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Integrated Analysis and Identification of Critical RNA-Binding Proteins in Bladder Cancer. Cancers (Basel) 2022; 14:cancers14153739. [PMID: 35954405 PMCID: PMC9367304 DOI: 10.3390/cancers14153739] [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: 06/15/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The role of RNA-binding proteins (RBPs) in bladder cancer (BC) remains unclear. Therefore, we analyzed the clinical information and RNA sequencing data from patients with BC and identified RBPs that may be promising predictors of BC. Abstract RBPs in the development and progression of BC remains unclear. Here, we elucidated the role of RBPs in predicting the survival of patients with BC. Clinical information and RNA sequencing data of the training and validation cohorts were downloaded from the Cancer Genome Atlas and Gene Expression Omnibus databases, respectively. Survival-related differentially expressed RBPs were identified using Cox regression analyses. A total of 113 upregulated and 54 downregulated RBPs were observed, with six showing prognostic values (AHNAK, MAP1B, LAMA2, P4HB, FASN, and GSDMB). In both the GSE32548 and GSE31684 datasets, patients with low-risk scores in survival-related six RBPs-based prognostic model showed longer overall survival than those with high-risk scores. AHNAK, MAP1B, P4HB, and FASN expression were significantly upregulated in both BC tissues and cell lines. BC tissues from high-risk group showed higher proportions of naive CD4+ T cells, M0 and M2 macrophages, and neutrophils and lower proportions of plasma cells, CD8+ T cells, and T-cell follicular helper compared to low-risk group. AHNAK knockdown significantly inhibited the proliferation, invasion, and migration of BC cells in vitro and inhibited the growth of subcutaneous tumors in vivo. We thus developed and functionally validated a novel six RBPs-based prognostic model for BC.
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Wang V, Geybels MS, Jordahl KM, Gerke T, Hamid A, Penney KL, Markt SC, Freedman M, Pomerantz M, Lee GSM, Rana H, Börnigen D, Rebbeck TR, Huttenhower C, Eeles RA, Stanford JL, Consortium P, Berndt SI, Claessens F, Sørensen KD, Park JY, Vega A, Usmani N, Mucci L, Sweeney CJ. A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer. Prostate 2021; 81:683-693. [PMID: 33956343 PMCID: PMC8491321 DOI: 10.1002/pros.24148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/19/2021] [Accepted: 04/22/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Inflammation and one of its mediators, NF-kappa B (NFκB), have been implicated in prostate cancer carcinogenesis. We assessed whether germline polymorphisms associated with NFκB are associated with the risk of developing lethal disease (metastases or death from prostate cancer). METHODS Using a Bayesian approach leveraging NFκB biology with integration of publicly available datasets we used a previously defined genome-wide functional association network specific to NFκB and lethal prostate cancer. A dense-module-searching method identified modules enriched with significant genes from a genome-wide association study (GWAS) study in a discovery data set, Physicians' Health Study and Health Professionals Follow-up Study (PHS/HPFS). The top 48 candidate single nucleotide polymorphisms (SNPs) from the dense-module-searching method were then assessed in an independent prostate cancer cohort and the one SNP reproducibly associated with lethality was tested in a third cohort. Logistic regression models evaluated the association between each SNP and lethal prostate cancer. The candidate SNP was assessed for association with lethal prostate cancer in 6 of 28 studies in the prostate cancer association group to investigate cancer associated alterations in the genome (PRACTICAL) Consortium where there was some medical record review for death ascertainment which also had SNP data from the ONCOARRAY platform. All men self-identified as Caucasian. RESULTS The rs1910301 SNP which was reproducibly associated with lethal disease was nominally associated with lethal disease (odds ratio [OR] = 1.40; p = .02) in the discovery cohort and the minor allele was also associated with lethal disease in two independent cohorts (OR = 1.35; p = .04 and OR = 1.35; p = .07). Fixed effects meta-analysis of all three cohorts found an association: OR = 1.37 (95% confidence interval [CI]: 1.15-1.62, p = .0003). This SNP is in the promoter region of FRAS1, a gene involved in epidermal-basement membrane adhesion and is present at a higher frequency in men with African ancestry. No association was found in the subset of studies from the PRACTICAL consortium studies which had a total of 106 deaths out total of 3263 patients and a median follow-up of 4.4 years. CONCLUSIONS Through its connection with the NFκB pathway, a candidate SNP with a higher frequency in men of African ancestry without cancer was found to be associated with lethal prostate cancer across three well-annotated independent cohorts of Caucasian men.
