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Yuan T, Wankhede D, Edelmann D, Kather JN, Tagscherer KE, Roth W, Bewerunge-Hudler M, Brobeil A, Kloor M, Bläker H, Brenner H, Hoffmeister M. Large-scale external validation and meta-analysis of gene methylation biomarkers in tumor tissue for colorectal cancer prognosis. EBioMedicine 2024; 105:105223. [PMID: 38917511 PMCID: PMC11255517 DOI: 10.1016/j.ebiom.2024.105223] [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: 02/15/2024] [Revised: 04/29/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND DNA methylation biomarkers in colorectal cancer (CRC) tissue hold potential as prognostic indicators. However, individual studies have yielded heterogeneous results, and external validation is largely absent. We conducted a comprehensive external validation and meta-analysis of previously suggested gene methylation biomarkers for CRC prognosis. METHODS We performed a systematic search to identify relevant studies investigating gene methylation biomarkers for CRC prognosis until March 2024. Our external validation cohort with long-term follow-up included 2303 patients with CRC from 22 hospitals in southwest Germany. We used Cox regression analyses to assess associations between previously suggested gene methylation biomarkers and prognosis, adjusting for clinical variables. We calculated pooled hazard ratios (HRs) and their 95% confidence intervals (CIs) using random-effects models. FINDINGS Of 151 single gene and 29 multiple gene methylation biomarkers identified from 121 studies, 37 single gene and seven multiple gene biomarkers were significantly associated with CRC prognosis after adjustment for clinical variables. Moreover, the directions of these associations with prognosis remained consistent between the original studies and our validation analyses. Seven single biomarkers and two multi-biomarker signatures were significantly associated with CRC prognosis in the meta-analysis, with a relatively strong level of evidence for CDKN2A, WNT5A, MLH1, and EVL. INTERPRETATION In a comprehensive evaluation of the so far identified gene methylation biomarkers for CRC prognosis, we identified candidates with potential clinical relevance for further investigation. FUNDING The German Research Council, the Interdisciplinary Research Program of the National Center for Tumor Diseases (NCT), Germany, the German Federal Ministry of Education and Research.
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Affiliation(s)
- Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Durgesh Wankhede
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany
| | | | - Wilfried Roth
- Institute of Pathology, University Medical Center Mainz, Mainz, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Alexander Brobeil
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias Kloor
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hendrik Bläker
- Institute of Pathology, University of Leipzig Medical Center, Leipzig, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Damasio MPS, Nascimento CS, Andrade LM, de Oliveira VL, Calzavara-Silva CE. The role of T-cells in head and neck squamous cell carcinoma: From immunity to immunotherapy. Front Oncol 2022; 12:1021609. [PMID: 36338731 PMCID: PMC9632296 DOI: 10.3389/fonc.2022.1021609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) encompass a group of complex entities of tumours affecting the aerodigestive upper tract. The main risk factors are strongly related to tobacco and alcohol consumption, but also HPV infection is often associated. Surgery, radiotherapy and/or chemotherapy are the standard treatments, though the 5-year overall survival is less than 50%. The advances in genomics, molecular medicine, immunology, and nanotechnology have shed a light on tumour biology which helps clinical researchers to obtain more efficacious and less toxic therapies. Head and neck tumours possess different immune escape mechanisms including diminishing the immune response through modulating immune checkpoints, in addition to the recruitment and differentiation of suppressive immune cells. The insights into the HNSCC biology and its strong interaction with the tumour microenvironment highlights the role of immunomodulating agents. Recently, the knowledge of the immunological features of these tumours has paved the way for the discovery of effective biomarkers that allow a better selection of patients with odds of improving overall survival through immunotherapy. Specially biomarkers regarding immune checkpoint inhibitors antibodies, such as anti-PD-1/PD-L1 and anti-CTLA-4 in combination with standard therapy or as monotherapy. New immunotherapies to treat head and neck cancer carcinomas, such as CAR T cells and nanoparticles have been the center of attention and in this review, we discuss the necessity of finding targets for the T cell in the cancer cells to generate CAR T cells, but also the relevance of evaluating specificity and safety of those therapies.
