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Liu Y, Yi J, Wu P, Zhang J, Li X, Li J, Zhou L, Liu Y, Xu H, Chen E, Zhang H, Liang M, Liu P, Pan X, Lu Y. Wemics: A Single-Base Resolution Methylation Quantification Method for Enhanced Prediction of Epigenetic Regulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308884. [PMID: 38544480 PMCID: PMC11151077 DOI: 10.1002/advs.202308884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/04/2024] [Indexed: 06/06/2024]
Abstract
DNA methylation, an epigenetic mechanism that alters gene expression without changing DNA sequence, is essential for organism development and key biological processes like genomic imprinting and X-chromosome inactivation. Despite tremendous efforts in DNA methylation research, accurate quantification of cytosine methylation remains a challenge. Here, a single-base methylation quantification approach is introduced by weighting methylation of consecutive CpG sites (Wemics) in genomic regions. Wemics quantification of DNA methylation better predicts its regulatory impact on gene transcription and identifies differentially methylated regions (DMRs) with more biological relevance. Most Wemics-quantified DMRs in lung cancer are epigenetically conserved and recurrently occurred in other primary cancers from The Cancer Genome Atlas (TCGA), and their aberrant alterations can serve as promising pan-cancer diagnostic markers. It is further revealed that these detected DMRs are enriched in transcription factor (TF) binding motifs, and methylation of these TF binding motifs and TF expression synergistically regulate target gene expression. Using Wemics on epigenomic-transcriptomic data from the large lung cancer cohort, a dozen novel genes with oncogenic potential are discovered that are upregulated by hypomethylation but overlooked by other quantification methods. These findings increase the understanding of the epigenetic mechanism by which DNA methylation regulates gene expression.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceDepartment of Respiratory Medicine, Department of Clinical LaboratorySir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310016China
- Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Jiani Yi
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceDepartment of Respiratory Medicine, Department of Clinical LaboratorySir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310016China
| | - Pin Wu
- Department of Thoracic SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineZhejiang UniversityHangzhou310009China
| | - Jun Zhang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceDepartment of Respiratory Medicine, Department of Clinical LaboratorySir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310016China
| | - Xufan Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceDepartment of Respiratory Medicine, Department of Clinical LaboratorySir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310016China
| | - Jia Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceDepartment of Respiratory Medicine, Department of Clinical LaboratorySir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310016China
| | - Liyuan Zhou
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceDepartment of Respiratory Medicine, Department of Clinical LaboratorySir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310016China
- Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Yong Liu
- Department of PhysiologyThe University of ArizonaTucsonAZ85721USA
| | - Haiming Xu
- Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Enguo Chen
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceDepartment of Respiratory Medicine, Department of Clinical LaboratorySir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310016China
| | - Honghe Zhang
- Department of PathologyResearch Unit of Intelligence Classification of Tumor Pathology and Precision TherapyChinese Academy of Medical SciencesZhejiang University School of MedicineHangzhou310058China
| | - Mingyu Liang
- Department of PhysiologyThe University of ArizonaTucsonAZ85721USA
| | - Pengyuan Liu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceDepartment of Respiratory Medicine, Department of Clinical LaboratorySir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310016China
- Department of PhysiologyThe University of ArizonaTucsonAZ85721USA
- Cancer centerZhejiang UniversityHangzhou310058China
| | - Xiaoqing Pan
- Department of MathematicsShanghai Normal UniversityShanghai200233China
| | - Yan Lu
- Cancer centerZhejiang UniversityHangzhou310058China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological DiseasesDepartment of Gynecologic OncologyWomen's Hospital and Institute of Translational MedicineZhejiang University School of MedicineHangzhouZhejiang310029China
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Qin T, Li S, Henry LE, Chou E, Cavalcante RG, Garb BF, D'Silva NJ, Rozek LS, Sartor MA. Whole-genome CpG-resolution DNA Methylation Profiling of HNSCC Reveals Distinct Mechanisms of Carcinogenesis for Fine-scale HPV+ Cancer Subtypes. CANCER RESEARCH COMMUNICATIONS 2023; 3:1701-1715. [PMID: 37654626 PMCID: PMC10467604 DOI: 10.1158/2767-9764.crc-23-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/24/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
DNA methylation is a vital early step in carcinogenesis. Most findings of aberrant DNA methylation in head and neck squamous cell carcinomas (HNSCC) are array based with limited coverage and resolution, and mainly explored by human papillomavirus (HPV) status, ignoring the high heterogeneity of this disease. In this study, we performed whole-genome bisulfite sequencing on a well-studied HNSCC cohort (n = 36) and investigated the methylation changes between fine-scaled HNSCC subtypes in relation to genomic instability, repetitive elements, gene expression, and key carcinogenic pathways. The previously observed hypermethylation phenotype in HPV-positive (HPV+) tumors compared with HPV-negative tumors was robustly present in the immune-strong (IMU) HPV+ subtype but absent in the highly keratinized (KRT) HPV+ subtype. Methylation levels of IMU tumors were significantly higher in repetitive elements, and methylation showed a significant correlation with genomic stability, consistent with the IMU subtype having more genomic stability and better prognosis. Expression quantitative trait methylation (cis-eQTM) analysis revealed extensive functionally-relevant differences, and differential methylation pathway analysis recapitulated gene expression pathway differences between subtypes. Consistent with their characteristics, KRT and HPV-negative tumors had high regulatory potential for multiple regulators of keratinocyte differentiation, which positively correlated with an expression-based keratinization score. Together, our findings revealed distinct mechanisms of carcinogenesis between subtypes in HPV+ HNSCC and uncovered previously ignored epigenomic differences and clinical implications, illustrating the importance of fine-scale subtype analysis in cancer. Significance This study revealed that the previously observed hypermethylation of HPV(+) HNSCC is due solely to the IMU subtype, illustrating the importance of fine-scale subtype analysis in such a heterogeneous disease. Particularly, IMU has significantly higher methylation of transposable elements, which can be tested as a prognosis biomarker in future translational studies.