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Affiliation(s)
- Victoria Wang
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Milan S Geybels
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Kristina M Jordahl
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, USA
| | - Travis Gerke
- Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Anis Hamid
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah C Markt
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Matthew Freedman
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Gwo-Shu M Lee
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Huma Rana
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniela Börnigen
- University Medical Center Hamburg-Eppendorf, Bioinformatics Core, Hamburg, Germany
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Timothy R Rebbeck
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ros A Eeles
- Oncogenetics, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, USA
| | - Practical Consortium
- Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, Santiago de Compostela, Spain
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Lorelei Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Christopher J Sweeney
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
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Berglund AE, Putney RM, Creed JH, Aden-Buie G, Gerke TA, Rounbehler RJ. Accessible Pipeline for Translational Research Using TCGA: Examples of Relating Gene Mechanism to Disease-Specific Outcomes. Methods Mol Biol 2021; 2194:127-142. [PMID: 32926365 DOI: 10.1007/978-1-0716-0849-4_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bioinformatic scientists are often asked to do widespread analyses of publicly available datasets in order to identify genetic alterations in cancer for genes of interest; therefore, we sought to create a set of tools to conduct common statistical analyses of The Cancer Genome Atlas (TCGA) data. These tools have been developed in response to requests from our collaborators to ask questions, validate findings, and better understand the function of their gene of interest. We describe here what data we have used, how to obtain it, and what figures we have found useful.
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Affiliation(s)
- Anders E Berglund
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
| | - Ryan M Putney
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jordan H Creed
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Garrick Aden-Buie
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Travis A Gerke
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Robert J Rounbehler
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
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Besso MJ, Montivero L, Lacunza E, Argibay MC, Abba M, Furlong LI, Colas E, Gil-Moreno A, Reventos J, Bello R, Vazquez-Levin MH. Identification of early stage recurrence endometrial cancer biomarkers using bioinformatics tools. Oncol Rep 2020; 44:873-886. [PMID: 32705231 PMCID: PMC7388212 DOI: 10.3892/or.2020.7648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 04/22/2020] [Indexed: 01/08/2023] Open
Abstract
Endometrial cancer (EC) is the sixth most common cancer in women worldwide. Early diagnosis is critical in recurrent EC management. The present study aimed to identify biomarkers of EC early recurrence using a workflow that combined text and data mining databases (DisGeNET, Gene Expression Omnibus), a prioritization algorithm to select a set of putative candidates (ToppGene), protein-protein interaction network analyses (Search Tool for the Retrieval of Interacting Genes, cytoHubba), association analysis of selected genes with clinicopathological parameters, and survival analysis (Kaplan-Meier and Cox proportional hazard ratio analyses) using a The Cancer Genome Atlas cohort. A total of 10 genes were identified, among which the targeting protein for Xklp2 (TPX2) was the most promising independent prognostic biomarker in stage I EC. TPX2 expression (mRNA and protein) was higher (P<0.0001 and P<0.001, respectively) in ETS variant transcription factor 5-overexpressing Hec1a and Ishikawa cells, a previously reported cell model of aggressive stage I EC. In EC biopsies, TPX2 mRNA expression levels were higher (P<0.05) in high grade tumors (grade 3) compared with grade 1–2 tumors (P<0.05), in tumors with deep myometrial invasion (>50% compared with <50%; P<0.01), and in intermediate-high recurrence risk tumors compared with low-risk tumors (P<0.05). Further validation studies in larger and independent EC cohorts will contribute to confirm the prognostic value of TPX2.