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Affiliation(s)
- Marcos Paulo S. Damasio
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Camila Sales Nascimento
- Grupo de pesquisa em Imunologia Celular e Molecular, Fundação Oswaldo Cruz, Instituto Rene Rachou, Belo Horizonte, MG, Brazil
| | - Lidia M. Andrade
- Departamento de Genética, Ecologia e Evolução, Departamento de Física, Nanobiomedical Research Group, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vivian L. de Oliveira
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, São Paulo, Brazil
- Laboratório de Imunologia, LIM19, Instituto do Coração (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil
| | - Carlos Eduardo Calzavara-Silva
- Grupo de pesquisa em Imunologia Celular e Molecular, Fundação Oswaldo Cruz, Instituto Rene Rachou, Belo Horizonte, MG, Brazil
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Huang J, Huo H, Lu R. A Novel Signature of Necroptosis-Associated Genes as a Potential Prognostic Tool for Head and Neck Squamous Cell Carcinoma. Front Genet 2022; 13:907985. [PMID: 35754840 PMCID: PMC9218670 DOI: 10.3389/fgene.2022.907985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) arises from squamous cells in the oral cavity, pharynx and larynx. Although HNSCC is sensitive to radiotherapy, patient prognosis is poor. Necroptosis is a novel programmed form of necrotic cell death. The prognostic value of necroptosis-associated gene expression in HNSCC has not been explored. Material and Methods: We downloaded mRNA expression data of HNSCC patients from TCGA databases and Gene Expression Omnibus (GEO) databases, and compared gene expression between tumor tissues and adjacent normal tissues to identify differentially expressed genes (DEGs) and necroptosis-related prognostic genes. A model with necroptosis-related genes was established to predict patient prognosis via LASSO method and Kaplan-Meier analysis. GSE65858 data set (n = 270) from GEO was used to verify the model's predictive ability. Gene set enrichment analyses, immune microenvironment analysis, principal component analysis, and anti-tumor compound IC50 prediction were also performed. Results: We identified 49 DEGs and found 10 DEGs were associated with patient survival (p < 0.05). A risk model of 6-gene signature was constructed using the TCGA training data set and further validated with the GEO data set. Patients in the low-risk group survived longer than those in the high-risk group (p < 0.05) in the GEO validation sets. Functional analysis showed the two patient groups were associated with distinct immunity conditions and IC50. Conclusion: We constructed a prognostic model with 6 necroptosis-associated genes for HNSCC. The model has potential usage to guide treatment because survival was different between the two groups.
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Affiliation(s)
- Jing Huang
- Department of Pharmacy, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Hongqi Huo
- Nuclear Medicine Department, Handan Central Hospital, Handan, China
| | - Rong Lu
- Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen Key Laboratory of Genetic Testing, School of Medicine, Xiamen University, Xiamen, China
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Bahrami A, Hassanian SM, Khazaei M, Gharib M, Rahmani M, Fiuji H, Jazayeri MH, Moetamani-Ahmadi M, Ferns GA, Avan A. The 9p21 locus as a potential therapeutic target and prognostic marker in colorectal cancer. Pharmacogenomics 2018; 19:463-474. [DOI: 10.2217/pgs-2017-0096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is a major cause of cancer-related-death worldwide. Despite extensive efforts to identify valid biomarkers for the risk stratification of CRC patients, there are few of proven clinical utility. It is recognized that genetic factors play a major role in determining susceptibility to CRC. Recent genome-wide association studies have demonstrated common genetic variants in a region on chromosome 9p21 associated with an increased risk of CRC. Several genetic polymorphisms have been identified in this region that are associated with CRC. Three genes are located at this locus; CDKN2B(encoding-p15ink4b), CDKN2A (encoding-p16ink4a/p14ARF) and 3′ end of CDKN2BAS (termed-antisense-noncoding-RNA in the INK4-locus [ANRIL]). ANRIL has a post-transcriptional modulatory activity, which has been shown to perturb the expression of nearby genes. It also plays an important role in coordinating tissue remodeling through regulation of cell proliferation, apoptosis, aging, extra-cellular matrix remodeling and inflammatory response. However, the role of ANRIL is not well understood in CRC. Hypermethylation of the p14ARF and p16INK4a genes is often found in some tumors, including CRC. However, further studies are necessary to explore the clinical utility of these putative markers in risk stratification, and in the assessment of prognosis. In this review, we have summarized the prognostic and therapeutic potential of the p14ARF and p16INK4a genes in patients with colorectal cancer.