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Affiliation(s)
- Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shiting Li
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Leanne E. Henry
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Elysia Chou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Raymond G. Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Bailey F. Garb
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Nisha J. D'Silva
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Laura S. Rozek
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
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Gaspar TB, Jesus TT, Azevedo MT, Macedo S, Soares MA, Martins RS, Leite R, Rodrigues L, Rodrigues DF, Cardoso L, Borges I, Canberk S, Gärtner F, Miranda-Alves L, Lopes JM, Soares P, Vinagre J. Generation of an Obese Diabetic Mouse Model upon Conditional Atrx Disruption. Cancers (Basel) 2023; 15:cancers15113018. [PMID: 37296979 DOI: 10.3390/cancers15113018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/15/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Atrx loss was recently ascertained as insufficient to drive pancreatic neuroendocrine tumour (PanNET) formation in mice islets. We have identified a preponderant role of Atrx in the endocrine dysfunction in a Rip-Cre;AtrxKO genetically engineered mouse model (GEMM). To validate the impact of a different Cre-driver line, we used similar methodologies and characterised the Pdx1-Cre;AtrxKO (P.AtrxKO) GEMM to search for PanNET formation and endocrine fitness disruption for a period of up to 24 months. Male and female mice presented different phenotypes. Compared to P.AtrxWT, P.AtrxHOM males were heavier during the entire study period, hyperglycaemic between 3 and 12 mo., and glucose intolerant only from 6 mo.; in contrast, P.AtrxHOM females started exhibiting increased weight gains later (after 6 mo.), but diabetes or glucose intolerance was detected by 3 mo. Overall, all studied mice were overweight or obese from early ages, which challenged the histopathological evaluation of the pancreas and liver, especially after 12 mo. Noteworthily, losing Atrx predisposed mice to an increase in intrapancreatic fatty infiltration (FI), peripancreatic fat deposition, and macrovesicular steatosis. As expected, no animal developed PanNETs. An obese diabetic GEMM of disrupted Atrx is presented as potentially useful for metabolic studies and as a putative candidate for inserting additional tumourigenic genetic events.
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Affiliation(s)
- Tiago Bordeira Gaspar
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Tito Teles Jesus
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Maria Teresa Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Sofia Macedo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Mariana Alves Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Laboratório de Endocrinologia Experimental (LEEx), Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Programa de Pós-Graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Rui Sousa Martins
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Faculty of Sciences of the University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Rúben Leite
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- School of Health (ESS), Polytechnic Institute of Porto (IPP), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Lia Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Daniela Ferreira Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular and Cell Biology (IBMC), University of Porto, 4200-135 Porto, Portugal
| | - Luís Cardoso
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Department of Endocrinology, Diabetes and Metabolism, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | - Inês Borges
- Centro de Diagnóstico Veterinário (Cedivet), 4200-071 Porto, Portugal
| | - Sule Canberk
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Fátima Gärtner
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Leandro Miranda-Alves
- Laboratório de Endocrinologia Experimental (LEEx), Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Programa de Pós-Graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - José Manuel Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário de São João (CHUSJ), 4200-319 Porto, Portugal
| | - Paula Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - João Vinagre
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
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Courant F, Bougras-Cartron G, Abadie C, Frenel JS, Cartron PF. Modulation of DNA Methylation/Demethylation Reactions Induced by Nutraceuticals and Pollutants of Exposome Can Promote a C > T Mutation in the Breast Cancer Predisposing Gene PALB2. EPIGENOMES 2022; 6:epigenomes6040032. [PMID: 36278678 PMCID: PMC9590087 DOI: 10.3390/epigenomes6040032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022] Open
Abstract
Background: Deregulation of DNA methylation/demethylation reactions may be the source of C > T mutation via active deamination of 5-methylcytosine to thymine. Exposome, that is to say, the totality of exposures to which an individual is subjected during their life, can deregulate these reactions. Thus, one may wonder whether the exposome can induce C > T mutations in the breast cancer-predisposing gene PALB2. Methods: Our work is based on the exposure of MCF10A mammary epithelial cells to seven compounds of our exposome (folate, Diuron, glyphosate, PFOA, iron, zinc, and ascorbic acid) alone or in cocktail. The qMSRE and RMS techniques were used to study the impact of these exposures on the level of methylation and mutation of the PALB2 gene. Results: Here, we have found that exposome compounds (nutriments, ions, pollutants) promoting the cytosine methylation and the 5-methylcytosine deamination have the ability to promote a specific C > T mutation in the PALB2 gene. Interestingly, we also noted that the addition of exposome compounds promoting the TET-mediated conversion of 5-methylcytosine (Ascorbic acid and iron) abrogates the presence of C > T mutation in the PALB2 gene. Conclusions: Our study provides a proof of concept supporting the idea that exposomes can generate genetic mutation by affecting DNA methylation/demethylation.
