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Trilla-Fuertes L, Gámez-Pozo A, Nogué M, Busquier I, Arias F, López-Campos F, Fernández-Montes A, Ruiz A, Velázquez C, Martín-Bravo C, Pérez-Ruiz E, Asensio E, Hernández-Yagüe X, Rodrigues A, Ghanem I, López-Vacas R, Hafez A, Arias P, Dapía I, Solís M, Dittmann A, Ramos R, Llorens C, Maurel J, Campos-Barros Á, Fresno Vara JÁ, Feliu J. Utility of CYP2D6 copy number variants as prognostic biomarker in localized anal squamous cell carcinoma. Cancer 2023. [PMID: 37096763 DOI: 10.1002/cncr.34797] [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] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND Anal squamous cell carcinoma (ASCC) is an infrequent tumor whose treatment has not changed since the 1970s. The aim of this study is the identification of biomarkers allowing personalized treatments and improvement of therapeutic outcomes. METHODS Forty-six paraffin tumor samples from ASCC patients were analyzed by whole-exome sequencing. Copy number variants (CNVs) were identified and their relation to disease-free survival (DFS) was studied and validated in an independent retrospective cohort of 101 ASCC patients from the Multidisciplinary Spanish Digestive Cancer Group (GEMCAD). GEMCAD cohort proteomics allowed assessing the biological features of these tumors. RESULTS On the discovery cohort, the median age was 61 years old, 50% were males, stages I/II/III: 3 (7%)/16 (35%)/27 (58%), respectively, median DFS was 33 months, and overall survival was 45 months. Twenty-nine genes whose duplication was related to DFS were identified. The most representative was duplications of the CYP2D locus, including CYP2D6, CYP2D7P, and CYP2D8P genes. Patients with CYP2D6 CNV had worse DFS at 5 years than those with two CYP2D6 copies (21% vs. 84%; p < .0002, hazard ratio [HR], 5.8; 95% confidence interval [CI], 2.7-24.9). In the GEMCAD validation cohort, patients with CYP2D6 CNV also had worse DFS at 5 years (56% vs. 87%; p = .02, HR = 3.6; 95% CI, 1.1-5.7). Mitochondria and mitochondrial cell-cycle proteins were overexpressed in patients with CYP2D6 CNV. CONCLUSIONS Tumor CYP2D6 CNV identified patients with a significantly worse DFS at 5 years among localized ASCC patients treated with 5-fluorouracil, mitomycin C, and radiotherapy. Proteomics pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets for these high-risk patients. PLAIN LANGUAGE SUMMARY Anal squamous cell carcinoma is an infrequent tumor whose treatment has not been changed since the 1970s. However, disease-free survival in late staged tumors is between 40% and 70%. The presence of an alteration in the number of copies of CYP2D6 gene is a biomarker of worse disease-free survival. The analysis of the proteins in these high-risk patients pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets. Therefore, the determination of the number of copies of CYP2D6 allows the identification of anal squamous carcinoma patients with a high-risk of relapse that could be redirected to a clinical trial. Additionally, this study may be useful to suggest new treatment strategies to increase current therapy efficacy.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
| | - Miguel Nogué
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital de Granollers, Barcelona, Spain
| | - Isabel Busquier
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Provincial de Castellón, Castellón, Spain
| | - Fernando Arias
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Radiotherapy Oncology Service, Complejo Hospitalario de Navarra, Navarra, Spain
| | - Fernando López-Campos
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Radiotherapy Oncology Service, Hospital Ramón y Cajal, Madrid, Spain
| | - Ana Fernández-Montes
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Ana Ruiz
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain
| | - Concepción Velázquez
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Miguel Servet, Zaragoza, Spain
| | | | - Elisabeth Pérez-Ruiz
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga, Hospitales Universitarios Regional y Virgen de la Victoria, Málaga, Spain
| | - Elena Asensio
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital General Universitario de Elche, Elche, Spain
| | - Xavier Hernández-Yagüe
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Instituto Catalán de Oncología-Girona, Girona, Spain
| | - Aline Rodrigues
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Ismael Ghanem
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario La Paz, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Ahmed Hafez
- Biotechvana SL, Parque Científico de Madrid, Madrid, Spain
| | - Pedro Arias
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Irene Dapía
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Mario Solís
- Bioinformatics Unit, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Antje Dittmann
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Ricardo Ramos
- Genomics Unit, Parque Científico de Madrid, Madrid, Spain
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, Madrid, Spain
| | - Joan Maurel
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics, IdiPAZ, Hospital Universitario La Paz/CIBERER Unit 753, ISCIII, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Jaime Feliu
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario La Paz, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
- Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Madrid, Spain
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Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite. Genes (Basel) 2023; 14:genes14020267. [PMID: 36833195 PMCID: PMC9957322 DOI: 10.3390/genes14020267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/08/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called "RNASeq" and "VariantSeq" to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, "RNASeq" and "VariantSeq" are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user's PC under any operating system or on remote servers, as a cloud solution. "RNASeq" and "VariantSeq" are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. "RNASeq" and "VariantSeq" also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software.