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Affiliation(s)
- Afsane Bahrami
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjnad, Iran
- Department of Modern Sciences & Technologies; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Department of Physiology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masoumeh Gharib
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Rahmani
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Fiuji
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mir Hadi Jazayeri
- Immunology Research Center, and Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex B. 9PH, UK
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Prognostic DNA methylation markers for sporadic colorectal cancer: a systematic review. Clin Epigenetics 2018; 10:35. [PMID: 29564023 PMCID: PMC5851322 DOI: 10.1186/s13148-018-0461-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/21/2018] [Indexed: 02/06/2023] Open
Abstract
Background Biomarkers that can predict the prognosis of colorectal cancer (CRC) patients and that can stratify high-risk early stage patients from low-risk early stage patients are urgently needed for better management of CRC. During the last decades, a large variety of prognostic DNA methylation markers has been published in the literature. However, to date, none of these markers are used in clinical practice. Methods To obtain an overview of the number of published prognostic methylation markers for CRC, the number of markers that was validated independently, and the current level of evidence (LoE), we conducted a systematic review of PubMed, EMBASE, and MEDLINE. In addition, we scored studies based on the REMARK guidelines that were established in order to attain more transparency and complete reporting of prognostic biomarker studies. Eighty-three studies reporting on 123 methylation markers fulfilled the study entry criteria and were scored according to REMARK. Results Sixty-three studies investigated single methylation markers, whereas 20 studies reported combinations of methylation markers. We observed substantial variation regarding the reporting of sample sizes and patient characteristics, statistical analyses, and methodology. The median (range) REMARK score for the studies was 10.7 points (4.5 to 17.5) out of a maximum of 20 possible points. The median REMARK score was lower in studies, which reported a p value below 0.05 versus those, which did not (p = 0.005). A borderline statistically significant association was observed between the reported p value of the survival analysis and the size of the study population (p = 0.051). Only 23 out of 123 markers (17%) were investigated in two or more study series. For 12 markers, and two multimarker panels, consistent results were reported in two or more study series. For four markers, the current LoE is level II, for all other markers, the LoE is lower. Conclusion This systematic review reflects that adequate reporting according to REMARK and validation of prognostic methylation markers is absent in the majority of CRC methylation marker studies. However, this systematic review provides a comprehensive overview of published prognostic methylation markers for CRC and highlights the most promising markers that have been published in the last two decades. Electronic supplementary material The online version of this article (10.1186/s13148-018-0461-8) contains supplementary material, which is available to authorized users.
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Cao B, Zhou X, Yang W, Ma J, Zhou W, Fan D, Hong L. The role of cell-free DNA in predicting colorectal cancer prognosis. Expert Rev Gastroenterol Hepatol 2018; 12:39-48. [PMID: 28838275 DOI: 10.1080/17474124.2017.1372191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colorectal cancer is a cancer of the digestive system with poor prognosis. Cell-free DNA has received much attention with its unique predominance, especially in colorectal cancer. Areas covered: This study has summarized recent advancements and challenges regarding cell-free DNA in predicting CRC prognosis. Furthermore, the authors make predictions on the potential developments concerning cell-free DNA in future prognosis prediction techniques. Expert commentary: Cell-free DNA has the value of predicting CRC prognosis as an important biomarke. Further clinical trials should be performed to promote translating cell-free DNA into clinical applications.
