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Church MC, Workman JL. The SWI/SNF chromatin remodeling complex: a critical regulator of metabolism. Biochem Soc Trans 2024; 52:1327-1337. [PMID: 38666605 PMCID: PMC11346436 DOI: 10.1042/bst20231141] [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: 02/06/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
The close relationship between chromatin and metabolism has been well-studied in recent years. Many metabolites have been found to be cofactors used to modify chromatin, and these modifications can in turn affect gene transcription. One chromatin-associated factor responsible for regulating transcription is the SWI/SNF complex, an ATP-dependent chromatin remodeler conserved throughout eukaryotes. SWI/SNF was originally described in yeast as regulating genes involved in carbon source metabolism and mating type switching, and its mammalian counterpart has been extensively studied for its role in diseases such as cancer. The yeast SWI/SNF complex is closely associated with activation of stress response genes, many of which have metabolic functions. It is now recognized that this is a conserved function of the complex, and recent work has shown that mammalian SWI/SNF is also a key regulator of metabolic transcription. Emerging evidence suggests that loss of SWI/SNF introduces vulnerabilities to cells due to this metabolic influence, and that this may present opportunities for treatment of SWI/SNF-deficient cancers.
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Affiliation(s)
- Michael C. Church
- Stowers Institute of Medical Research, 1000 E 50th Street, Kansas City, MO 64118, U.S.A
| | - Jerry L. Workman
- Stowers Institute of Medical Research, 1000 E 50th Street, Kansas City, MO 64118, U.S.A
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Li K, Qi L, Tang G, Xu H, Li Z, Fan B, Li Z, Li Y. Epigenetic Regulation in Urothelial Carcinoma. Curr Mol Med 2024; 24:85-97. [PMID: 36545729 DOI: 10.2174/1566524023666221221094432] [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: 05/24/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022]
Abstract
Urothelial carcinoma (UC) is a common malignancy that remains a clinical challenge: Non-muscle-invasive urothelial carcinoma (NMIUC) has a high rate of recurrence and risk of progression, while muscle-invasive urothelial carcinoma (MIUC) has a high mortality. Although some new treatments, such as immunotherapies, have shown potential effects on some patients, most cases of advanced UC remain incurable. While treatments based on epigenetic mechanisms, whether combined with traditional platinum-based chemotherapy or emerging immunotherapy, show therapeutic advantages. With the advancement of sequencing and bioinformatics, the study of epigenomics, containing DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA, is increasingly linked with the occurrence and progression of UC. Since the epigenetics of UC is a constantly developing field of medicine, this review aims to summarize the latest research on epigenetic regulation of UC, generalize the mechanism of epigenetics in UC, and reveal the potential epigenetic therapies in the clinical setting, in order to provide some new clues on the discovery of new drugs based on the epigenetics.
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Affiliation(s)
- Ke Li
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Lin Qi
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Guyu Tang
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Haozhe Xu
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhi Li
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Bo Fan
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhongbei Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Yuan Li
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, China
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Li Z, Zhao J, Tang Y. Advances in the role of SWI/SNF complexes in tumours. J Cell Mol Med 2023; 27:1023-1031. [PMID: 36883311 PMCID: PMC10098296 DOI: 10.1111/jcmm.17709] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
Cancer development is a complex process involving both genetic and epigenetic changes. The SWI/SNF (switch/sucrose non-fermentable) chromatin remodelling complex, one of the most studied ATP-dependent complexes, plays an important role in coordinating chromatin structural stability, gene expression and post-translational modifications. The SWI/SNF complex can be classified into BAF, PBAF and GBAF according to their constituent subunits. Cancer genome sequencing studies have shown a high incidence of mutations in genes encoding subunits of the SWI/SNF chromatin remodelling complex, with abnormalities in one or more of these genes present in nearly 25% of all cancers, which indicating that stabilizing normal expression of genes encoding subunits in the SWI/SNF complex may prevent tumorigenesis. In this paper, we will review the relationship between the SWI/SNF complex and some clinical tumours and its mechanism of action. The aim is to provide a theoretical basis to guide the diagnosis and treatment of tumours caused by mutations or inactivation of one or more genes encoding subunits of the SWI/SNF complex in the clinical setting.
