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Zhu T, Tong H, Du Z, Beck S, Teschendorff AE. An improved epigenetic counter to track mitotic age in normal and precancerous tissues. Nat Commun 2024; 15:4211. [PMID: 38760334 PMCID: PMC11101651 DOI: 10.1038/s41467-024-48649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
The cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA methylation (DNAm) clocks are promising tools to molecularly track mitotic age, yet their relationship is underexplored and their potential for cancer risk prediction in normal tissues remains to be demonstrated. Here we build and validate an improved pan-tissue DNAm counter of total mitotic age called stemTOC. We demonstrate that stemTOC's mitotic age proxy increases with the tumor cell-of-origin fraction in each of 15 cancer-types, in precancerous lesions, and in normal tissues exposed to major cancer risk factors. Extensive benchmarking against 6 other mitotic counters shows that stemTOC compares favorably, specially in the preinvasive and normal-tissue contexts. By cross-correlating stemTOC to two clock-like somatic mutational signatures, we confirm the mitotic-like nature of only one of these. Our data points towards DNAm as a promising molecular substrate for detecting mitotic-age increases in normal tissues and precancerous lesions, and hence for developing cancer-risk prediction strategies.
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Affiliation(s)
- Tianyu Zhu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Zhaozhen Du
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- Medical Genomics Group, UCL Cancer Institute, University College London, 72 Huntley Street, WC1E 6BT, London, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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2
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Tong H, Dwaraka VB, Chen Q, Luo Q, Lasky-Su JA, Smith R, Teschendorff AE. Quantifying the stochastic component of epigenetic aging. NATURE AGING 2024:10.1038/s43587-024-00600-8. [PMID: 38724732 DOI: 10.1038/s43587-024-00600-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/21/2024] [Indexed: 05/15/2024]
Abstract
DNA methylation clocks can accurately estimate chronological age and, to some extent, also biological age, yet the process by which age-associated DNA methylation (DNAm) changes are acquired appears to be quasi-stochastic, raising a fundamental question: how much of an epigenetic clock's predictive accuracy could be explained by a stochastic process of DNAm change? Here, using DNAm data from sorted immune cells, we build realistic simulation models, subsequently demonstrating in over 22,770 sorted and whole-blood samples from 25 independent cohorts that approximately 66-75% of the accuracy underpinning Horvath's clock could be driven by a stochastic process. This fraction increases to 90% for the more accurate Zhang's clock, but is lower (63%) for the PhenoAge clock, suggesting that biological aging is reflected by nonstochastic processes. Confirming this, we demonstrate that Horvath's age acceleration in males and PhenoAge's age acceleration in severe coronavirus disease 2019 cases and smokers are not driven by an increased rate of stochastic change but by nonstochastic processes. These results significantly deepen our understanding and interpretation of epigenetic clocks.
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Affiliation(s)
- Huige Tong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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3
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Künstner A, Schwarting J, Witte HM, Xing P, Bernard V, Stölting S, Lohneis P, Janke F, Salehi M, Chen X, Kusch K, Sültmann H, Chteinberg E, Fischer A, Siebert R, von Bubnoff N, Merz H, Busch H, Feller AC, Gebauer N. Genome-wide DNA methylation-analysis of blastic plasmacytoid dendritic cell neoplasm identifies distinct molecular features. Leukemia 2024; 38:1086-1098. [PMID: 38600314 DOI: 10.1038/s41375-024-02240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) constitutes a rare and aggressive malignancy originating from plasmacytoid dendritic cells (pDCs) with a primarily cutaneous tropism followed by dissemination to the bone marrow and other organs. We conducted a genome-wide analysis of the tumor methylome in an extended cohort of 45 BPDCN patients supplemented by WES and RNA-seq as well as ATAC-seq on selected cases. We determined the BPDCN DNA methylation profile and observed a dramatic loss of DNA methylation during malignant transformation from early and mature DCs towards BPDCN. DNA methylation profiles further differentiate between BPDCN, AML, CMML, and T-ALL exhibiting the most striking global demethylation, mitotic stress, and merely localized DNA hypermethylation in BPDCN resulting in pronounced inactivation of tumor suppressor genes by comparison. DNA methylation-based analysis of the tumor microenvironment by MethylCIBERSORT yielded two, prognostically relevant clusters (IC1 and IC2) with specific cellular composition and mutational spectra. Further, the transcriptional subgroups of BPDCN (C1 and C2) differ by DNA methylation signatures in interleukin/inflammatory signaling genes but also by higher transcription factor activity of JAK-STAT and NFkB signaling in C2 in contrast to an EZH2 dependence in C1-BPDCN. Our integrative characterization of BPDCN offers novel molecular insights and potential diagnostic applications.