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Affiliation(s)
- Florestan Courant
- Nantes Université, Inserm, CNRS, Université d’Angers, CRCI2NA, 44000 Nantes, France
- SIRIC ILIAD, 44000 Nantes, France
| | - Gwenola Bougras-Cartron
- Nantes Université, Inserm, CNRS, Université d’Angers, CRCI2NA, 44000 Nantes, France
- SIRIC ILIAD, 44000 Nantes, France
- Institut de Cancérologie de l’Ouest, 44800 Saint-Herblain, France
| | - Caroline Abadie
- Institut de Cancérologie de l’Ouest, 44800 Saint-Herblain, France
| | - Jean-Sébastien Frenel
- Nantes Université, Inserm, CNRS, Université d’Angers, CRCI2NA, 44000 Nantes, France
- SIRIC ILIAD, 44000 Nantes, France
- Institut de Cancérologie de l’Ouest, 44800 Saint-Herblain, France
| | - Pierre-François Cartron
- Nantes Université, Inserm, CNRS, Université d’Angers, CRCI2NA, 44000 Nantes, France
- SIRIC ILIAD, 44000 Nantes, France
- Institut de Cancérologie de l’Ouest, 44800 Saint-Herblain, France
- Correspondence:
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Gaspar TB, Macedo S, Sá A, Soares MA, Rodrigues DF, Sousa M, Mendes N, Martins RS, Cardoso L, Borges I, Canberk S, Gärtner F, Miranda-Alves L, Sobrinho-Simões M, Lopes JM, Soares P, Vinagre J. Characterisation of an Atrx Conditional Knockout Mouse Model: Atrx Loss Causes Endocrine Dysfunction Rather Than Pancreatic Neuroendocrine Tumour. Cancers (Basel) 2022; 14:cancers14163865. [PMID: 36010860 PMCID: PMC9406167 DOI: 10.3390/cancers14163865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/22/2022] Open
Abstract
Simple Summary ATRX and DAXX mutations occur in 30–40% of pancreatic neuroendocrine tumours (PanNETs), and there are no reports in the literature of any genetically engineered mouse model (GEMM) evaluating the effect of Atrx disruption as a putative driver event on PanNET initiation. We created a novel GEMM with Atrx conditional disruption in β cells. We observed that this genetic alteration, per se, was not tumourigenic, but we reported novel roles of Atrx on endocrine function, which resulted in dysglycaemia and the exacerbation of inflammageing (increased pancreatic inflammation and hepatic steatosis). Abstract ATRX is a chromatin remodeller that maintains telomere homeostasis. Loss of ATRX is described in approximately 10% of pancreatic neuroendocrine tumours (PanNETs) and associated with poorer prognostic features. Here, we present a genetically engineered mouse model (GEMM) addressing the role of Atrx loss (AtrxKO) in pancreatic β cells, evaluating a large cohort of ageing mice (for up to 24 months (mo.)). Atrx loss did not cause PanNET formation but rather resulted in worsening of ageing-related pancreatic inflammation and endocrine dysfunction in the first year of life. Histopathological evaluation highlighted an exacerbated prevalence and intensity of pancreatic inflammation, ageing features, and hepatic steatosis in AtrxKO mice. Homozygous floxed mice presented hyperglycaemia, increased weights, and glucose intolerance after 6 months, but alterations in insulinaemia were not detected. Floxed individuals presented an improper growth of their pancreatic endocrine fraction that may explain such an endocrine imbalance. A pilot study of BRACO-19 administration to AtrxKO mice resulted in telomere instability, reinforcing the involvement of Atrx in the maintenance of β cell telomere homeostasis. Thereby, a non-obese dysglycaemic GEMM of disrupted Atrx is here presented as potentially useful for metabolic studies and putative candidate for inserting additional tumourigenic genetic events.
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Affiliation(s)
- Tiago Bordeira Gaspar
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Sofia Macedo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Ana Sá
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Mariana Alves Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Laboratório de Endocrinologia Experimental (LEEx), Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil
- Programa de Pós-Graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-905, Brazil
| | - Daniela Ferreira Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute for Molecular and Cell Biology (IBMC), University of Porto, 4200-135 Porto, Portugal
| | - Mafalda Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute for Molecular and Cell Biology (IBMC), University of Porto, 4200-135 Porto, Portugal
| | - Nuno Mendes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Rui Sousa Martins
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Sciences of the University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Luís Cardoso
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Department of Endocrinology, Diabetes and Metabolism, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | - Inês Borges
- Centro de Diagnóstico Veterinário (Cedivet), 4200-071 Porto, Portugal
| | - Sule Canberk
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Fátima Gärtner
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Leandro Miranda-Alves
- Laboratório de Endocrinologia Experimental (LEEx), Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil
- Programa de Pós-Graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-905, Brazil
| | - Manuel Sobrinho-Simões
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário de São João (CHUSJ), 4200-319 Porto, Portugal
| | - José Manuel Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário de São João (CHUSJ), 4200-319 Porto, Portugal
| | - Paula Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - João Vinagre
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Correspondence: ; Tel.: +351-225-570-700
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Marini F, Giusti F, Brandi ML. Epigenetic-based targeted therapies for well-differentiated pancreatic neuroendocrine tumors: recent advances and future perspectives. Expert Rev Endocrinol Metab 2021; 16:295-307. [PMID: 34554891 DOI: 10.1080/17446651.2021.1982382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Well-differentiated pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous group of primary tumors of the endocrine pancreas. Dysregulation of chromatin remodeling, gene expression alteration, global DNA hypomethylation of non-coding regions, DNA hypermethylation and silencing of tumor suppressor gene promoters are frequent epigenetic changes in PanNETs. These changes exert a role in neoplastic transformation and progression. As epigenetic mechanisms, converse to genetic mutations, are potentially reversible, they are an interesting and promising therapeutic target for the treatment of PanNETs. AREAS COVERED We reviewed main epigenetic alterations associated with the development, biological and clinical features and progression of PanNETs, as well as emerging therapies targeting epigenetic changes, which may prove effective for the treatment of human PanNETs. EXPERT OPINION Constant advances in the PanNET medical approach, as reported in the clinical and therapeutic recommendations of ESMO, improved the overall survival of patients over the years. However, over 60% of the patients with metastatic disease still have poor prognosis. Epigenetic regulator drugs, currently approved to treat some human malignancies, that showed anti-tumoral activity also on PanNETs, in pre-clinical and clinical studies, could concur to ameliorate the prognosis and OS of advanced and metastatic PanNET, in combination with surgery and currently employed medical therapies.