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Affiliation(s)
- Ziwei Li
- Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jiumei Zhao
- Chongqing Nanchuan District People's Hospital, Chongqing, China
| | - Yu Tang
- The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China.,Department of Genetics, Zunyi Medical University, Guizhou, China
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Adhikari S, Guha D, Mohan C, Mukherjee S, Tyler JK, Das C. Reprogramming Carbohydrate Metabolism in Cancer and Its Role in Regulating the Tumor Microenvironment. Subcell Biochem 2022; 100:3-65. [PMID: 36301490 PMCID: PMC10760510 DOI: 10.1007/978-3-031-07634-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Altered metabolism has become an emerging feature of cancer cells impacting their proliferation and metastatic potential in myriad ways. Proliferating heterogeneous tumor cells are surrounded by other resident or infiltrating cells, along with extracellular matrix proteins, and other secretory factors constituting the tumor microenvironment. The diverse cell types of the tumor microenvironment exhibit different molecular signatures that are regulated at their genetic and epigenetic levels. The cancer cells elicit intricate crosstalks with these supporting cells, exchanging essential metabolites which support their anabolic processes and can promote their survival, proliferation, EMT, angiogenesis, metastasis and even therapeutic resistance. In this context, carbohydrate metabolism ensures constant energy supply being a central axis from which other metabolic and biosynthetic pathways including amino acid and lipid metabolism and pentose phosphate pathway are diverged. In contrast to normal cells, increased glycolytic flux is a distinguishing feature of the highly proliferative cancer cells, which supports them to adapt to a hypoxic environment and also protects them from oxidative stress. Such rewired metabolic properties are often a result of epigenetic alterations in the cancer cells, which are mediated by several factors including, DNA, histone and non-histone protein modifications and non-coding RNAs. Conversely, epigenetic landscapes of the cancer cells are also dictated by their diverse metabolomes. Altogether, this metabolic and epigenetic interplay has immense potential for the development of efficient anti-cancer therapeutic strategies. In this book chapter we emphasize upon the significance of reprogrammed carbohydrate metabolism in regulating the tumor microenvironment and cancer progression, with an aim to explore the different metabolic and epigenetic targets for better cancer treatment.
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Affiliation(s)
- Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Deblina Guha
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Chitra Mohan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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Szarkowska J, Cwiek P, Szymanski M, Rusetska N, Jancewicz I, Stachowiak M, Swiatek M, Luba M, Konopinski R, Kubala S, Zub R, Kucharz J, Wiechno P, Siedlecki JA, Markowicz S, Sarnowska E, Sarnowski TJ. RRM2 gene expression depends on BAF180 subunit of SWISNF chromatin remodeling complex and correlates with abundance of tumor infiltrating lymphocytes in ccRCC. Am J Cancer Res 2021; 11:5965-5978. [PMID: 35018236 PMCID: PMC8727810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/12/2021] [Indexed: 06/14/2023] Open
Abstract
About 40% of clear cell renal cell carcinoma (ccRCC) cases carry the pbrm1 mutation inactivating BAF180 subunit of the SWI/SNF chromatin remodeling complex (CRC). Here we show that the majority of transcriptomic changes appear at the stage I of ccRCC development. By contrast, the stage II ccRCC exhibits hyperactivation of DNA replication demonstrated by the overexpression of several genes, e.g., RRM1 and RRM2 genes encoding subunits of ribonucleotide reductase (RNR) complex. We found that the degree of RRM1 and RRM2 upregulation in ccRCC patients depends on pbrm1 mutation. We show that the BAF180 protein product of the PBRM1 gene directly binds to RRM1 and RRM2 loci. The BAF180 binding regions are targeted by regulatory proteins previously reported as SWI/SNF CRC interacting partners. BAF180 binding to RRMs loci correlates with enrichment of H3K27me3 in case of RRM1 and H3K14Ac on RRM2, indicating the existence of differential regulatory mechanism controlling expression of these genes. We found that the strong overexpression of RRM2 in ccRCC patient samples correlates with T cell infiltration. Surprisingly, the majority of tumor infiltrating lymphocytes (TILs) consisted of CD4+ T cells. Furthermore, we show that exhausted CD4+ T cells induced the expression of the RRM2 gene in the primary ccRCC cell line. Collectively, our results provide the link between PBRM1 loss, RRM2 expression and T cell infiltration, which may lead to the establishment of new treatment of this disease.