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Astaras C, De Vito C, Chaskar P, Bornand A, Khanfir K, Sciarra A, Letovanec I, Corro C, Dietrich PY, Tsantoulis P, Koessler T. The first comprehensive genomic characterization of rectal squamous cell carcinoma. J Gastroenterol 2023; 58:125-134. [PMID: 36357817 PMCID: PMC9876866 DOI: 10.1007/s00535-022-01937-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/31/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Rectal cancers represent 35% of colorectal cancers; 90% are adenocarcinomas, while squamous cell carcinoma accounts for 0.3% of them. Given its rarity, little is known concerning its pathogenesis, molecular profile and therapeutic management. The current treatment trend is to treat rectal squamous cell carcinoma by analogy to anal squamous cell carcinoma with definitive chemo-radiotherapy, setting aside surgery in case of local recurrence. METHODS We performed an in-depth genomic analysis (next-generation sequencing, copy number variation, and human papilloma virus characterization) on 10 rectal squamous cell carcinoma samples and compared them in silico to those of anal squamous cell carcinoma and rectal adenocarcinoma. RESULTS Rectal squamous cell carcinoma shows 100% HPV positivity. It has a mutational (PIK3CA, PTEN, TP53, ATM, BCL6, SOX2) and copy number variation profile (3p, 10p, 10q, 16q deletion and 1q, 3q, 5p, 8q, 20p gain) similar to anal squamous cell carcinoma. PI3K/Akt/mTOR is the most commonly affected signaling pathway similarly to anal squamous cell carcinoma. Most commonly gained or lost genes seen in rectal adenocarcinoma (FLT3, CDX2, GNAS, BCL2, SMAD4, MALT1) are not found in rectal squamous cell carcinoma. CONCLUSION This study presents the first comprehensive genomic characterization of rectal squamous cell carcinoma. We confirm the existence of this rare histology and its molecular similarity with anal squamous cell carcinoma. This molecular proximity confirms the adequacy of therapeutic management based on histology and not localization, suggesting that rectal squamous cell carcinoma should be treated like anal squamous cell carcinoma and not as a rectal adenocarcinoma.
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Affiliation(s)
- Christoforos Astaras
- grid.150338.c0000 0001 0721 9812Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland
| | - Claudio De Vito
- grid.150338.c0000 0001 0721 9812Pathology Department, Geneva University Hospitals, Geneva, Switzerland
| | - Prasad Chaskar
- grid.150338.c0000 0001 0721 9812Pathology Department, Geneva University Hospitals, Geneva, Switzerland
| | - Aurelie Bornand
- grid.150338.c0000 0001 0721 9812Pathology Department, Geneva University Hospitals, Geneva, Switzerland
| | - Kaouthar Khanfir
- grid.418149.10000 0000 8631 6364Radiation Oncology Department, Valais Hospital, Sion, Switzerland
| | - Amedeo Sciarra
- grid.418149.10000 0000 8631 6364Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
| | - Igor Letovanec
- grid.418149.10000 0000 8631 6364Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
| | - Claudia Corro
- grid.150338.c0000 0001 0721 9812Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland ,grid.511014.0Swiss Cancer Center Léman, Lausanne, Geneva Switzerland ,grid.8591.50000 0001 2322 4988Translational Research Center in Onco-Hematology, Department of Medicine, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Pierre-Yves Dietrich
- grid.150338.c0000 0001 0721 9812Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland ,grid.511014.0Swiss Cancer Center Léman, Lausanne, Geneva Switzerland ,grid.8591.50000 0001 2322 4988Translational Research Center in Onco-Hematology, Department of Medicine, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Petros Tsantoulis
- grid.150338.c0000 0001 0721 9812Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Translational Research Center in Onco-Hematology, Department of Medicine, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Thibaud Koessler
- Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland. .,Swiss Cancer Center Léman, Lausanne, Geneva, Switzerland.