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Affiliation(s)
- Axel Künstner
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Julian Schwarting
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hanno M Witte
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Hematology and Oncology, Federal Armed Forces Hospital Ulm, Oberer Eselsberg 40, 89081, Ulm, Germany
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Veronica Bernard
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Stephanie Stölting
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Philipp Lohneis
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Maede Salehi
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Kathrin Kusch
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Emil Chteinberg
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Hartmut Merz
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Alfred C Feller
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Niklas Gebauer
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany.
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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4
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Zhao N, Lai C, Wang Y, Dai S, Gu H. Understanding the role of DNA methylation in colorectal cancer: Mechanisms, detection, and clinical significance. Biochim Biophys Acta Rev Cancer 2024; 1879:189096. [PMID: 38499079 DOI: 10.1016/j.bbcan.2024.189096] [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: 10/05/2023] [Revised: 02/18/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Colorectal cancer (CRC) is one of the deadliest malignancies worldwide, ranking third in incidence and second in mortality. Remarkably, early stage localized CRC has a 5-year survival rate of over 90%; in stark contrast, the corresponding 5-year survival rate for metastatic CRC (mCRC) is only 14%. Compounding this problem is the staggering lack of effective therapeutic strategies. Beyond genetic mutations, which have been identified as critical instigators of CRC initiation and progression, the importance of epigenetic modifications, particularly DNA methylation (DNAm), cannot be underestimated, given that DNAm can be used for diagnosis, treatment monitoring and prognostic evaluation. This review addresses the intricate mechanisms governing aberrant DNAm in CRC and its profound impact on critical oncogenic pathways. In addition, a comprehensive review of the various techniques used to detect DNAm alterations in CRC is provided, along with an exploration of the clinical utility of cancer-specific DNAm alterations.
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Affiliation(s)
- Ningning Zhao
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China
| | - Chuanxi Lai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou 310000, China
| | - Sheng Dai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China.
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5
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Lu YW, Ding ZL, Mao R, Zhao GG, He YQ, Li XL, Liu J. Early results of the integrative epigenomic-transcriptomic landscape of colorectal adenoma and cancer. World J Gastrointest Oncol 2024; 16:414-435. [PMID: 38425399 PMCID: PMC10900154 DOI: 10.4251/wjgo.v16.i2.414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/24/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Aberrant methylation is common during the initiation and progression of colorectal cancer (CRC), and detecting these changes that occur during early adenoma (ADE) formation and CRC progression has clinical value. AIM To identify potential DNA methylation markers specific to ADE and CRC. METHODS Here, we performed SeqCap targeted bisulfite sequencing and RNA-seq analysis of colorectal ADE and CRC samples to profile the epigenomic-transcriptomic landscape. RESULTS Comparing 22 CRC and 25 ADE samples, global methylation was higher in the former, but both showed similar methylation patterns regarding differentially methylated gene positions, chromatin signatures, and repeated elements. High-grade CRC tended to exhibit elevated methylation levels in gene promoter regions compared to those in low-grade CRC. Combined with RNA-seq gene expression data, we identified 14 methylation-regulated differentially expressed genes, of which only AGTR1 and NECAB1 methylation had prognostic significance. CONCLUSION Our results suggest that genome-wide alterations in DNA methylation occur during the early stages of CRC and demonstrate the methylation signatures associated with colorectal ADEs and CRC, suggesting prognostic biomarkers for CRC.
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Affiliation(s)
- You-Wang Lu
- Department of Dermatology and Venereology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
| | - Zhao-Li Ding
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Public Technical Service Center, Kunming Institute of Zoology, Kunming 650223, Yunnan Province, China
| | - Rui Mao
- School of Stomatology, Kunming Medical University, Kunming 650500, Yunnan Province, China
| | - Gui-Gang Zhao
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, Yunnan Province, China
| | - Yu-Qi He
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, Yunnan Province, China
| | - Xiao-Lu Li
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, Yunnan Province, China
| | - Jiang Liu
- Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
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6
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Gallardo-Gómez M, Rodríguez-Girondo M, Planell N, Moran S, Bujanda L, Etxart A, Castells A, Balaguer F, Jover R, Esteller M, Cubiella J, Gómez-Cabrero D, De Chiara L. Serum methylation of GALNT9, UPF3A, WARS, and LDB2 as noninvasive biomarkers for the early detection of colorectal cancer and advanced adenomas. Clin Epigenetics 2023; 15:157. [PMID: 37794510 PMCID: PMC10552320 DOI: 10.1186/s13148-023-01570-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Early detection has proven to be the most effective strategy to reduce the incidence and mortality of colorectal cancer (CRC). Nevertheless, most current screening programs suffer from low participation rates. A blood test may improve both the adherence to screening and the selection to colonoscopy. In this study, we conducted a serum-based discovery and validation of cfDNA methylation biomarkers for CRC screening in a multicenter cohort of 433 serum samples including healthy controls, benign pathologies, advanced adenomas (AA), and CRC. RESULTS First, we performed an epigenome-wide methylation analysis with the MethylationEPIC array using a sample pooling approach, followed by a robust prioritization of candidate biomarkers for the detection of advanced neoplasia (AN: AA and CRC). Then, candidate biomarkers were validated by pyrosequencing in independent individual cfDNA samples. We report GALNT9, UPF3A, WARS, and LDB2 as new noninvasive biomarkers for the early detection of AN. The combination of GALNT9/UPF3A by logistic regression discriminated AN with 78.8% sensitivity and 100% specificity, outperforming the commonly used fecal immunochemical test and the methylated SEPT9 blood test. CONCLUSIONS Overall, this study highlights the utility of cfDNA methylation for CRC screening. Our results suggest that the combination methylated GALNT9/UPF3A has the potential to serve as a highly specific and sensitive blood-based test for screening and early detection of CRC.