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Affiliation(s)
- Francesca Marini
- Department of Experimental and Clinical Biomedical Sciences, University of refereFlorence, Florence, Italy
- F.I.R.M.O. Italian Foundation for the Research on Bone Diseases, Florence, Italy
| | - Francesca Giusti
- Department of Experimental and Clinical Biomedical Sciences, University of refereFlorence, Florence, Italy
| | - Maria Luisa Brandi
- F.I.R.M.O. Italian Foundation for the Research on Bone Diseases, Florence, Italy
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7
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Byun S, Affolter KE, Snow AK, Curtin K, Cannon AR, Cannon-Albright LA, Thota R, Neklason DW. Differential methylation of G-protein coupled receptor signaling genes in gastrointestinal neuroendocrine tumors. Sci Rep 2021; 11:12303. [PMID: 34112938 PMCID: PMC8192774 DOI: 10.1038/s41598-021-91934-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
Neuroendocrine tumors (NETs) of the small intestine undergo large chromosomal and methylation changes. The objective of this study was to identify methylation differences in NETs and consider how the differentially methylated genes may impact patient survival. Genome-wide methylation and chromosomal copy number variation (CNV) of NETs from the small intestine and appendix were measured. Tumors were divided into three molecular subtypes according to CNV results: chromosome 18 loss (18LOH), Multiple CNV, and No CNV. Comparison of 18LOH tumors with MultiCNV and NoCNV tumors identified 901 differentially methylated genes. Genes from the G-protein coupled receptor (GPCR) pathways are statistically overrepresented in the differentially methylated genes. One of the highlighted genes from the GPCR pathway is somatostatin (SST), a clinical target for NETs. Patient survival based on low versus high methylation in all samples identified four significant genes (p < 0.05) OR2S2, SMILR, RNU6-653P, and AC010543.1. Within the 18LOH molecular subtype tumors, survival differences were identified in high versus low methylation of 24 genes. The most significant is TRHR (p < 0.01), a GPCR with multiple FDA-approved drugs. By separating NETs into different molecular subtypes based on chromosomal changes, we find that multiple GPCRs and their ligands appear to be regulated through methylation and correlated with survival. These results suggest opportunities for better treatment strategies for NETs based on molecular features.
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Affiliation(s)
- Seyoun Byun
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112-5550, USA
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, USA
| | - Kajsa E Affolter
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112-5550, USA
- Department of Pathology, University of Utah, Salt Lake City, USA
| | - Angela K Snow
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112-5550, USA
| | - Karen Curtin
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112-5550, USA
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, USA
| | - Austin R Cannon
- Division of General Surgery, Department of Surgery, University of Utah School of Medicine, Salt Lake City, USA
| | - Lisa A Cannon-Albright
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112-5550, USA
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, USA
| | - Ramya Thota
- Medical Oncology, Intermountain Healthcare, Salt Lake City, USA
| | - Deborah W Neklason
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112-5550, USA.
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, USA.
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8
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Lakis V, Lawlor RT, Newell F, Patch AM, Mafficini A, Sadanandam A, Koufariotis LT, Johnston RL, Leonard C, Wood S, Rusev B, Corbo V, Luchini C, Cingarlini S, Landoni L, Salvia R, Milella M, Chang D, Bailey P, Jamieson NB, Duthie F, Gingras MC, Muzny DM, Wheeler DA, Gibbs RA, Milione M, Pederzoli P, Samra JS, Gill AJ, Johns AL, Pearson JV, Biankin AV, Grimmond SM, Waddell N, Nones K, Scarpa A. DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association. Commun Biol 2021; 4:155. [PMID: 33536587 PMCID: PMC7859232 DOI: 10.1038/s42003-020-01469-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Here we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information. We identified three subgroups of PanNETs, termed T1, T2 and T3, with distinct patterns of methylation. The T1 subgroup was enriched for functional tumors and ATRX, DAXX and MEN1 wild-type genotypes. The T2 subgroup contained tumors with mutations in ATRX, DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent loss and methylation levels. T2 tumors were larger and had lower methylation in the MGMT gene body, which showed positive correlation with gene expression. The T3 subgroup harboured mutations in MEN1 with recurrent loss of chromosome 11, was enriched for grade G1 tumors and showed histological parameters associated with better prognosis. Our results suggest a role for methylation in both driving tumorigenesis and potentially stratifying prognosis in PanNETs.
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Affiliation(s)
- Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Rita T Lawlor
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Andrea Mafficini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Rebecca L Johnston
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Borislav Rusev
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Vincenzo Corbo
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Claudio Luchini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Sara Cingarlini
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - David Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of General Surgery, University of Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Baden-Württemberg, Germany
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Fraser Duthie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of Pathology, Queen Elizabeth University Hospital, Greater Glasgow & Clyde NHS, Glasgow, G51 4TF, UK
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
- Michael E. DeBakey Department of Surgery and The Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030-3411, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Massimo Milione
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | | | | | - Anthony J Gill
- University of Sydney, Sydney, New South Wales, 2006, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, 2010, Australia
| | - Amber L Johns
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, 2010, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, Victoria, 3000, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia.
| | - Aldo Scarpa
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy.
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy.
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9
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Jiang R, Hong X, Zhao Y, Wu W. Application of multiomics sequencing and advances in the molecular mechanisms of pancreatic neuroendocrine neoplasms. Cancer Lett 2020; 499:39-48. [PMID: 33246093 DOI: 10.1016/j.canlet.2020.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/10/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022]
Abstract
The incidence of pancreatic neuroendocrine neoplasms (PanNENs) has gradually increased. PanNENs comprise two subtypes with different clinical manifestations and molecular mechanisms: functional PanNENs and nonfunctional PanNENs. Excessive hormones and tumor progression severely affect the quality of life of patients or are even life threatening. However, the molecular mechanisms of hormone secretion and tumor progression in PanNENs have not yet been fully elucidated. At present, advancements in sequencing technologies have led to the exploration of new biological markers and an advanced understanding of molecular mechanisms in PanNENs. Multiomics sequencing could reveal differences and similarities in molecular features in different fields. However, sequencing studies of PanNENs are booming and should be summarized to integrate the current findings. In this review, we summarize the current status of multiomics sequencing in PanNENs to further guide its application. We explore mainly advancements in the genome, transcriptome, and DNA methylation fields. In addition, the cell origin of PanNENs, which has been a hot issue in sequencing research, is described in multiple fields.