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Carr RM, Jin Z, Hubbard J. Research on Anal Squamous Cell Carcinoma: Systemic Therapy Strategies for Anal Cancer. Cancers (Basel) 2021; 13:cancers13092180. [PMID: 34062753 PMCID: PMC8125190 DOI: 10.3390/cancers13092180] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Anal cancer is rare with an estimated 9000 new cases predicted to occur in the United States in 2021. However, rates of new anal cancer cases and deaths from the disease are increasing by about 2% and 3% per year respectively. In light of these trends it is critical to better understand the nature of this disease and progress in its management. The present review focuses on the history and development of the role of systemic therapy in the treatment of anal cancer. Major trials establishing the role of chemotherapy in the management of locoregional and metastatic anal cancer are summarized. In addition, the rapidly evolving role of immunotherapy is discussed. Finally, major insights into the molecular pathobiology of anal cancer and opportunities for advancement in precision medicine in treatment of the disease. Abstract Anal squamous cell carcinoma (ASCC) is a rare malignancy, with most cases associated with human papilloma virus and an increased incidence in immunocompromised patients. Progress in management of ASCC has been limited not only due to its rarity, but also the associated lack of research funding and social stigma. Historically, standard of care for invasive ASCC has been highly morbid surgical resection, requiring a permanent colostomy. Surgery was associated with disease recurrence in approximately half of the patients. However, the use of chemotherapy (5-fluorouracil and mitomycin C) concomitantly with radiation in the 1970s resulted in disease regression, curing a subset of patients and sparing them from morbid surgery. Validation of the use of systemic therapy in prospective trials was not achieved until approximately 20 years later. In this review, advancements and shortcomings in the use of systemic therapy in the management of ASCC will be discussed. Not only will standard-of-care systemic therapies for locoregional and metastatic disease be reviewed, but the evolving role of novel treatment strategies such as immune checkpoint inhibitors, HPV-based vaccines, and molecularly targeted therapies will also be covered. While advances in ASCC treatment have remained largely incremental, with increased biological insight, an increasing number of promising systemic treatment modalities are being explored.
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Iseas S, Golubicki M, Robbio J, Ruiz G, Guerra F, Mariani J, Salanova R, Cabanne A, Eleta M, Gonzalez JV, Basiletti J, Picconi MA, Masciangioli G, Carballido M, Roca E, Mendez G, Coraglio M, Abba MC. A clinical and molecular portrait of non-metastatic anal squamous cell carcinoma. Transl Oncol 2021; 14:101084. [PMID: 33789221 PMCID: PMC8026912 DOI: 10.1016/j.tranon.2021.101084] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/20/2022] Open
Abstract
High-risk HPV infection is less frequently detected in HIV-positive non-metastatic ASCC compared with HIV-negative cases. Mutational profile identified in the non-metastatic ASCC cohort revealed expected similarities with metastatic ASCC. High PD-L1 expression levels are associated with high CD3 and CD8 TIL density, complete response to treatment, and good survival outcome of ASCC patients. PD-L1 is a reliable predictive and prognostic biomarker that allows the stratification in low- vs. high-risk ASCC patients at their initial therapeutic approach.