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Affiliation(s)
- Bo Cao
- a The First Brigade of Student , Fourth Military Medical University , Xi'an , China
| | - Xin Zhou
- a The First Brigade of Student , Fourth Military Medical University , Xi'an , China
| | - Wanli Yang
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
| | - Jiaojiao Ma
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
| | - Wei Zhou
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
| | - Daiming Fan
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
| | - Liu Hong
- b State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , Fourth Military Medical University , Xi'an , China
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Wu D, Chen X, Xu Y, Wang H, Yu G, Jiang L, Hong Q, Duan S. Prognostic value of MLH1 promoter methylation in male patients with esophageal squamous cell carcinoma. Oncol Lett 2017; 13:2745-2750. [PMID: 28454461 DOI: 10.3892/ol.2017.5759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/06/2017] [Indexed: 10/20/2022] Open
Abstract
The DNA mismatch repair (MMR) gene MutL homolog 1 (MLH1) is critical for the maintenance of genomic integrity. Methylation of the MLH1 gene promoter was identified as a prognostic marker for numerous types of cancer including glioblastoma, colorectal, ovarian and gastric cancer. The present study aimed to determine whether MLH1 promoter methylation was associated with survival in male patients with esophageal squamous cell carcinoma (ESCC). Formalin-fixed, paraffin-embedded ESCC tissues were collected from 87 male patients. MLH1 promoter methylation was assessed using the methylation-specific polymerase chain reaction approach. Kaplan-Meier survival curves and log-rank tests were used to evaluate the association between MLH1 promoter methylation and overall survival (OS) in patients with ESCC. Cox regression analysis was used to obtain crude and multivariate hazard ratios (HR), and 95% confidence intervals (CI). The present study revealed that MLH1 promoter methylation was observed in 53/87 (60.9%) of male patients with ESCC. Kaplan-Meier survival analysis demonstrated that MLH1 promoter hypermethylation was significantly associated with poorer prognosis in patients with ESCC (P=0.048). Multivariate survival analysis revealed that MLH1 promoter hypermethylation was an independent predictor of poor OS in male patients with ESCC (HR=1.716; 95% CI=1.008-2.921). Therefore, MLH1 promoter hypermethylation may be a predictor of prognosis in male patients with ESCC.
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Affiliation(s)
- Dongping Wu
- Department of Medical Oncology, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Zhejiang 312000, P.R. China
| | - Xiaoying Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yan Xu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Haiyong Wang
- Thoracic Surgery, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Zhejiang 312000. P.R. China
| | - Guangmao Yu
- Thoracic Surgery, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Zhejiang 312000. P.R. China
| | - Luping Jiang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Qingxiao Hong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
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Zhao R, Choi BY, Lee MH, Bode AM, Dong Z. Implications of Genetic and Epigenetic Alterations of CDKN2A (p16(INK4a)) in Cancer. EBioMedicine 2016; 8:30-39. [PMID: 27428416 PMCID: PMC4919535 DOI: 10.1016/j.ebiom.2016.04.017] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/01/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022] Open
Abstract
Aberrant gene silencing is highly associated with altered cell cycle regulation during carcinogenesis. In particular, silencing of the CDKN2A tumor suppressor gene, which encodes the p16(INK4a) protein, has a causal link with several different types of cancers. The p16(INK4a) protein plays an executional role in cell cycle and senescence through the regulation of the cyclin-dependent kinase (CDK) 4/6 and cyclin D complexes. Several genetic and epigenetic aberrations of CDKN2A lead to enhanced tumorigenesis and metastasis with recurrence of cancer and poor prognosis. In these cases, the restoration of genetic and epigenetic reactivation of CDKN2A is a practical approach for the prevention and therapy of cancer. This review highlights the genetic status of CDKN2A as a prognostic and predictive biomarker in various cancers.
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Affiliation(s)
- Ran Zhao
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Bu Young Choi
- Department of Pharmaceutical Science and Engineering, Seowon University, Cheongju 361-742, South Korea
| | - Mee-Hyun Lee
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China.
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Zigang Dong
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China; The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
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