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Affiliation(s)
- Rui Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, 100730, China
| | - Xiafei Hong
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, 100730, China
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, 100730, China.
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, 100730, China.
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10
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Liu Y, Han Y, Zhou L, Pan X, Sun X, Liu Y, Liang M, Qin J, Lu Y, Liu P. A comprehensive evaluation of computational tools to identify differential methylation regions using RRBS data. Genomics 2020; 112:4567-4576. [PMID: 32712292 DOI: 10.1016/j.ygeno.2020.07.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 01/01/2023]
Abstract
DNA methylation plays a vital role in transcription regulation. Reduced representation bisulfite sequencing (RRBS) is becoming common for analyzing genome-wide methylation profiles at the single nucleotide level. A major goal of RRBS studies is to detect differentially methylated regions (DMRs) between different biological conditions. The previous tools to predict DMRs lack consistency. Here, we simulated RRBS datasets with significant attributes of real sequencing data under a wide range of scenarios, and systematically evaluated seven DMR detection tools in terms of type I error rate, precision/recall (PR), and area under ROC curve (AUC) using different methylation levels, sequencing coverage depth, length of DMRs, read length, and sample sizes. DMRfinder, methylSig, and methylKit were our preferred tools for RRBS data analysis, in terms of their AUC and PR curves. Our comparison highlights the different applicability of DMR detection tools and provides information to guide researchers towards the advancement of sequence-based DMR analysis.
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Affiliation(s)
- Yi Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yi Han
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Liyuan Zhou
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Xiaoqing Pan
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiwei Sun
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jiale Qin
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China.
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China.
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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11
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Bocchini M, Nicolini F, Severi S, Bongiovanni A, Ibrahim T, Simonetti G, Grassi I, Mazza M. Biomarkers for Pancreatic Neuroendocrine Neoplasms (PanNENs) Management-An Updated Review. Front Oncol 2020; 10:831. [PMID: 32537434 PMCID: PMC7267066 DOI: 10.3389/fonc.2020.00831] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022] Open
Abstract
Pancreatic neuroendocrine tumors (PanNENs) are rare sporadic cancers or develop as part of hereditary syndromes. PanNENs can be both functioning and non-functioning based on whether they produce bioactive peptides. Some PanNENs are well differentiated while others-poorly. Symptoms, thus, depend on both oncological and hormonal causes. PanNEN diagnosis and treatment benefit from and in some instances are guided by biomarker monitoring. However, plasmatic monoanalytes are only suggestive of PanNEN pathological status and their positivity is typically followed by deepen diagnostic analyses through imaging techniques. There is a strong need for new biomarkers and follow-up modalities aimed to improve the outcome of PanNEN patients. Liquid biopsy follow-up, i.e., sequential analysis on tumor biomarkers in body fluids offers a great potential, that need to be substantiated by additional studies focusing on the specific markers and the timing of the analyses. This review provides the most updated panorama on PanNEN biomarkers.
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Affiliation(s)
- Martine Bocchini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Fabio Nicolini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Stefano Severi
- Nuclear Medicine and Radiometabolic Units, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Alberto Bongiovanni
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Toni Ibrahim
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Ilaria Grassi
- Nuclear Medicine and Radiometabolic Units, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Massimiliano Mazza
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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12
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Clift AK, Kidd M, Bodei L, Toumpanakis C, Baum RP, Oberg K, Modlin IM, Frilling A. Neuroendocrine Neoplasms of the Small Bowel and Pancreas. Neuroendocrinology 2020; 110:444-476. [PMID: 31557758 PMCID: PMC9175236 DOI: 10.1159/000503721] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/24/2019] [Indexed: 12/12/2022]
Abstract
The traditionally promulgated perspectives of neuroendocrine neoplasms (NEN) as rare, indolent tumours are blunt and have been outdated for the last 2 decades. Clear increments in their incidence over the past decades render them increasingly clinically relevant, and at initial diagnosis many present with nodal and/or distant metastases (notably hepatic). The molecular pathogenesis of these tumours is increasingly yet incompletely understood. Those arising from the small bowel (SB) or pancreas typically occur sporadically; the latter may occur within the context of hereditary tumour predisposition syndromes. NENs can also be associated with endocrinopathy of hormonal hypersecretion. Tangible advances in the development of novel biomarkers, functional imaging modalities and therapy are especially applicable to this sub-set of tumours. The management of SB and pancreatic neuroendocrine tumours (NET) may be challenging, and often comprises a multidisciplinary approach wherein surgical, medical, interventional radiological and radiotherapeutic modalities are implemented. This review provides a comprehensive overview of the epidemiology, pathophysiology, diagnosis and treatment of SB and pancreatic NETs. Moreover, we provide an outlook of the future in these tumour types which will include the development of precision oncology frameworks for individualised therapy, multi-analyte predictive biomarkers, artificial intelligence-derived clinical decision support tools and elucidation of the role of the microbiome in NEN development and clinical behaviour.
