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Zhang F, Zheng L, Zhou W, He X, Liao S. HNRNPL Increases WSB1 mRNA Stability to Promote Proliferation and Lipid Droplets in Clear Cell Renal Cell Carcinoma. Cell Biochem Biophys 2024:10.1007/s12013-024-01309-6. [PMID: 38822203 DOI: 10.1007/s12013-024-01309-6] [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] [Accepted: 05/09/2024] [Indexed: 06/02/2024]
Abstract
This study aims to explore the possible effect and mechanism of heterogeneous nuclear ribonucleoprotein L (HNRNPL) on the lipid droplet and proliferation ability of clear cell renal cell carcinoma (ccRCC). The mRNA and protein expressions of HNRNPL and WSB1 on ccRCC tissues and cells were detected using qRT-PCR and western blot. The lipid droplet of cells was assessed after Oil Red O staining and BODIPY 493/503 staining. Cell proliferation was detected by CCK-8 assay. The interaction between HNRNPL and WSB1 was verified using RNA immunoprecipitation (RIP) and RNA-pull down assay. WSB1 mRNA stability was measured by Actinomycin D. Elevated expressions of HNRNPL and WSB1 were found in both ccRCC tissues and cells. HNRNPL knockdown can lead to suppressed lipid droplet and cell proliferation ability of ccRCC cells, while expression pattern was found in cells with HNRNPL overexpression. RIP and RNA-pull down assay clarified the binding of HNRNPL with WSB1. HNRNPL can facilitate the stability and expression of WSB1 mRNA. Rescue assay identified the promotive effect of HNRNPL on lipid droplets and cell proliferation of ccRCC cells can be abolished in response to WSB1 knockdown. Collected evidence summarized that HNRNPL can increase the stability of WSB1 mRNA to promote lipid droplet and proliferation ability in ccRCC cells.
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Affiliation(s)
- Fabiao Zhang
- Department of Urology, Fujian Medical University Affiliated Sanming First Hospital, Sanming, Fujian, 365000, PR China
| | - Luoping Zheng
- Department of Urology, Fujian Medical University Affiliated Sanming First Hospital, Sanming, Fujian, 365000, PR China
| | - Wenhu Zhou
- Department of Urology, Fujian Medical University Affiliated Sanming First Hospital, Sanming, Fujian, 365000, PR China
| | - Xiyuan He
- Department of Urology, Zhangjiajie People's Hospital, Zhangjiajie, Hunan, 427000, PR China
| | - Shangfan Liao
- Department of Urology, Fujian Medical University Affiliated Sanming First Hospital, Sanming, Fujian, 365000, PR China.
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2
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Zhou L, Zhou W, Li Y, Hua R. m1A Regulatory gene signatures are associated with certain immune cell compositions of the tumor microenvironment and predict survival in kidney renal clear cell carcinoma. Eur J Med Res 2023; 28:321. [PMID: 37679761 PMCID: PMC10483733 DOI: 10.1186/s40001-023-01292-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
Adenosine N1 methylation (m1A) of RNA, a type of post-transcriptional modification, has been shown to play a significant role in the progression of cancer. The objective of the current research was to analyze the genetic alteration and prognostic significance of m1A regulators in kidney renal clear cell carcinoma (KIRC). Genomic and clinicopathological characteristics were obtained from 558 KIRC patients in the Cancer Genome Atlas (TCGA) and Gene Omnibus Expression (GEO) databases. Alterations in the gene expression of ten m1A-regulators were analyzed and survival analysis was performed using the Cox regression method. We also identified three clusters of patients based on their distinct m1A alteration patterns, using integrated analysis of the ten m1A-related regulators, which were significantly related to overall survival (OS), disease-free survival (DFS) and tumor microenvironment (TME) immune cell infiltration cells in KIRC. Our findings showed that m1A alteration patterns have critical roles in determining TME complexity and its immune cell composition. Furthermore, different m1A expression patterns were significantly associated with DFS and OS rates in KIRC patients. In conclusion, the identified m1A RNA modification patterns offer a potentially effective way to classify KIRC patients based on their TME immune cell infiltration, enabling the development of more personalized and successful treatment strategies for these patients.
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Affiliation(s)
- Linjun Zhou
- Department of Nephrology, Ganzhou Hospital of Guangdong Provincial People's Hospital, Ganzhou Municipal Hospital, Ganzhou, China
| | - Weidong Zhou
- Department of Emergency, Zhanggongqu Hospital Of Traditional Chinese Medicine, Ganzhou, China
| | - Yuan Li
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA, 91016, USA.
| | - Ruifang Hua
- Department of Nephrology, Ganzhou Hospital of Guangdong Provincial People's Hospital, Ganzhou Municipal Hospital, Ganzhou, China.