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Affiliation(s)
- María Gallardo-Gómez
- CINBIO, Universidade de Vigo, Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, CINBIO, Universidade de Vigo, Campus As Lagoas-Marcosende s/n. 36310, Vigo, Spain
- Translational Oncology Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Mar Rodríguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Núria Planell
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de La Granvia, 199. 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Biodonostia Health Research Institute, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Ane Etxart
- Department of Surgery, Hospital Universitario Donostia, San Sebastián, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Rodrigo Jover
- Department of Gastroenterology, Hospital General Universitario de Alicante, Alicante, Spain
- Servicio de Medicina Digestiva. ISABIAL. Universidad Miguel Hernández, Hospital General Universitario Dr. Balmis, Alicante, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Joaquín Cubiella
- Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Biomédica Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - David Gómez-Cabrero
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
- Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
- Mucosal & Salivary Biology Division, King's College London Dental Institute, London, SE1 9RT, UK
| | - Loretta De Chiara
- CINBIO, Universidade de Vigo, Vigo, Spain.
- Department of Biochemistry, Genetics and Immunology, CINBIO, Universidade de Vigo, Campus As Lagoas-Marcosende s/n. 36310, Vigo, Spain.
- Translational Oncology Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
- Cancer Genomics Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
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7
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Bhandari YR, Krishna V, Powers R, Parmar S, Thursby SJ, Gupta E, Kulak O, Gokare P, Reumers J, Van Wesenbeeck L, Bachman KE, Baylin SB, Easwaran H. Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers. Proc Natl Acad Sci U S A 2023; 120:e2301536120. [PMID: 37487069 PMCID: PMC10401032 DOI: 10.1073/pnas.2301536120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/15/2023] [Indexed: 07/26/2023] Open
Abstract
Colorectal cancers (CRCs) form a heterogenous group classified into epigenetic and transcriptional subtypes. The basis for the epigenetic subtypes, exemplified by varying degrees of promoter DNA hypermethylation, and its relation to the transcriptional subtypes is not well understood. We link cancer-specific transcription factor (TF) expression alterations to methylation alterations near TF-binding sites at promoter and enhancer regions in CRCs and their premalignant precursor lesions to provide mechanistic insights into the origins and evolution of the CRC molecular subtypes. A gradient of TF expression changes forms a basis for the subtypes of abnormal DNA methylation, termed CpG-island promoter DNA methylation phenotypes (CIMPs), in CRCs and other cancers. CIMP is tightly correlated with cancer-specific hypermethylation at enhancers, which we term CpG-enhancer methylation phenotype (CEMP). Coordinated promoter and enhancer methylation appears to be driven by downregulation of TFs with common binding sites at the hypermethylated enhancers and promoters. The altered expression of TFs related to hypermethylator subtypes occurs early during CRC development, detectable in premalignant adenomas. TF-based profiling further identifies patients with worse overall survival. Importantly, altered expression of these TFs discriminates the transcriptome-based consensus molecular subtypes (CMS), thus providing a common basis for CIMP and CMS subtypes.
