1
|
Sharma S, Mittal M, Shukla A, Khan J, Dinand V, Saluja D. Exploring serine-arginine rich splicing factors: potential predictive markers for dysregulation in oral cancer. BMC Cancer 2024; 24:1094. [PMID: 39227899 PMCID: PMC11373262 DOI: 10.1186/s12885-024-12750-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/01/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Dysregulated splicing events are a common phenomenon in cancer with the Serine-arginine-rich splicing factor (SRSF) family emerging as pivotal regulators of gene expression, exerting influence over constitutive and alternative splicing processes. Although aberrations in a few SRSF family members have been implicated in various cancers, the comprehensive roles of other family constituents remain underexplored. METHODS This study delves into the expression profile of the entire SRSF family (SRSF1-SRSF12) in 23 cancerous cell lines originating from diverse tissues using quantitative Real-Time PCR. Further, the transcript levels of the SRSF family were examined in oral cancer patient samples stratified into Pre-cancer (n = 15), Early cancer (n = 11), Late cancer (n = 14), and adjacent non-tumor tissues (n = 26) as controls. The results were corroborated by a parallel investigation utilizing the transcriptomics data of oral squamous cell carcinoma (OSCC) patients (n = 319) and controls (n = 35) available in The Cancer Genome Atlas (TCGA) database. RESULTS Our investigation reveals a notable upregulation in the expression levels of key splicing factors, namely SRSF3, SRSF9, and SRSF10 in all oral cancer cell lines (SCC-4, UM-SCC-84, CAL33, SAS-H1). Conversely, no significant associations between SRSF family members and other cancer cell lines were discerned. Further, the expression profile of the SRSF family in oral cancer patient samples revealed significant upregulation of SRSF1, SRSF3, SRSF7, SRSF9, SRSF10, and SRSF11 in patients with late-stage oral cancer compared to controls. Transcriptomics data from TCGA database demonstrated remarkable upregulation of SRSF1, SRSF4, SRSF9, SRSF10, and SRSF11 in OSCC patients. CONCLUSION Collectively our results underscore the critical involvement of SRSF family members in the context of oral cancer, highlighting their potential as key players in the altered splicing dynamics associated with cancer progression.
Collapse
Affiliation(s)
- Sakshi Sharma
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India
| | - Manasi Mittal
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India
| | - Akanksha Shukla
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India
| | - Jiyauddin Khan
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India
| | - Veronique Dinand
- Bai Jerbai Wadia Hospital for Children, Parel, Mumbai, 400014, Maharashtra, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India.
- Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
2
|
Wang X, Guan X, Zhu X, Zhang L, Ma C, He S, Bai J, Mei J, Li Q, Sun N, Wu B, Zhu D. CircNAP1L4 regulates pulmonary artery smooth muscle cell proliferation via the NAP1L4-mediated super-enhancer-driven glycolysis gene hexokinase II (HK II) in pulmonary hypertension. FASEB J 2024; 38:e23868. [PMID: 39102213 DOI: 10.1096/fj.202400585rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/12/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Glycolysis is a major determinant of pulmonary artery smooth muscle cell (PASMC) proliferation in pulmonary hypertension (PH). Circular RNAs (circRNAs) are powerful regulators of glycolysis in multiple diseases; however, the role of circRNAs in glycolysis in PH has been poorly characterized. The aim of this study was to uncover the regulatory mechanism of a new circRNA, circNAP1L4, in human pulmonary artery smooth muscle cell (HPASMC) proliferation through the host protein NAP1L4 to regulate the super-enhancer-driven glycolysis gene hexokinase II (HK II). CircNAP1L4 was downregulated in hypoxic HPASMCs and plasma of PH patients. Functionally, circNAP1L4 overexpression inhibited glycolysis and proliferation in hypoxic HPASMCs. Mechanistically, circNAP1L4 directly bound to its host protein NAP1L4 and affected the ability of NAP1L4 to move into the nucleus to regulate the epigenomic signals of the super-enhancer of HK II. Intriguingly, circNAP1L4 overexpression inhibited the proliferation but not the migration of human pulmonary arterial endothelial cells (HPAECs) cocultured with HPASMCs. Furthermore, pre-mRNA-processing-splicing Factor 8 (PRP8) was found to regulate the production ratio of circNAP1L4 and linear NAP1L4. In vivo, targeting circNAP1L4 alleviates SU5416 combined with hypoxia (SuHx)-induced PH. Overall, these findings reveal a new circRNA that inhibits PASMC proliferation and serves as a therapeutic target for PH.