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Meng K, Hu Y, Wang D, Li Y, Shi F, Lu J, Wang Y, Cao Y, Zhang CZ, He QY. EFHD1, a novel mitochondrial regulator of tumor metastasis in clear cell renal cell carcinoma. Cancer Sci 2023; 114:2029-2040. [PMID: 36747492 PMCID: PMC10154798 DOI: 10.1111/cas.15749] [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: 10/18/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
The biological function of many mitochondrial proteins in mechanistic detail has not been well investigated in clear cell renal cell carcinoma (ccRCC). A seven-mitochondrial-gene signature was generated by Lasso regression analysis to improve the prediction of prognosis of patients with ccRCC, using The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium cohort. Among those seven genes, EFHD1 is less studied and its role in the progression of ccRCC remains unknown. The decreased expression of EFHD1 was validated in clinical samples and was correlated with unfavorable outcome. Overexpression of EFHD1 in ccRCC cells resulted in the reduction of mitochondrial Ca2+ , and the inhibition of cell migration and invasion in vitro and tumor metastasis in vivo. Mechanistically, EFHD1 physically bound to the core mitochondrial calcium transporter (mitochondrial calcium uniporter, MCU) through its N-terminal domain. The interaction between EFHD1 and MCU suppressed the uptake of Ca2+ into mitochondria, and deactivated the Hippo/YAP signaling pathway. Further data revealed that the ectopic expression of EFHD1 upregulated STARD13 to enhance the phosphorylation of YAP protein at Ser-127. The knockdown of STARD13 or the overexpression of MCU partly abrogated the EFHD1-mediated induction of phosphorylation of YAP at Ser-127 and suppression of cell migration. Taken together, the newly identified EFHD1-MCU-STARD13 axis participates in the modulation of the Hippo/YAP pathway and serves as a novel regulator in the progression of ccRCC.
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Affiliation(s)
- Kun Meng
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China.,The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuyu Hu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Dingkang Wang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Yuying Li
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Fujin Shi
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Jiangli Lu
- Department of Pathology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yang Wang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Yun Cao
- Department of Pathology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chris Zhiyi Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China.,The First Affiliated Hospital of Jinan University, Guangzhou, China
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Tang Y, Jin Y, Li H, Xin H, Chen J, Li X, Pan Y. PBRM1
deficiency oncogenic addiction is associated with activated
AKT–mTOR
signalling and aerobic glycolysis in clear cell renal cell carcinoma cells. J Cell Mol Med 2022; 26:3837-3849. [PMID: 35672925 PMCID: PMC9279584 DOI: 10.1111/jcmm.17418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/16/2022] Open
Abstract
The PBRM1 (PB1) gene which encodes the specific subunit BAF180 of the PBAF SWI/SNF complex, is highly mutated (~ 40%) in clear cell renal cell carcinoma (ccRCC). However, its functions and impact on cell signalling are still not fully understood. Aerobic glycolysis, also known as the ‘Warburg Effect’, is a hallmark of cancer, whether PB1 is involved in this metabolic shift in clear cell renal cell carcinoma remains unclear. Here, with established stable knockdown PB1 cell lines, we performed functional assays to access the effects on 786‐O and SN12C cells. Based on the RNA‐seq data, we selected some genes encoding key glycolytic enzymes, including PFKP, ENO1, PKM and LDHA, and examined the expression levels. The AKT–mTOR signalling pathway activity and expression of HIF1α were also analysed. Our data demonstrate that PB1 deficiency promotes the proliferation, migration, Xenograft growth of 786‐O and SN12C cells. Notably, knockdown of PB1 activates AKT–mTOR signalling and increases the expression of key glycolytic enzymes at both mRNA and protein levels. Furthermore, we provide evidence that deficient PB1 and hypoxic conditions exert a synergistic effect on HIF 1α expression and lactate production. Thus, our study provides novel insights into the roles of tumour suppressor PB1 and suggests that the AKT–mTOR signalling pathway, as well as glycolysis, is a potential drug target for ccRCC patients with deficient PB1.
