI: 10.1093/carcin/bgad049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/15/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism in cancer development and progression. Poly(A) binding protein nuclear 1 (PABPN1) is a gene that encodes abundant nuclear protein, binds with high affinity to nascent poly(A) tails, and is crucial for 3'-UTR (3'-untranslated region) APA. Although PABPN1 has been recently reported as a dominant master APA regulator in clear cell renal cell carcinoma (ccRCC), the underlying functional mechanism remain unclear and the genes subject to PABPN1 regulation that contribute to ccRCC progression have not been identified. Here, we found that PABPN1 is upregulated in ccRCC, and its expression is highly associated with the clinical prognosis of ccRCC patients. PABPN1 promotes ccRCC cell proliferation, migration, invasion, and exerts an influence on sphingolipid metabolism and cell cycle. Moreover, PABPN1 depletion significantly suppressed cancer cell growth via induction of cell cycle arrest and apoptosis. In particular, we characterized PABPN1-regulated 3'-UTR APA of sphingosine-1-phosphate lyase 1 (SGPL1) and cellular repressor of E1A stimulated genes 1 (CREG1), which contribute to ccRCC progression. Collectively, our data revealed that PABPN1 promotes ccRCC progression at least in part, by suppressing SGPL1 and CREG1. Thus, PABPN1 may be a potential therapeutic target in ccRCC.
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Affiliation(s)
- Ming Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyu Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wencheng Li
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huiling Jiang
- Department of Urology, South China Hospital, Medical School, Shenzhen University, Shenzhen, 518116, China
| | - Wulin Long
- Department of Urology, Wuhan Union Jiangbei Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Menghao Zhou
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenlu Yang
- Department of Gynecology and Obstetrics, Women and Children Hospital of Guangdong Province, Guangzhou 510080, China
| | - Gallina Kazobinka
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Urology Unit, La Nouvelle Polyclinique Centrale de Bujumbura, Bujumbura 378, Burundi
| | - Yi Sun
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Zhao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Teng Hou
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Urology, South China Hospital, Medical School, Shenzhen University, Shenzhen, 518116, China
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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Dharmalingam P, Mahalingam R, Yalamanchili HK, Weng T, Karmouty-Quintana H, Guha A, A Thandavarayan R. Emerging roles of alternative cleavage and polyadenylation (APA) in human disease. J Cell Physiol 2021; 237:149-160. [PMID: 34378793 DOI: 10.1002/jcp.30549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022]
Abstract
In the messenger RNA (mRNA) maturation process, the 3'-end of pre-mRNA is cleaved and a poly(A) sequence is added, this is an important determinant of mRNA stability and its cellular functions. More than 60%-70% of human genes have three or more polyadenylation (APA) sites and can be cleaved at different sites, generating mRNA transcripts of varying lengths. This phenomenon is termed as alternative cleavage and polyadenylation (APA) and it plays role in key biological processes like gene regulation, cell proliferation, senescence, and also in various human diseases. Loss of regulatory microRNA binding sites and interactions with RNA-binding proteins leading to APA are largely investigated in human diseases. However, the functions of the core APA machinery and related factors during disease conditions remain largely unknown. In this review, we discuss the roles of polyadenylation machinery in relation to brain disease, cardiac failure, pulmonary fibrosis, cancer, infectious conditions, and other human diseases. Collectively, we believe this review will be a useful avenue for understanding the emerging role of APA in the pathobiology of various human diseases.
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Affiliation(s)
- Prakash Dharmalingam
- Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai, India
| | - Rajasekaran Mahalingam
- Laboratory of Neuroimmunology, Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics - Neurology, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas, USA
| | - Tingting Weng
- Department of Biochemistry and Molecular Biology & Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology & Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ashrith Guha
- Department of Cardiology, Houston Methodist DeBakey Heart & Vascular Center, Houston, Texas, USA
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