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Affiliation(s)
- Yuba R. Bhandari
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Vinod Krishna
- Infectious Diseases and Vaccines Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Rachael Powers
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sehej Parmar
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sara-Jayne Thursby
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ekta Gupta
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ozlem Kulak
- Division of Gastrointestinal and Liver Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Prashanth Gokare
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Joke Reumers
- Discovery Technologies and Molecular Pharmacology, Therapeutics Discovery, Janssen Research and Development, Turnhoutseweg 30, 2340Beerse, Belgiumg
| | - Liesbeth Van Wesenbeeck
- Infectious Diseases and Vaccines Therapeutic Area, Janssen Research and Development, Turnhoutseweg 30, 2340Beerse, Belgium
| | - Kurtis E. Bachman
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Stephen B. Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
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8
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Chen Z, Lau KS. Advances in Mapping Tumor Progression from Precancer Atlases. Cancer Prev Res (Phila) 2023; 16:439-447. [PMID: 37167978 PMCID: PMC10523872 DOI: 10.1158/1940-6207.capr-22-0473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/22/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Tissue profiling technologies present opportunities for understanding transition from precancerous lesions to malignancy, which may impact risk stratification, prevention, and even cancer treatment. A human precancer atlas building effort is ongoing to tackle the significant challenge of decoding the heterogeneity among cells, specimens, and patients. Here, we discuss the findings resulting from atlases built across precancer types, including those found in colon, breast, lung, stomach, cervix, and skin, using bulk, single-cell, and spatial profiling strategies. We highlight two main themes that emerge across precancer types: the ordering of molecular events that occur during tumor progression and the fluctuation of microenvironmental response during precancer progression. We further highlight the key challenges of data integration across large cohorts of patients, and the need for computational tools to reliably annotate and quality control high-volume, high-dimensional data.
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Affiliation(s)
- Zhengyi Chen
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ken S. Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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9
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Suppiah S, Mansouri S, Mamatjan Y, Liu JC, Bhunia MM, Patil V, Rath P, Mehani B, Heir P, Bunda S, Velez-Reyes GL, Singh O, Ijad N, Pirouzmand N, Dalcourt T, Meng Y, Karimi S, Wei Q, Nassiri F, Pugh TJ, Bader GD, Aldape KD, Largaespada DA, Zadeh G. Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities. Nat Commun 2023; 14:2696. [PMID: 37164978 PMCID: PMC10172395 DOI: 10.1038/s41467-023-38432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/28/2023] [Indexed: 05/12/2023] Open
Abstract
Malignant peripheral nerve sheath tumor (MPNST) is a highly aggressive sarcoma, and a lethal neurofibromatosis type 1-related malignancy, with little progress made on treatment strategies. Here, we apply a multiplatform integrated molecular analysis on 108 tumors spanning the spectrum of peripheral nerve sheath tumors to identify candidate drivers of MPNST that can serve as therapeutic targets. Unsupervised analyses of methylome and transcriptome profiles identify two distinct subgroups of MPNSTs with unique targetable oncogenic programs. We establish two subgroups of MPNSTs: SHH pathway activation in MPNST-G1 and WNT/ß-catenin/CCND1 pathway activation in MPNST-G2. Single nuclei RNA sequencing characterizes the complex cellular architecture and demonstrate that malignant cells from MPNST-G1 and MPNST-G2 have neural crest-like and Schwann cell precursor-like cell characteristics, respectively. Further, in pre-clinical models of MPNST we confirm that inhibiting SHH pathway in MPNST-G1 prevent growth and malignant progression, providing the rational for investigating these treatments in clinical trials.
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Affiliation(s)
- Suganth Suppiah
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Division of Neurosurgery, Department of Neurosurgery, University of Toronto, Toronto, ON, Canada
| | - Sheila Mansouri
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Yasin Mamatjan
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Jeffrey C Liu
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Minu M Bhunia
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Vikas Patil
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Prisni Rath
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Bharati Mehani
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Pardeep Heir
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Severa Bunda
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Olivia Singh
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Nazanin Ijad
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Neda Pirouzmand
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Tatyana Dalcourt
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Ying Meng
- Division of Neurosurgery, Department of Neurosurgery, University of Toronto, Toronto, ON, Canada
| | - Shirin Karimi
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Qingxia Wei
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Farshad Nassiri
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Division of Neurosurgery, Department of Neurosurgery, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Gary D Bader
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Gelareh Zadeh
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Neurosurgery, University of Toronto, Toronto, ON, Canada.