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Affiliation(s)
- Joanna Szarkowska
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Pawel Cwiek
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Michal Szymanski
- Department of Urology and Urological Oncology, Central Clinical Hospital of Ministry of the Interior and Administration in WarsawWarsaw, Poland
| | - Natalia Rusetska
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Iga Jancewicz
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Malgorzata Stachowiak
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Monika Swiatek
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Maciej Luba
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Ryszard Konopinski
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Szymon Kubala
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Renata Zub
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Jakub Kucharz
- Department of Uro-oncology, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Pawel Wiechno
- Department of Uro-oncology, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Sergiusz Markowicz
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Elzbieta Sarnowska
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
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Ding H, Huang Y, Shi J, Wang L, Liu S, Zhao B, Liu Y, Yang J, Chen Z. Attenuated expression of SNF5 facilitates progression of bladder cancer via STAT3 activation. Cancer Cell Int 2021; 21:655. [PMID: 34876150 PMCID: PMC8650342 DOI: 10.1186/s12935-021-02363-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SWI/SNF, a well-known ATP-dependent chromatin-remodeling complex, plays an essential role in several biological processes. SNF5, the core subunit of the SWI/SNF remodeling complex, inactivated in 95% of malignant rhabdoid tumors (MRT), highlighting its significance in tumorigenesis. However, the role of SNF5 in bladder cancer (BC) remains unknown. In this study, we aimed to investigate the function and potential clinical applicability of SNF5 in BC. METHODS Data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and Cancer Cell Line Encyclopedia (CCLE) databases were used to evaluate the clinical significance of SNF5 in BC. We performed Gene Set Enrichment Analysis (GSEA) and functional assays to investigate the role of SNF5 in BC. Genomics of Drug Sensitivity in Cancer (GDSC) and drug-susceptibility tests were performed to identify the potential value of SNF5 in the treatment of BC. RESULTS Low SNF5 expression conferred a poor prognosis and was significantly associated with the N-stage in BC. ROC curves indicated that SNF5 could distinguish BC from the normal tissues. In vitro and in vivo functional assays demonstrated that attenuated SNF5 expression could promote cell proliferation and enhance migration by STAT3 activation. We imputed that low SNF5 expression could confer greater resistance against conventional first-line drugs, including cisplatin and gemcitabine in BC. GDSC and drug-resistance assays suggested that low SNF5 expression renders T24 and 5637 cells high sensitivity to EGFR inhibitor gefitinib, and combination of EZH2 inhibitor GSK126 and cisplatin. CONCLUSIONS To the best of our knowledge, the present study, for the first time, showed that low SNF5 expression could promote cell proliferation and migration by activating STAT3 and confer poor prognosis in BC. Importantly, SNF5 expression may be a promising candidate for identifying BC patients who could benefit from EGFR-targeted chemotherapy or cisplatin in combination with EZH2 inhibitor treatment regimens.