Collapse
MESH Headings
- Humans
- Hexokinase/metabolism
- Hexokinase/genetics
- Cell Proliferation
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/genetics
- Glycolysis
- Myocytes, Smooth Muscle/metabolism
- RNA, Circular/genetics
- RNA, Circular/metabolism
- Animals
- Mice
- Male
- Cells, Cultured
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/cytology
Collapse
Affiliation(s)
- Xiaoying Wang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Pharmacy, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Xiaoyu Guan
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Pharmacy, Harbin Medical University, Harbin, P. R. China
| | - Xiangrui Zhu
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Lixin Zhang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Cui Ma
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Siyu He
- Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, Shenzhen, P. R. China
| | - June Bai
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Pharmacy, Harbin Medical University, Harbin, P. R. China
| | - Jian Mei
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Qian Li
- College of Pharmacy, Harbin Medical University, Harbin, P. R. China
| | - Na Sun
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Myocardial Ischemia, Ministry Education, Harbin Medical University, Harbin, P. R. China
| | - Bingxiang Wu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Myocardial Ischemia, Ministry Education, Harbin Medical University, Harbin, P. R. China
| | - Daling Zhu
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Pharmacy, Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, Harbin, P. R. China
| |
Collapse
|
3
|
Li Q, Xia Z, Wu Y, Ma Y, Zhang D, Wang S, Fan J, Xu P, Li X, Bai L, Zhou X, Xue M. Lysophospholipid acyltransferase-mediated formation of saturated glycerophospholipids maintained cell membrane integrity for hypoxic adaptation. FEBS J 2024; 291:3191-3210. [PMID: 38602252 DOI: 10.1111/febs.17132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/11/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
Adaptation to hypoxia has attracted much public interest because of its clinical significance. However, hypoxic adaptation in the body is complicated and difficult to fully explore. To explore previously unknown conserved mechanisms and key proteins involved in hypoxic adaptation in different species, we first used a yeast model for mechanistic screening. Further multi-omics analyses in multiple species including yeast, zebrafish and mice revealed that glycerophospholipid metabolism was significantly involved in hypoxic adaptation with up-regulation of lysophospholipid acyltransferase (ALE1) in yeast, a key protein for the formation of dipalmitoyl phosphatidylcholine [DPPC (16:0/16:0)], which is a saturated phosphatidylcholine. Importantly, a mammalian homolog of ALE1, lysophosphatidylcholine acyltransferase 1 (LPCAT1), enhanced DPPC levels at the cell membrane and exhibited the same protective effect in mammalian cells under hypoxic conditions. DPPC supplementation effectively attenuated growth restriction, maintained cell membrane integrity and increased the expression of epidermal growth factor receptor under hypoxic conditions, but unsaturated phosphatidylcholine did not. In agreement with these findings, DPPC treatment could also repair hypoxic injury of intestinal mucosa in mice. Taken together, ALE1/LPCAT1-mediated DPPC formation, a key pathway of glycerophospholipid metabolism, is crucial for cell viability under hypoxic conditions. Moreover, we found that ALE1 was also involved in glycolysis to maintain sufficient survival conditions for yeast. The present study offers a novel approach to understanding lipid metabolism under hypoxia and provides new insights into treating hypoxia-related diseases.
Collapse
Affiliation(s)
- Qiang Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Zhengchao Xia
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yi Wu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yi Ma
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
| | - Di Zhang
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Sihan Wang
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jingxin Fan
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Pingxiang Xu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xiaorong Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Lu Bai
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xuelin Zhou
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Ming Xue
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| |
Collapse
|
4
|
Pandey A, Kakani P, Shukla S. CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer. J Biol Chem 2024; 300:107416. [PMID: 38810696 PMCID: PMC11254729 DOI: 10.1016/j.jbc.2024.107416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Autophagy is a pivotal regulatory and catabolic process, induced under various stressful conditions, including hypoxia. However, little is known about alternative splicing of autophagy genes in the hypoxic landscape in breast cancer. Our research unravels the hitherto unreported alternative splicing of BNIP3L, a crucial hypoxia-induced autophagic gene. We showed that BNIP3L, under hypoxic condition, forms two isoforms, a full-length isoform (BNIP3L-F) and a shorter isoform lacking exon 1 (BNIP3L-Δ1). The hypoxia-induced BNIP3L-F promotes autophagy, while under normoxia, the BNIP3L-Δ1 inhibits autophagy. We discovered a novel dimension of hypoxia-mediated epigenetic modification that regulates the alternative splicing of BNIP3L. Here, we showed differential DNA methylation of BNIP3L intron 1, causing reciprocal binding of epigenetic factor CCCTC-binding factor (CTCF) and its paralog BORIS. Additionally, we highlighted the role of CTCF and BORIS impacting autophagy in breast cancer. The differential binding of CTCF and BORIS results in alternative splicing of BNIP3L forming BNIP3L-F and BNIP3L-Δ1, respectively. The binding of CTCF on unmethylated BNIP3L intron 1 under hypoxia results in RNA Pol-II pause and inclusion of exon 1, promoting BNIP3L-F and autophagy. Interestingly, the binding of BORIS on methylated BNIP3L intron 1 under normoxia also results in RNA Pol-II pause but leads to the exclusion of exon 1 from BNIP3L mRNA. Finally, we reported the critical role of BORIS-mediated RNA Pol-II pause, which subsequently recruits SRSF6, redirecting the proximal splice-site selection, promoting BNIP3L-Δ1, and inhibiting autophagy. Our study provides novel insights into the potential avenues for breast cancer therapy by targeting autophagy regulation, specifically under hypoxic condition.