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Affiliation(s)
- Ashley Kieran Clift
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Mark Kidd
- Wren Laboratories, Branford, Connecticut, USA
| | - Lisa Bodei
- Department of Nuclear Medicine, Memorial Sloan Kettering Cancer Centre, New York, New York, USA
| | - Christos Toumpanakis
- Centre for Gastroenterology/Neuroendocrine Tumour Unit, Royal Free Hospital, London, United Kingdom
| | - Richard P Baum
- Theranostics Centre for Molecular Radiotherapy and Precision Oncology, Zentralklinik, Bad Berka, Germany
| | - Kjell Oberg
- Department of Endocrine Oncology, Uppsala University, Uppsala, Sweden
| | - Irvin M Modlin
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrea Frilling
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom,
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13
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Reduced DAXX Expression Is Associated with Reduced CD24 Expression in Colorectal Cancer. Cells 2019; 8:cells8101242. [PMID: 31614769 PMCID: PMC6830082 DOI: 10.3390/cells8101242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/23/2019] [Accepted: 10/11/2019] [Indexed: 12/14/2022] Open
Abstract
The presence of an activating mutation of the Wnt/β-catenin signaling pathway is found in ~90% of colorectal cancer (CRC) cases. Death domain-associated protein (DAXX), a nuclear protein, interacts with β-catenin in CRC cells. We investigated DAXX expression in 106 matched sample pairs of CRC and adjacent normal tissue by Western blotting. This study evaluated DAXX expression and its clinical implications in CRC. The results revealed that DAXX expression was significantly lower in the patients with the positive serum carcinoembryonic antigen (CEA) screening results compared to the patients with negative CEA screening levels (p < 0.001). It has been reported that CD24 is a Wnt target in CRC cells. Here, we further revealed that DAXX expression was significantly correlated with CD24 expression (rho = 0.360, p < 0.001) in 106 patients. Consistent with this, in the CEA-positive subgroup, of which the carcinomas expressed DAXX at low levels, they were significantly correlated with CD24 expression (rho = 0.461, p < 0.005). Therefore, reduced DAXX expression is associated with reduced CD24 expression in CRC. Notably, in the Hct116 cells, DAXX knockdown using short-hairpin RNA against DAXX (shDAXX) not only caused significant cell proliferation, but also promoted metastasis. The DAXX-knockdown cells also demonstrated significantly decreased CD24 expression, however the intracellular localization of CD24 did not change. Thus, DAXX might be considered as a potential regulator of CD24 or β-catenin expression, which might be correlated with proliferative and metastatic potential of CRC.
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14
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Scarpa A. The landscape of molecular alterations in pancreatic and small intestinal neuroendocrine tumours. ANNALES D'ENDOCRINOLOGIE 2019; 80:153-158. [PMID: 31072588 DOI: 10.1016/j.ando.2019.04.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastroenteropancreatic Neuroendocrine Neoplasms (GEP-NENs) arise throughout the gut and feature varying biological behaviour and malignant potential. GEP-NENs include two genetically different entities, well-differentiated neuroendocrine tumours (NETs) and poorly differentiated neuroendocrine carcinomas (NEC). NECs are characterized by a dismal prognosis and by distinctive TP53 and RB1 inactivation which sets them apart from NETs. The latter, conversely, have a wide spectrum of aggressiveness and molecular alterations. Knowledge on their biology has recently expanded thanks to high-throughput studies focused on two important groups of well-differentiated neuroendocrine neoplasms: pancreatic (PanNETs) and small intestinal (SiNETs) tumours. PanNETs have been among the most studied also due to genetic syndromes featuring their onset. Research stemming from this observation has uncovered the inactivation of MEN1, VHL, TSC1/2, and the hyperactivation of the PI3K/mTOR pathway as distinctive biological features of these neoplasms. Next-Generation Sequencing added information on the role of telomere lengthening via ATRX/DAXX inactivation in a fraction of PanNETs, while other display shortened telomeres and recurrent chromosomal alterations. The data so far disclosed a heterogeneous combination of driver events, yet converging into four pathways including DNA damage repair, cell cycle regulation, PI3K/mTOR signalling and telomere maintenance. SiNETs showed a lesser relationship with mutational driver events, even in the case of familial cases. High throughput studies identified putative driver mutations in CDKN1 and APC which, however, were reported in a minor fraction (∼10%) of cases. Tumorigenesis of SiNETs seems to depend more on chromosomal alterations (loss of chromosome 8, gains at 4, 5 and 20) and epigenetic events, which converge to hyperactivate the PI3K/mTOR, MAPK and Wnt pathways. While calling for further integrative studies, these data lay previous and recent findings in a more defined frame and provide clinical research with several candidate markers for patient stratification and companion diagnostics.
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Affiliation(s)
- Aldo Scarpa
- RC-Net Centre for applied research on cancer, University and Hospital Trust of Verona, 37134 Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy.
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15
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Mafficini A, Scarpa A. Genetics and Epigenetics of Gastroenteropancreatic Neuroendocrine Neoplasms. Endocr Rev 2019; 40:506-536. [PMID: 30657883 PMCID: PMC6534496 DOI: 10.1210/er.2018-00160] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 12/27/2018] [Indexed: 12/11/2022]
Abstract
Gastroenteropancreatic (GEP) neuroendocrine neoplasms (NENs) are heterogeneous regarding site of origin, biological behavior, and malignant potential. There has been a rapid increase in data publication during the last 10 years, mainly driven by high-throughput studies on pancreatic and small intestinal neuroendocrine tumors (NETs). This review summarizes the present knowledge on genetic and epigenetic alterations. We integrated the available information from each compartment to give a pathway-based overview. This provided a summary of the critical alterations sustaining neoplastic cells. It also highlighted similarities and differences across anatomical locations and points that need further investigation. GEP-NENs include well-differentiated NETs and poorly differentiated neuroendocrine carcinomas (NECs). NENs are graded as G1, G2, or G3 based on mitotic count and/or Ki-67 labeling index, NECs are G3 by definition. The distinction between NETs and NECs is also linked to their genetic background, as TP53 and RB1 inactivation in NECs set them apart from NETs. A large number of genetic and epigenetic alterations have been reported. Recurrent changes have been traced back to a reduced number of core pathways, including DNA damage repair, cell cycle regulation, and phosphatidylinositol 3-kinase/mammalian target of rapamycin signaling. In pancreatic tumors, chromatin remodeling/histone methylation and telomere alteration are also affected. However, also owing to the paucity of disease models, further research is necessary to fully integrate and functionalize data on deregulated pathways to recapitulate the large heterogeneity of behaviors displayed by these tumors. This is expected to impact diagnostics, prognostic stratification, and planning of personalized therapy.