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Affiliation(s)
- Yu Tang
- Department of Medical Genetics Zunyi Medical University Zunyi China
- Key Laboratory of Gene Detection and Treatment in Guizhou Province Zunyi China
| | - Yan‐Hong Jin
- Department of Medical Genetics Zunyi Medical University Zunyi China
- Key Laboratory of Gene Detection and Treatment in Guizhou Province Zunyi China
| | - Hu‐Li Li
- Department of Medical Genetics Zunyi Medical University Zunyi China
| | - Hui Xin
- Department of Medical Genetics Zunyi Medical University Zunyi China
- Key Laboratory of Gene Detection and Treatment in Guizhou Province Zunyi China
| | - Jin‐Dong Chen
- Department of Urology University of Rochester Medical Center Rochester New York USA
- Exploring Health LLC Guangzhou China
| | - Xue‐Ying Li
- Department of Medical Genetics Zunyi Medical University Zunyi China
| | - You‐Fu Pan
- Department of Medical Genetics Zunyi Medical University Zunyi China
- Key Laboratory of Gene Detection and Treatment in Guizhou Province Zunyi China
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5
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Huang M, Zhang T, Yao ZY, Xing C, Wu Q, Liu YW, Xing XL. MicroRNA related prognosis biomarkers from high throughput sequencing data of kidney renal clear cell carcinoma. BMC Med Genomics 2021; 14:72. [PMID: 33750388 PMCID: PMC7941961 DOI: 10.1186/s12920-021-00932-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC) is the most common type of kidney cell carcinoma which has the worst overall survival rate. Almost 30% of patients with localized cancers eventually develop to metastases despite of early surgical treatment carried out. MicroRNAs (miRNAs) play a critical role in human cancer initiation, progression, and prognosis. The aim of our study was to identify potential prognosis biomarkers to predict overall survival of KIRC. METHODS All data were downloaded from an open access database The Cancer Genome Atlas. DESeq2 package in R was used to screening the differential expression miRNAs (DEMs) and genes (DEGs). RegParallel and Survival packages in R was used to analysis their relationships with the KIRC patients. David version 6.8 and STRING version 11 were used to take the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. RESULTS We found 2 DEGs (TIMP3 and HMGCS1) and 3 DEMs (hsa-miR-21-5p, hsa-miR-223-3p, and hsa-miR-365a-3p) could be prognosis biomarkers for the prediction of KIRC patients. The constructed prognostic model based on those 2 DEGs could effectively predict the survival status of KIRC. And the constructed prognostic model based on those 3 DEMs could effectively predict the survival status of KIRC in 3-year and 5-year. CONCLUSION The current study provided novel insights into the miRNA related mRNA network in KIRC and those 2 DEGs biomarkers and 3 DEMs biomarkers may be independent prognostic signatures in predicting the survival of KIRC patients.
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Affiliation(s)
- Minjiang Huang
- Hunan University of Medicine, Huaihua, 418000, Hunan, People's Republic of China
| | - Ti Zhang
- Hunan University of Medicine, Huaihua, 418000, Hunan, People's Republic of China
| | - Zhi-Yong Yao
- Hunan University of Medicine, Huaihua, 418000, Hunan, People's Republic of China
| | - Chaoqung Xing
- The First Affiliated Hospital of Hunan University of Medicine, Huaihua, 418000, Hunan, People's Republic of China
| | - Qingyi Wu
- Hunan University of Medicine, Huaihua, 418000, Hunan, People's Republic of China
| | - Yuan-Wu Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Xiao-Liang Xing
- Hunan University of Medicine, Huaihua, 418000, Hunan, People's Republic of China.
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6
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Perron G, Jandaghi P, Solanki S, Safisamghabadi M, Storoz C, Karimzadeh M, Papadakis AI, Arseneault M, Scelo G, Banks RE, Tost J, Lathrop M, Tanguay S, Brazma A, Huang S, Brimo F, Najafabadi HS, Riazalhosseini Y. A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes. Cell Rep 2018; 23:1639-1650. [PMID: 29742422 DOI: 10.1016/j.celrep.2018.04.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 03/03/2018] [Accepted: 04/06/2018] [Indexed: 01/13/2023] Open
Abstract
Widespread remodeling of the transcriptome is a signature of cancer; however, little is known about the post-transcriptional regulatory factors, including RNA-binding proteins (RBPs) that regulate mRNA stability, and the extent to which RBPs contribute to cancer-associated pathways. Here, by modeling the global change in gene expression based on the effect of sequence-specific RBPs on mRNA stability, we show that RBP-mediated stability programs are recurrently deregulated in cancerous tissues. Particularly, we uncovered several RBPs that contribute to the abnormal transcriptome of renal cell carcinoma (RCC), including PCBP2, ESRP2, and MBNL2. Modulation of these proteins in cancer cell lines alters the expression of pathways that are central to the disease and highlights RBPs as driving master regulators of RCC transcriptome. This study presents a framework for the screening of RBP activities based on computational modeling of mRNA stability programs in cancer and highlights the role of post-transcriptional gene dysregulation in RCC.
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Affiliation(s)
- Gabrielle Perron
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Pouria Jandaghi
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Shraddha Solanki
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Maryam Safisamghabadi
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Cristina Storoz
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Mehran Karimzadeh
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Andreas I Papadakis
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Madeleine Arseneault
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), 150 cours Albert Thomas, Lyon 69008, France
| | - Rosamonde E Banks
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Jorg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, 2 rue Gaston Crémieux, 91000 Evry, France
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Simon Tanguay
- Department of Urology, McGill University, Montreal, QC H3G 1A4, Canada
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Fadi Brimo
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada.
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada.
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