Collapse
Affiliation(s)
- Anchala Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Parik Kakani
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India.
| |
Collapse
|
5
|
Gimeno-Valiente F, López-Rodas G, Castillo J, Franco L. The Many Roads from Alternative Splicing to Cancer: Molecular Mechanisms Involving Driver Genes. Cancers (Basel) 2024; 16:2123. [PMID: 38893242 PMCID: PMC11171328 DOI: 10.3390/cancers16112123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer driver genes are either oncogenes or tumour suppressor genes that are classically activated or inactivated, respectively, by driver mutations. Alternative splicing-which produces various mature mRNAs and, eventually, protein variants from a single gene-may also result in driving neoplastic transformation because of the different and often opposed functions of the variants of driver genes. The present review analyses the different alternative splicing events that result in driving neoplastic transformation, with an emphasis on their molecular mechanisms. To do this, we collected a list of 568 gene drivers of cancer and revised the literature to select those involved in the alternative splicing of other genes as well as those in which its pre-mRNA is subject to alternative splicing, with the result, in both cases, of producing an oncogenic isoform. Thirty-one genes fall into the first category, which includes splicing factors and components of the spliceosome and splicing regulators. In the second category, namely that comprising driver genes in which alternative splicing produces the oncogenic isoform, 168 genes were found. Then, we grouped them according to the molecular mechanisms responsible for alternative splicing yielding oncogenic isoforms, namely, mutations in cis splicing-determining elements, other causes involving non-mutated cis elements, changes in splicing factors, and epigenetic and chromatin-related changes. The data given in the present review substantiate the idea that aberrant splicing may regulate the activation of proto-oncogenes or inactivation of tumour suppressor genes and details on the mechanisms involved are given for more than 40 driver genes.
Collapse
Affiliation(s)
- Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London WC1E 6DD, UK;
| | - Gerardo López-Rodas
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
| | - Josefa Castillo
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Luis Franco
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
| |
Collapse
|
6
|
Kerry J, Specker EJ, Mizzoni M, Brumwell A, Fell L, Goodbrand J, Rosen MN, Uniacke J. Autophagy-dependent alternative splicing of ribosomal protein S24 produces a more stable isoform that aids in hypoxic cell survival. FEBS Lett 2024; 598:503-520. [PMID: 38281767 DOI: 10.1002/1873-3468.14804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/08/2023] [Accepted: 12/24/2023] [Indexed: 01/30/2024]
Abstract
Cells remodel splicing and translation machineries to mount specialized gene expression responses to stress. Here, we show that hypoxic human cells in 2D and 3D culture models increase the relative abundance of a longer mRNA variant of ribosomal protein S24 (RPS24L) compared to a shorter mRNA variant (RPS24S) by favoring the inclusion of a 22 bp cassette exon. Mechanistically, RPS24L and RPS24S are induced and repressed, respectively, by distinct pathways in hypoxia: RPS24L is induced in an autophagy-dependent manner, while RPS24S is reduced by mTORC1 repression in a hypoxia-inducible factor-dependent manner. RPS24L produces a more stable protein isoform that aids in hypoxic cell survival and growth, which could be exploited by cancer cells in the tumor microenvironment.
Collapse
Affiliation(s)
- Jenna Kerry
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Erin J Specker
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Morgan Mizzoni
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Andrea Brumwell
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Leslie Fell
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Jenna Goodbrand
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - Michael N Rosen
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| | - James Uniacke
- Department of Molecular and Cellular Biology, University of Guelph, Canada
| |
Collapse
|