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Affiliation(s)
- Andrea Mafficini
- ARC-Net Center for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Center for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
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16
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Sahnane N, Ottini G, Turri-Zanoni M, Furlan D, Battaglia P, Karligkiotis A, Albeni C, Cerutti R, Mura E, Chiaravalli AM, Castelnuovo P, Sessa F, Facco C. Comprehensive analysis of HPV infection, EGFR exon 20 mutations and LINE1 hypomethylation as risk factors for malignant transformation of sinonasal-inverted papilloma to squamous cell carcinoma. Int J Cancer 2018; 144:1313-1320. [PMID: 30411788 DOI: 10.1002/ijc.31971] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/10/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022]
Abstract
Different risk factors are suspected to be involved in malignant transformation of sinonasal papillomas and include HPV infection, tobacco smoking, occupational exposure, EGFR/KRAS mutations and DNA methylation alterations. In our study, 25 inverted sinonasal papillomas (ISPs), 5 oncocytic sinonasal papillomas (OSP) and 35 squamous cell carcinomas (SCCs) from 54 patients were genotyped for 10 genes involved in EGFR signalling. HPV-DNA detection was performed by in-situ hybridisation and LINE-1 methylation was quantitatively determined by bisulphite-pyrosequencing. High-risk HPV was observed only in 13% of ISP-associated SCC and in 8% of de novo-SCC patients. EGFR mutations occurred in 72% of ISPs, 30% of ISP-associated SCCs and 17% of de novo-SCCs. At 5-year follow-up, SCC arose in only 30% (6/20) of patients with EGFR-mutated ISPs compared to 76% (13/17) of patients with EGFR-wild-type ISP (p = 0.0044). LINE-1 hypomethylation significantly increased from papilloma/early stage SCC to advanced stage SCC (p = 0.03) and was associated with occupational exposure (p = 0.01) and worse prognosis (p = 0.09). In conclusion, our results suggest that a small subset of these tumours could be related to HPV infection; EGFR mutations characterise those ISPs with a lower risk of developing into SCC; LINE-1 hypomethylation is associated with occupational exposure and could identify more aggressive nasal SCC.
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Affiliation(s)
- Nora Sahnane
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Giorgia Ottini
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Mario Turri-Zanoni
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Daniela Furlan
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Paolo Battaglia
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Apostolos Karligkiotis
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Chiara Albeni
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Roberta Cerutti
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Eleonora Mura
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Anna Maria Chiaravalli
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Paolo Castelnuovo
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Fausto Sessa
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy
| | - Carla Facco
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy
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17
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Iyer S, Agarwal SK. Epigenetic regulation in the tumorigenesis of MEN1-associated endocrine cell types. J Mol Endocrinol 2018; 61:R13-R24. [PMID: 29615472 PMCID: PMC5966343 DOI: 10.1530/jme-18-0050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 04/03/2018] [Indexed: 12/15/2022]
Abstract
Epigenetic regulation is emerging as a key feature in the molecular characteristics of various human diseases. Epigenetic aberrations can occur from mutations in genes associated with epigenetic regulation, improper deposition, removal or reading of histone modifications, DNA methylation/demethylation and impaired non-coding RNA interactions in chromatin. Menin, the protein product of the gene causative for the multiple endocrine neoplasia type 1 (MEN1) syndrome, interacts with chromatin-associated protein complexes and also regulates some non-coding RNAs, thus participating in epigenetic control mechanisms. Germline inactivating mutations in the MEN1 gene that encodes menin predispose patients to develop endocrine tumors of the parathyroids, anterior pituitary and the duodenopancreatic neuroendocrine tissues. Therefore, functional loss of menin in the various MEN1-associated endocrine cell types can result in epigenetic changes that promote tumorigenesis. Because epigenetic changes are reversible, they can be targeted to develop therapeutics for restoring the tumor epigenome to the normal state. Irrespective of whether epigenetic alterations are the cause or consequence of the tumorigenesis process, targeting the endocrine tumor-associated epigenome offers opportunities for exploring therapeutic options. This review presents epigenetic control mechanisms relevant to the interactions and targets of menin, and the contribution of epigenetics in the tumorigenesis of endocrine cell types from menin loss.
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Affiliation(s)
- Sucharitha Iyer
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Sunita K Agarwal
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
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18
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Ueda H, Akiyama Y, Shimada S, Mogushi K, Serizawa M, Matsumura S, Mitsunori Y, Aihara A, Ban D, Ochiai T, Kudo A, Tanabe M, Tanaka S. Tumor suppressor functions of DAXX through histone H3.3/H3K9me3 pathway in pancreatic NETs. Endocr Relat Cancer 2018; 25:619-631. [PMID: 29599123 DOI: 10.1530/erc-17-0328] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 03/28/2018] [Indexed: 12/13/2022]
Abstract
Pancreatic neuroendocrine tumors (PanNETs) have considerable malignant potential. Frequent somatic mutations and loss of DAXX protein expression have been found in PanNETs. DAXX is known as a transcriptional repressor; however, molecular functions underlying DAXX loss remain unclear in PanNETs. We evaluated DAXX expression by immunohistochemistry in 44 PanNETs. DAXX-knockdown (KD) and -knockout (KO) PanNET cells were analyzed for in vitro and vivo The target genes were screened by microarray and chromatin immunoprecipitation (ChIP) assays for DAXX, histone H3.3 and H3K9me3 complex. In clinicopathological features, low DAXX expression was significantly correlated with nonfunctional tumors, higher Ki-67 index and WHO grade. Microarray and ChIP assays of DAXX-KD/KO identified 12 genes as the direct targets of DAXX transcriptional repressor. Among them, expression of five genes including STC2 was suppressed by DAXX/H3.3/H3K9me3 pathway. DAXX-KD/KO cells enhanced sphere forming activity, but its effect was suppressed by knockdown of STC2 In xenograft models, tumorigenicity and tumor vessel density were significantly increased in DAXX-KO cells with high expression of STC2. Clinically, higher recurrence rate was recognized in PanNETs with low expression of DAXX and high expression of STC2 than others (P = 0.018). Our data suggest that DAXX plays as a tumor suppressor and DAXX/H3.3 complex suppresses target genes by promoting H3K9me3 in PanNETs. Combination of DAXX loss and its target gene STC2 overexpression might be effective biomarkers and therapeutic candidates.