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10
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Alom Z, Tran QT, Bag AK, Lucas JT, Orr BA. Predicting methylation class from diffusely infiltrating adult gliomas using multimodality MRI data. Neurooncol Adv 2023; 5:vdad045. [PMID: 37215955 PMCID: PMC10195196 DOI: 10.1093/noajnl/vdad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Background Radiogenomic studies of adult-type diffuse gliomas have used magnetic resonance imaging (MRI) data to infer tumor attributes, including abnormalities such as IDH-mutation status and 1p19q deletion. This approach is effective but does not generalize to tumor types that lack highly recurrent alterations. Tumors have intrinsic DNA methylation patterns and can be grouped into stable methylation classes even when lacking recurrent mutations or copy number changes. The purpose of this study was to prove the principle that a tumor's DNA-methylation class could be used as a predictive feature for radiogenomic modeling. Methods Using a custom DNA methylation-based classification model, molecular classes were assigned to diffuse gliomas in The Cancer Genome Atlas (TCGA) dataset. We then constructed and validated machine learning models to predict a tumor's methylation family or subclass from matched multisequence MRI data using either extracted radiomic features or directly from MRI images. Results For models using extracted radiomic features, we demonstrated top accuracies above 90% for predicting IDH-glioma and GBM-IDHwt methylation families, IDH-mutant tumor methylation subclasses, or GBM-IDHwt molecular subclasses. Classification models utilizing MRI images directly demonstrated average accuracies of 80.6% for predicting methylation families, compared to 87.2% and 89.0% for differentiating IDH-mutated astrocytomas from oligodendrogliomas and glioblastoma molecular subclasses, respectively. Conclusions These findings demonstrate that MRI-based machine learning models can effectively predict the methylation class of brain tumors. Given appropriate datasets, this approach could generalize to most brain tumor types, expanding the number and types of tumors that could be used to develop radiomic or radiogenomic models.
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Affiliation(s)
- Zahangir Alom
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Quynh T Tran
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Asim K Bag
- Department of Diagnostic Imaging, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - John T Lucas
- Department of Radiation Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Brent A Orr
- Corresponding Author: Brent A. Orr MD, PhD, Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS 250, Memphis, TN 38-105-3678, USA ()
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11
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Devall MA, Sun X, Eaton S, Cooper GS, Willis JE, Weisenberger DJ, Casey G, Li L. A Race-Specific, DNA Methylation Analysis of Aging in Normal Rectum: Implications for the Biology of Aging and Its Relationship to Rectal Cancer. Cancers (Basel) 2022; 15:cancers15010045. [PMID: 36612042 PMCID: PMC9817986 DOI: 10.3390/cancers15010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/01/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the important role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA) and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epigenome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n = 140 samples). We identified increased epigenetic age acceleration in EA than AA rectum (p = 3.91 × 10-4) using linear regression. We also identified differentially methylated regions (DMRs) associated with chronological aging in AA and EA, separately using DMRcate. Next, a consensus set of regions associated with cancer was identified through DMR analysis of two rectal cancer cohorts. The vast majority of AA DMRs were present in our analysis of aging in rectum of EA subjects, though rates of epigenetic drift were significantly greater in AA (p = 1.94 × 10-45). However, 3.66-fold more DMRs were associated with aging in rectum of EA subjects, many of which were also associated with rectal cancer. Our findings reveal a novel relationship between race, age, DNA methylation and rectal cancer risk that warrants further investigation.
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Affiliation(s)
- Matthew A. Devall
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Xiangqing Sun
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gregory S. Cooper
- Department of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: ; Tel.: +1-434-982-3975
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12
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Kim H, Sim M, Park N, Kwon K, Kim J, Kim J. msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data. BMC Bioinformatics 2022; 23:383. [PMID: 36123620 PMCID: PMC9487059 DOI: 10.1186/s12859-022-04925-2] [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: 02/03/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole genome. However, it is difficult to obtain methylation profiles using the WGBS raw reads and is necessary to be proficient in all types of bioinformatic tools for the study of DNA methylation. In addition, recent end-to-end pipelines for DNA methylation analyses are not sufficient for addressing those difficulties. RESULTS Here we present msPIPE, a pipeline for DNA methylation analyses with WGBS data seamlessly connecting all the required tasks ranging from data pre-processing to multiple downstream DNA methylation analyses. The msPIPE can generate various methylation profiles to analyze methylation patterns in the given sample, including statistical summaries and methylation levels. Also, the methylation levels in the functional regions of a genome are computed with proper annotation. The results of methylation profiles, hypomethylation, and differential methylation analysis are plotted in publication-quality figures. The msPIPE can be easily and conveniently used with a Docker image, which includes all dependent packages and software related to DNA methylation analyses. CONCLUSION msPIPE is a new end-to-end pipeline designed for methylation calling, profiling, and various types of downstream DNA methylation analyses, leading to the creation of publication-quality figures. msPIPE allows researchers to process and analyze the WGBS data in an easy and convenient way. It is available at https://github.com/jkimlab/msPIPE and https://hub.docker.com/r/jkimlab/mspipe .