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Affiliation(s)
- Hua Ding
- Department of Urology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yaqin Huang
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Jiazhong Shi
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Liwei Wang
- Department of Urology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.,Unit 32357 of People's Liberation Army, Pujiang, 611630, China
| | - Sha Liu
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Baixiong Zhao
- Department of Urology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yuting Liu
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Jin Yang
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Zhiwen Chen
- Department of Urology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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Xiao ZM, Lv DJ, Yu YZ, Wang C, Xie T, Wang T, Song XL, Zhao SC. SMARCC1 Suppresses Tumor Progression by Inhibiting the PI3K/AKT Signaling Pathway in Prostate Cancer. Front Cell Dev Biol 2021; 9:678967. [PMID: 34249931 PMCID: PMC8267926 DOI: 10.3389/fcell.2021.678967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
Background SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily C member 1 (SMARCC1) protein is a potential tumor suppressor in various cancers. However, its role in prostate cancer (PCa) remains controversial. The aim of this study was to determine the biological function of SMARCC1 in PCa and explore the underlying regulatory mechanisms. Methods The expression of SMARCC1 was validated in PCa tissues by immunohistochemistry. Meanwhile, function experiments were used to evaluate the regulatory role on cell proliferation and metastasis in PCa cells with SMARCC1 depletion both in vitro and in vivo. The expression levels of relevant proteins were detected by Western blotting. Results Our finding showed that SMARCC1 was significantly downregulated in prostate adenocarcinoma, with a higher Gleason score (GS) than that in low GS. The decreased expression of SMARCC1 was significantly correlated with a higher GS and poor prognosis. Additionally, we found that silencing of SMARCC1 dramatically accelerated cell proliferation by promoting cell cycle progression and enhancing cell migration by inducing epithelial mesenchymal transition (EMT). Furthermore, depletion of SMARCC1 facilitated PCa xenograft growth and lung metastasis in murine models. Mechanistically, the loss of SMARCC1 activated the PI3K/AKT pathway in PCa cells. Conclusion SMARCC1 suppresses PCa cell proliferation and metastasis via the PI3K/AKT signaling pathway and is a novel therapeutic target.
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Affiliation(s)
- Zhao-Ming Xiao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dao-Jun Lv
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu-Zhong Yu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chong Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Xie
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xian-Lu Song
- Department of Radiotherapy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Urology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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Liu Z, Sun T, Zhang Z, Bi J, Kong C. An 18-gene signature based on glucose metabolism and DNA methylation improves prognostic prediction for urinary bladder cancer. Genomics 2021; 113:896-907. [PMID: 33096258 DOI: 10.1016/j.ygeno.2020.10.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/23/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Glucose metabolism and DNA methylation play important roles in cancers. We aimed to identify glucose metabolism-related genes that were DNA methylation associated to establish a prognostic signature of bladder cancer (BLCA). METHODS With BLCA sample transcriptome data from The Cancer Genome Atlas (TCGA) and methylation data from TCGA 450 K microarray, glucose metabolism-related genes associated to prognosis and DNA methylation were identified and a prognostic signature was established. GSEA and WGCNA analysis were performed and two genes, UCHL1 and PYCR1, were selected for functional validations. RESULTS 18 target genes were identified and the signature based on them was considered an effective and independent prognostic factor. Several pathways were enriched in the high-risk group by GSEA and three modules of genes were identified by WGCNA. UCHL1 and PYCR1 proliferated proliferation, migration and invasion ability of bladder cancer cells. CONCLUSIONS The 18-gene signature is an independent prognostic factor for bladder cancer patients.
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Affiliation(s)
- Zhuonan Liu
- Department of Urology, Fist Hospital of China Medical University, School of China Medical University, No. 155 Nanjing North Street, Heping District, Shenyang City, Liaoning Province 110004, PR China
| | - Tianshui Sun
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Zhe Zhang
- Department of Urology, Fist Hospital of China Medical University, School of China Medical University, No. 155 Nanjing North Street, Heping District, Shenyang City, Liaoning Province 110004, PR China
| | - Jianbin Bi
- Department of Urology, Fist Hospital of China Medical University, School of China Medical University, No. 155 Nanjing North Street, Heping District, Shenyang City, Liaoning Province 110004, PR China.
| | - Chuize Kong
- Department of Urology, Fist Hospital of China Medical University, School of China Medical University, No. 155 Nanjing North Street, Heping District, Shenyang City, Liaoning Province 110004, PR China.