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Affiliation(s)
- Hiroki Ueda
- Department of Molecular OncologyGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshimitsu Akiyama
- Department of Molecular OncologyGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shu Shimada
- Department of Molecular OncologyGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kaoru Mogushi
- Department of Molecular OncologyGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Misaki Serizawa
- Department of Molecular OncologyGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoshi Matsumura
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Mitsunori
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Arihiro Aihara
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Daisuke Ban
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Ochiai
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Atsushi Kudo
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Minoru Tanabe
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shinji Tanaka
- Department of Molecular OncologyGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Hepatobiliary and Pancreatic SurgeryGraduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
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19
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Mafficini A, Scarpa A. Genomic landscape of pancreatic neuroendocrine tumours: the International Cancer Genome Consortium. J Endocrinol 2018; 236:R161-R167. [PMID: 29321190 PMCID: PMC5811627 DOI: 10.1530/joe-17-0560] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/10/2018] [Indexed: 12/22/2022]
Abstract
Neuroendocrine tumours (NETs) may arise throughout the body and are a highly heterogeneous, relatively rare class of neoplasms difficult to study also for the lack of disease models. Despite this, knowledge on their molecular alterations has expanded in the latest years, also building from genetic syndromes causing their onset. Pancreatic NETs (PanNETs) have been among the most studied, and research so far has outlined a series of recurring features, as inactivation of MEN1, VHL, TSC1/2 genes and hyperactivation of the PI3K/mTOR pathway. Next-generation sequencing has added new information by showing the key role of alternative lengthening of telomeres, driven in a fraction of PanNETs by inactivation of ATRX/DAXX. Despite this accumulation of knowledge, single studies often relied on few cases or were limited to the DNA, RNA, protein or epigenetic level with lack of integrative analysis. The International Cancer Genome Consortium aimed at removing these barriers through a strict process of data and samples collection, to produce whole-genome integrated analyses for many tumour types. The results of this effort on PanNETs have been recently published and, while confirming previous observations provide a first snapshot of how heterogeneous is the combination of genetic alterations that drive this tumour type, yet converging into four pathways whose alteration has been enriched by newly discovered mechanisms. While calling for further integration of genetic and epigenetic analyses, these data allow to reconcile previous findings in a defined frame and may provide clinical research with markers for patients stratification and to guide targeted therapy decisions.
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Affiliation(s)
- Andrea Mafficini
- ARC-Net Centre for Applied Research on CancerUniversity and Hospital Trust of Verona, Verona, Italy
- Department of Diagnostics and Public HealthSection of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Centre for Applied Research on CancerUniversity and Hospital Trust of Verona, Verona, Italy
- Department of Diagnostics and Public HealthSection of Pathology, University and Hospital Trust of Verona, Verona, Italy
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20
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Di Domenico A, Wiedmer T, Marinoni I, Perren A. Genetic and epigenetic drivers of neuroendocrine tumours (NET). Endocr Relat Cancer 2017; 24:R315-R334. [PMID: 28710117 DOI: 10.1530/erc-17-0012] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 12/13/2022]
Abstract
Neuroendocrine tumours (NET) of the gastrointestinal tract and the lung are a rare and heterogeneous group of tumours. The molecular characterization and the clinical classification of these tumours have been evolving slowly and show differences according to organs of origin. Novel technologies such as next-generation sequencing revealed new molecular aspects of NET over the last years. Notably, whole-exome/genome sequencing (WES/WGS) approaches underlined the very low mutation rate of well-differentiated NET of all organs compared to other malignancies, while the engagement of epigenetic changes in driving NET evolution is emerging. Indeed, mutations in genes encoding for proteins directly involved in chromatin remodelling, such as DAXX and ATRX are a frequent event in NET. Epigenetic changes are reversible and targetable; therefore, an attractive target for treatment. The discovery of the mechanisms underlying the epigenetic changes and the implication on gene and miRNA expression in the different subgroups of NET may represent a crucial change in the diagnosis of this disease, reveal new therapy targets and identify predictive markers. Molecular profiles derived from omics data including DNA mutation, methylation, gene and miRNA expression have already shown promising results in distinguishing clinically and molecularly different subtypes of NET. In this review, we recapitulate the major genetic and epigenetic characteristics of pancreatic, lung and small intestinal NET and the affected pathways. We also discuss potential epigenetic mechanisms leading to NET development.
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Affiliation(s)
- Annunziata Di Domenico
- Institute of PathologyUniversity of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical SciencesUniversity of Bern, Bern, Switzerland
| | - Tabea Wiedmer
- Institute of PathologyUniversity of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical SciencesUniversity of Bern, Bern, Switzerland
| | | | - Aurel Perren
- Institute of PathologyUniversity of Bern, Bern, Switzerland
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21
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Shukla R. Retrotransposons and genetic instability in hepatocellular carcinoma. Hepat Oncol 2017; 4:5-8. [PMID: 30191048 DOI: 10.2217/hep-2017-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 06/06/2017] [Indexed: 11/21/2022] Open
Affiliation(s)
- Ruchi Shukla
- Northern Institute for Cancer Research, Newcastle University, NE2 4HH, UK
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