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Affiliation(s)
- Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Junyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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13
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Parmar S, Easwaran H. Genetic and epigenetic dependencies in colorectal cancer development. Gastroenterol Rep (Oxf) 2022; 10:goac035. [PMID: 35975243 PMCID: PMC9373935 DOI: 10.1093/gastro/goac035] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/24/2022] [Accepted: 05/22/2022] [Indexed: 11/12/2022] Open
Abstract
Recent studies have mapped key genetic changes in colorectal cancer (CRC) that impact important pathways contributing to the multistep models for CRC initiation and development. In parallel with genetic changes, normal and cancer tissues harbor epigenetic alterations impacting regulation of critical genes that have been shown to play profound roles in the tumor initiation. Cumulatively, these molecular changes are only loosely associated with heterogenous transcriptional programs, reflecting the heterogeneity in the various CRC molecular subtypes and the paths to CRC development. Studies from mapping molecular alterations in early CRC lesions and use of experimental models suggest that the intricate dependencies of various genetic and epigenetic hits shape the early development of CRC via different pathways and its manifestation into various CRC subtypes. We highlight the dependency of epigenetic and genetic changes in driving CRC development and discuss factors affecting epigenetic alterations over time and, by extension, risk for cancer.
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Affiliation(s)
- Sehej Parmar
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hariharan Easwaran
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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14
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Zuo Y, Zhong J, Bai H, Xu B, Wang Z, Li W, Chen Y, Jin S, Wang S, Wang X, Wan R, Xu J, Fei K, Han J, Yang Z, Bao H, Shao Y, Ying J, Song Q, Duan J, Wang J. Genomic and epigenomic profiles distinguish pulmonary enteric adenocarcinoma from lung metastatic colorectal cancer. EBioMedicine 2022; 82:104165. [PMID: 35901658 PMCID: PMC9334343 DOI: 10.1016/j.ebiom.2022.104165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ying Zuo
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jia Zhong
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bin Xu
- Cancer center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yedan Chen
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Shi Jin
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Shuhang Wang
- GCP Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xin Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiachen Xu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Kailun Fei
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiefei Han
- Department of Neuro-oncology, Cancer Center Beijing Tiantan Hospital, Capital Medical University, China
| | - Zhenlin Yang
- Thoracic Surgery Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hua Bao
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China; School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qibin Song
- Cancer center, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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15
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Gore S, Azad RK. CancerNet: a unified deep learning network for pan-cancer diagnostics. BMC Bioinformatics 2022; 23:229. [PMID: 35698059 PMCID: PMC9195411 DOI: 10.1186/s12859-022-04783-y] [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: 02/03/2022] [Accepted: 06/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Despite remarkable advances in cancer research, cancer remains one of the leading causes of death worldwide. Early detection of cancer and localization of the tissue of its origin are key to effective treatment. Here, we leverage technological advances in machine learning or artificial intelligence to design a novel framework for cancer diagnostics. Our proposed framework detects cancers and their tissues of origin using a unified model of cancers encompassing 33 cancers represented in The Cancer Genome Atlas (TCGA). Our model exploits the learned features of different cancers reflected in the respective dysregulated epigenomes, which arise early in carcinogenesis and differ remarkably between different cancer types or subtypes, thus holding a great promise in early cancer detection. Results Our comprehensive assessment of the proposed model on the 33 different tissues of origin demonstrates its ability to detect and classify cancers to a high accuracy (> 99% overall F-measure). Furthermore, our model distinguishes cancers from pre-cancerous lesions to metastatic tumors and discriminates between hypomethylation changes due to age related epigenetic drift and true cancer. Conclusions Beyond detection of primary cancers, our proposed computational model also robustly detects tissues of origin of secondary cancers, including metastatic cancers, second primary cancers, and cancers of unknown primaries. Our assessment revealed the ability of this model to characterize pre-cancer samples, a significant step forward in early cancer detection. Deployed broadly this model can deliver accurate diagnosis for a greatly expanded target patient population. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04783-y.
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Affiliation(s)
- Steven Gore
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA. .,Department of Mathematics, University of North Texas, Denton, TX, 76203, USA.
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16
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Complex Elucidation of Cells-of-Origin in Pediatric Soft Tissue Sarcoma: From Concepts to Real Life, Hide-and-Seek through Epigenetic and Transcriptional Reprogramming. Int J Mol Sci 2022; 23:ijms23116310. [PMID: 35682989 PMCID: PMC9181261 DOI: 10.3390/ijms23116310] [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: 04/11/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 02/01/2023] Open
Abstract
Soft tissue sarcoma (STS) comprise a large group of mesenchymal malignant tumors with heterogeneous cellular morphology, proliferative index, genetic lesions and, more importantly, clinical features. Full elucidation of this wide diversity remains a central question to improve their therapeutic management and the identity of cell(s)-of-origin from which these tumors arise is part of this enigma. Cellular reprogramming allows transitions of a mature cell between phenotypes, or identities, and represents one key driver of tumoral heterogeneity. Here, we discuss how cellular reprogramming mediated by driver genes in STS can profoundly reshape the molecular and morphological features of a transformed cell and lead to erroneous interpretation of its cell-of-origin. This review questions the fact that the epigenetic context in which a genetic alteration arises has to be taken into account as a key determinant of STS tumor initiation and progression. Retracing the cancer-initiating cell and its clonal evolution, notably via epigenetic approach, appears as a key lever for understanding the origin of these tumors and improving their clinical management.