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Affiliation(s)
- María José Besso
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET)‑Fundación IBYME (FIBYME), Ciudad Autónoma de Buenos Aires 1428ADN, Argentina
| | - Luciana Montivero
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET)‑Fundación IBYME (FIBYME), Ciudad Autónoma de Buenos Aires 1428ADN, Argentina
| | - Ezequiel Lacunza
- Centro de Investigaciones Inmunológicas, Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires 1900, Argentina
| | - María Cecilia Argibay
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET)‑Fundación IBYME (FIBYME), Ciudad Autónoma de Buenos Aires 1428ADN, Argentina
| | - Martín Abba
- Centro de Investigaciones Inmunológicas, Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires 1900, Argentina
| | - Laura Inés Furlong
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Eva Colas
- Biomedical Research Group in Gynecology, Vall d´Hebron Research Institute (VHIR), Universitat Autónoma de Barcelona, CIBERONC, 08035 Barcelona, Spain
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall d´Hebron Research Institute (VHIR), Universitat Autónoma de Barcelona, CIBERONC, 08035 Barcelona, Spain
| | - Jaume Reventos
- Biomedical Research Group in Gynecology, Vall d´Hebron Research Institute (VHIR), Universitat Autónoma de Barcelona, CIBERONC, 08035 Barcelona, Spain
| | - Ricardo Bello
- Departamento de Metodología, Estadística y Matemática, Universidad de Tres de Febrero, Sáenz Peña, Buenos Aires B1674AHF, Argentina
| | - Mónica Hebe Vazquez-Levin
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET)‑Fundación IBYME (FIBYME), Ciudad Autónoma de Buenos Aires 1428ADN, Argentina
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The Tristetraprolin Family of RNA-Binding Proteins in Cancer: Progress and Future Prospects. Cancers (Basel) 2020; 12:cancers12061539. [PMID: 32545247 PMCID: PMC7352335 DOI: 10.3390/cancers12061539] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays a key role in cellular proliferation, differentiation, migration, and apoptosis. Increasing evidence suggests dysregulated post-transcriptional gene expression as an important mechanism in the pathogenesis of cancer. The tristetraprolin family of RNA-binding proteins (RBPs), which include Zinc Finger Protein 36 (ZFP36; commonly referred to as tristetraprolin (TTP)), Zinc Finger Protein 36 like 1 (ZFP36L1), and Zinc Finger Protein 36 like 2 (ZFP36L2), play key roles in the post-transcriptional regulation of gene expression. Mechanistically, these proteins function by binding to the AU-rich elements within the 3′-untranslated regions of their target mRNAs and, in turn, increasing mRNA turnover. The TTP family RBPs are emerging as key regulators of multiple biological processes relevant to cancer and are aberrantly expressed in numerous human cancers. The TTP family RBPs have tumor-suppressive properties and are also associated with cancer prognosis, metastasis, and resistance to chemotherapy. Herein, we summarize the various hallmark molecular traits of cancers that are reported to be regulated by the TTP family RBPs. We emphasize the role of the TTP family RBPs in the regulation of trait-associated mRNA targets in relevant cancer types/cell lines. Finally, we highlight the potential of the TTP family RBPs as prognostic indicators and discuss the possibility of targeting these TTP family RBPs for therapeutic benefits.
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Legrand N, Dixon DA, Sobolewski C. AU-rich element-binding proteins in colorectal cancer. World J Gastrointest Oncol 2019; 11:71-90. [PMID: 30788036 PMCID: PMC6379757 DOI: 10.4251/wjgo.v11.i2.71] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/11/2018] [Accepted: 01/01/2019] [Indexed: 02/05/2023] Open
Abstract
Trans-acting factors controlling mRNA fate are critical for the post-transcriptional regulation of inflammation-related genes, as well as for oncogene and tumor suppressor expression in human cancers. Among them, a group of RNA-binding proteins called “Adenylate-Uridylate-rich elements binding proteins” (AUBPs) control mRNA stability or translation through their binding to AU-rich elements enriched in the 3’UTRs of inflammation- and cancer-associated mRNA transcripts. AUBPs play a central role in the recruitment of target mRNAs into small cytoplasmic foci called Processing-bodies and stress granules (also known as P-body/SG). Alterations in the expression and activities of AUBPs and P-body/SG assembly have been observed to occur with colorectal cancer (CRC) progression, indicating the significant role AUBP-dependent post-transcriptional regulation plays in controlling gene expression during CRC tumorigenesis. Accordingly, these alterations contribute to the pathological expression of many early-response genes involved in prostaglandin biosynthesis and inflammation, along with key oncogenic pathways. In this review, we summarize the current role of these proteins in CRC development. CRC remains a major cause of cancer mortality worldwide and, therefore, targeting these AUBPs to restore efficient post-transcriptional regulation of gene expression may represent an appealing therapeutic strategy.
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Affiliation(s)
- Noémie Legrand
- Department of Microbiology, Faculty of Medicine, University of Geneva, Geneva CH-1211, Switzerland
| | - Dan A Dixon
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, and University of Kansas Cancer Center, Kansas City, KS 66045, United States
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva CH-1211, Switzerland
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