Anal squamous cell carcinoma (ASCC) is a rare gastrointestinal malignancy associated with high-risk Human papillomavirus (HPV) infection. Despite improved outcomes in non-metastatic ASCC, definitive chemoradiotherapy constitutes the standard treatment for localized disease. Evidences for predictive and prognostic biomarkers are limited. Here, we performed a viral, immune, and mutational characterization of 79 non-metastatic ASCC patients with complete definitive chemoradiotherapy. HPV-16 was detected in 91% of positive cases in single infections (78%) or in coinfections with multiple genotypes (22%). Fifty-four percent of non-metastatic ASCC cases displayed mutations affecting cancer driver genes such as PIK3CA (21% of cases), TP53 (15%), FBXW7 (9%), and APC (6%). PD-L1 expression was detected in 57% of non-metastatic ASCC. Increased PD-L1 positive cases (67%) were detected in patients with complete response compared with non-complete response to treatment (37%) (p = 0.021). Furthermore, patients with PD-L1 positive tumors were significantly associated with better disease-free survival (DFS) and overall survival (OS) compared with patients with PD-L1 negative tumors (p = 0.006 and p = 0.002, respectively). PD-L1 expression strongly impacts CR rate and survival of non-metastatic ASCC patients after standard definitive chemoradiotherapy. PD-L1 expression could be used to stratify good versus poor responders avoiding the associated morbidity with abdominal perineal resection.
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Affiliation(s)
- Soledad Iseas
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina.
| | - Mariano Golubicki
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Juan Robbio
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Gonzalo Ruiz
- Pathology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Florencia Guerra
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Javier Mariani
- Department of Cardiology, "El Cruce" Hospital. Av. Calchaquí 5401, Florencio Varela, Buenos Aires, C1888, Argentina
| | - Ruben Salanova
- Pathology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Ana Cabanne
- Pathology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Martin Eleta
- Imaxe Image Diagnosis Center, Av. Córdoba 2340, Ciudad Autónoma de Buenos Aires C1120, Argentina
| | - Joaquin V Gonzalez
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires C1282, Argentina
| | - Jorge Basiletti
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires C1282, Argentina
| | - María Alejandra Picconi
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires C1282, Argentina
| | - Guillermo Masciangioli
- Proctology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Marcela Carballido
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Enrique Roca
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Guillermo Mendez
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Mariana Coraglio
- Proctology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo". Av. Caseros 2061, Ciudad Autónoma de Buenos Aires C1264, Argentina
| | - Martin C Abba
- Basic and Applied Immunological Research Center (CINIBA), School of Medical Sciences, National University of La Plata, Calle 60 y 120, La Plata C1900, Argentina.
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Huang Y, Chen S, Qin W, Wang Y, Li L, Li Q, Yuan X. A Novel RNA Binding Protein-Related Prognostic Signature for Hepatocellular Carcinoma. Front Oncol 2020; 10:580513. [PMID: 33251144 PMCID: PMC7673432 DOI: 10.3389/fonc.2020.580513] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly malignant and aggressive cancer with high recurrence rates and mortality. Some studies have illustrated that RNA binding proteins (RBPs) were involved in the carcinogenesis and development of multiple cancers, but the roles in HCC were still unclear. We downloaded the RNA-seq and corresponding clinical information of HCC from The Cancer Genome Atlas (TCGA) database, and 330 differentially expressed RBPs were identified between normal and HCC tissues. Through series of the univariate, the least absolute shrinkage selection operator (LASSO), and the stepwise multivariate Cox regression analyses, six prognosis-related key RBPs (CNOT6, UPF3B, MRPL54, ZC3H13, IFIT5, and PPARGC1A) were screened out from DE RBPs, and a six-RBP gene risk score signature was constructed in training set. Survival analysis indicated that HCC patients with high-risk scores had significantly worse overall survival than low-risk patients, and furthermore, the signature can be used as an independent prognostic indicator. The good accuracy of this prognostic signature was confirmed by the ROC curve analysis and was further validated in the International Cancer Genome Consortium (ICGC) HCC cohort. Besides, a nomogram based on six RBP genes was established and internally validated in the TCGA cohort. Gene set enrichment analysis demonstrated some cancer-related phenotypes were significantly gathered in the high-risk group. Overall, our study first identified an RBP-related six-gene prognostic signature, which could serve as a promising prognostic biomarker and provide some potential therapeutic targets for HCC.
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Affiliation(s)
- Yongbiao Huang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Long Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
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