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17
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Woltering N, Albers A, Müther M, Stummer W, Paulus W, Hasselblatt M, Holling M, Thomas C. DNA
methylation profiling of central nervous system hemangioblastomas identifies two distinct subgroups. Brain Pathol 2022; 32:e13083. [PMID: 35637626 PMCID: PMC9616087 DOI: 10.1111/bpa.13083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/10/2022] [Indexed: 12/01/2022] Open
Abstract
Hemangioblastomas (HBs) of the central nervous system are highly vascular neoplasms that occur sporadically or as a manifestation of von Hippel–Lindau (VHL) disease. Despite their benign nature, HBs are clinically heterogeneous and can be associated with significant morbidity due to mass effects of peritumoral cysts or tumor progression. Underlying molecular factors involved in HB tumor biology remain elusive. We investigated genome‐wide DNA methylation profiles and clinical and histopathological features in a series of 47 HBs from 42 patients, including 28 individuals with VHL disease. Thirty tumors occurred in the cerebellum, 8 in the brainstem and 8 HBs were of spinal location, while 1 HB was located in the cerebrum. Histologically, 12 HBs (26%) belonged to the cellular subtype and exclusively occurred in the cerebellum, whereas 35 HBs were reticular (74%). Unsupervised clustering and dimensionality reduction of DNA methylation profiles revealed two distinct subgroups. Methylation cluster 1 comprised 30 HBs of mainly cerebellar location (29/30, 97%), whereas methylation cluster 2 contained 17 HBs predominantly located in non‐cerebellar compartments (16/17, 94%). The sum of chromosomal regions being affected by copy‐number alterations was significantly higher in methylation cluster 1 compared to cluster 2 (mean 262 vs. 109 Mb, p = 0.001). Of note, loss of chromosome 6 occurred in 9/30 tumors (30%) of methylation cluster 1 and was not observed in cluster 2 tumors (p = 0.01). No relevant methylation differences between sporadic and VHL‐related HBs or cystic and non‐cystic HBs could be detected. Deconvolution of the bulk DNA methylation profiles revealed four methylation components that were associated with the two methylation clusters suggesting cluster‐specific cell‐type compositions. In conclusion, methylation profiling of HBs reveals 2 distinct subgroups that mainly associate with anatomical location, cytogenetic profiles and differences in cell type composition, potentially reflecting different cells of origin.
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Affiliation(s)
- Niklas Woltering
- Institute of Neuropathology University Hospital Münster Münster Germany
| | - Anne Albers
- Institute of Neuropathology University Hospital Münster Münster Germany
| | - Michael Müther
- Department of Neurosurgery University Hospital Münster Münster Germany
| | - Walter Stummer
- Department of Neurosurgery University Hospital Münster Münster Germany
| | - Werner Paulus
- Institute of Neuropathology University Hospital Münster Münster Germany
| | | | - Markus Holling
- Department of Neurosurgery University Hospital Münster Münster Germany
| | - Christian Thomas
- Institute of Neuropathology University Hospital Münster Münster Germany
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18
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Laurent A, Madigou T, Bizot M, Turpin M, Palierne G, Mahé E, Guimard S, Métivier R, Avner S, Le Péron C, Salbert G. TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis. Life Sci Alliance 2022; 5:5/7/e202101283. [PMID: 35351824 PMCID: PMC8963717 DOI: 10.26508/lsa.202101283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
TET2-mediated oxidation of 5-methylcytosine establishes an antiviral state and contributes to MYC-dependent down-regulation of genes involved in lysosome biogenesis and function in breast cancer cells. Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression by controlling the chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs, and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. The TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC-binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease–like state that contributes to an exacerbated sensitivity to autophagy inducers.