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Identification of metabolism-associated genes and construction of a prognostic signature in bladder cancer. Cancer Cell Int 2020; 20:538. [PMID: 33292266 PMCID: PMC7643334 DOI: 10.1186/s12935-020-01627-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Bladder cancer (BC) is a commonly diagnosed malignant tumor in the urinary system, with a high morbidity and a high recurrence rate. Current studies indicated that metabolism-associated genes (MAGs) having critical roles in the etiology of BC. The present study aims to identify differentially expressed MAGs and construct a MAGs based prognostic risk signature for BC by using The Cancer Genome Atlas (TCGA) database and proteomics data. METHODS RNA-sequence data from the TCGA database and proteomics data from our BC samples were used to identify differentially expressed MAGs and construct a MAGs based prognostic signature in BC. Subsequently, survival analysis and nomogram were used to evaluate the prognostic and predictive value of the MAGs based signature in BC. RNA isolation and reverse transcription‑quantitative PCR (RT-qPCR) were further performed to investigate the expression levels of MAGs in BC cells and explore the relationship between MAGs and M2 tumor associated macrophages (TAMs) secreted transforming growth factor-β1 (TGF-β1) in BC cells. RESULTS A total of 23 differentially expressed MAGs were identified and five MAGs were finally used to construct a MAGs based signature. Survival analysis revealed that the MAGs based signature was closely correlated with the survival outcomes of patients with BC. A nomogram with the MAGs based signature risk score and clinical features was also constructed to facilitate the individualized prediction of BC patients. RT-qPCR showed that five MAGs were significantly differentially expressed and the expression levels of three MAGs were positively correlated with M2 TAMs secreted TGF-β1 in T24 cells. CONCLUSIONS Our study identified novel prognostic MAGs and constructed a MAGs based signature, which can be used as an independent factor in evaluating the prognosis of patients with BC. Furthermore, M2 TAMs may promote the expression of MAGs via the TGF-β1 signaling pathway in the microenvironment of BC. Further clinical trials and experimental explorations are needed to validate our observations in BC.
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Stachowiak M, Szymanski M, Ornoch A, Jancewicz I, Rusetska N, Chrzan A, Demkow T, Siedlecki JA, Sarnowski TJ, Sarnowska E. SWI/SNF chromatin remodeling complex and glucose metabolism are deregulated in advanced bladder cancer. IUBMB Life 2020; 72:1175-1188. [PMID: 32073734 PMCID: PMC7317882 DOI: 10.1002/iub.2254] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 02/03/2020] [Indexed: 12/18/2022]
Abstract
Bladder cancer (BC) is a frequently diagnosed malignancy affecting predominantly adult and elderly populations. It is expected that due to the longer life time, BC will become even more frequent in the future; thus in consequence, it will represent serious health problem of older society part. The treatment of advanced BC is mostly ineffective due to its very aggressive behavior. So far, no effective targeted therapy is used for BC treatment. Here, we found that BC is characterized by lower protein levels of BRM, INI1, and BAF155 main subunits of SWI/SNF chromatin remodeling complex (CRC) which is involved in global control of gene expression and influences various important cellular processes like: cell cycle control, apoptosis, DNA repair, etc. Moreover, the expression of SMARCA2, a BRM encoding gene, strongly correlated with BC metastasis and expression of such metabolic genes as PKM2 and PRKAA1. Furthermore, the analysis of T24 and 5637 commonly used BC cell lines revealed different expression levels of metabolic genes including FBP1 gene encoding Frutose-1,6-Bisphosphatase, an enzyme controlling glycolysis flux and gluconeogenesis. The tested BC cell lines exhibited various molecular and metabolic alterations as well as differential glucose uptake, growth rate, and migration potential. We have shown that BRM subunit is involved in the transcriptional control of genes encoding metabolic enzymes. Moreover, we found that the FBP1 expression level and the SWI/SNF CRCs may serve as markers of molecular subtypes of BC. Collectively, this study may provide a new knowledge about the molecular and metabolic BC subtypes which likely will be of high importance for the clinic in the future.
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Affiliation(s)
- Malgorzata Stachowiak
- Department of Molecular and Translational OncologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Michal Szymanski
- Department of Uro‐oncologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Anna Ornoch
- Department of Molecular and Translational OncologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Iga Jancewicz
- Department of Molecular and Translational OncologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Natalia Rusetska
- Department of Molecular and Translational OncologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Alicja Chrzan
- Department of PathologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Tomasz Demkow
- Department of Uro‐oncologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Janusz A. Siedlecki
- Department of Molecular and Translational OncologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Tomasz J. Sarnowski
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Elzbieta Sarnowska
- Department of Molecular and Translational OncologyMaria Sklodowska‐Curie National Research Institute of OncologyWarsawPoland
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