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Affiliation(s)
- Audrey Laurent
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Thierry Madigou
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Maud Bizot
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Marion Turpin
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gaëlle Palierne
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Elise Mahé
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Sarah Guimard
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Raphaël Métivier
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Stéphane Avner
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Christine Le Péron
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gilles Salbert
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
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19
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Simon T, Riemer P, Jarosch A, Detjen K, Di Domenico A, Bormann F, Menne A, Khouja S, Monjé N, Childs LH, Lenze D, Leser U, Rossner F, Morkel M, Blüthgen N, Pavel M, Horst D, Capper D, Marinoni I, Perren A, Mamlouk S, Sers C. DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors. Genome Med 2022; 14:24. [PMID: 35227293 PMCID: PMC8886788 DOI: 10.1186/s13073-022-01018-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/28/2022] [Indexed: 02/07/2023] Open
Abstract
Background Pancreatic neuroendocrine neoplasms (PanNENs) fall into two subclasses: the well-differentiated, low- to high-grade pancreatic neuroendocrine tumors (PanNETs), and the poorly-differentiated, high-grade pancreatic neuroendocrine carcinomas (PanNECs). While recent studies suggest an endocrine descent of PanNETs, the origin of PanNECs remains unknown. Methods We performed DNA methylation analysis for 57 PanNEN samples and found that distinct methylation profiles separated PanNENs into two major groups, clearly distinguishing high-grade PanNECs from other PanNETs including high-grade NETG3. DNA alterations and immunohistochemistry of cell-type markers PDX1, ARX, and SOX9 were utilized to further characterize PanNECs and their cell of origin in the pancreas. Results Phylo-epigenetic and cell-type signature features derived from alpha, beta, acinar, and ductal adult cells suggest an exocrine cell of origin for PanNECs, thus separating them in cell lineage from other PanNENs of endocrine origin. Conclusions Our study provides a robust and clinically applicable method to clearly distinguish PanNECs from G3 PanNETs, improving patient stratification. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01018-w.
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Affiliation(s)
- Tincy Simon
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Pamela Riemer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Armin Jarosch
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Katharina Detjen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hepatology and Gastroenterology, Berlin, Germany
| | | | | | - Andrea Menne
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Slim Khouja
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Nanna Monjé
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Liam H Childs
- Humboldt-Universität zu Berlin, Knowledge Management in Bioinformatics, Berlin, Germany
| | - Dido Lenze
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Ulf Leser
- Humboldt-Universität zu Berlin, Knowledge Management in Bioinformatics, Berlin, Germany
| | - Florian Rossner
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Nils Blüthgen
- Integrative Research Institute (IRI) Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marianne Pavel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hepatology and Gastroenterology, Berlin, Germany
| | - David Horst
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - David Capper
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neuropathology, Berlin, Germany.,German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilaria Marinoni
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Aurel Perren
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Soulafa Mamlouk
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Christine Sers
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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20
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Zhang CD, Takeshima H, Sekine S, Yamashita S, Liu YY, Hattori N, Abe H, Yamashita H, Fukuda M, Imamura Y, Ushiku T, Katai H, Makino H, Watanabe M, Seto Y, Ushijima T. Prediction of tissue origin of adenocarcinomas in the esophagogastric junction by DNA methylation. Gastric Cancer 2022; 25:336-345. [PMID: 34557982 DOI: 10.1007/s10120-021-01252-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Prediction of tissue origin of esophagogastric junction (EGJ) adenocarcinomas can be important for therapeutic decision, but no molecular marker is available. Here, we aimed to develop such a marker taking advantage of tissue-specific profiles of DNA methylation. METHODS DNA methylation profiles of gastric adenocarcinomas (GACs) were obtained by an Infinium HumanMethylation450 BeadChip array, and those of esophageal adenocarcinoma (EACs) were obtained from the TCGA database. DNA from formalin-fixed paraffin-embedded (FFPE) samples was analyzed by bisulfite pyrosequencing. RESULTS In the screening set, 51 of 145,841 CpG sites in CpG islands were methylated at significantly higher levels in 30 GACs compared to those in 30 EACs. Among them, SLC46A3 and cg09177106 were unmethylated in all the 30 EACs. Predictive powers of these two markers were successfully confirmed in an independent validation set (18 GACs and 18 EACs) (SLC46A3, sensitivity = 77.8%, specificity = 100%; cg09177106, sensitivity = 83.3%, specificity = 94.4%), and could be applied to FFPE samples (37 GACs and 18 EACs) (SLC46A3, P = 0.0001; cg09177106, P = 0.0028). On the other hand, EAC-specific markers informative in the FFPE samples could not be isolated. Using these GAC-specific markers, nine of 46 (19.6%) TCGA EGJ adenocarcinomas were predicted to be GACs. CONCLUSIONS Two GAC-specific markers, SLC46A3 and cg09177106, had a high specificity for identifying the tissue origin of EGJ adenocarcinoma.
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Affiliation(s)
- Chun-Dong Zhang
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yu-Yu Liu
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroharu Yamashita
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Masahide Fukuda
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hitoshi Katai
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Hiroshi Makino
- Department of Surgery, Tama-Nagayama Hospital, Nippon Medical School, Tokyo, 206-8512, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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21
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Feng J, Zhao D, Lv F, Yuan Z. Epigenetic Inheritance From Normal Origin Cells Can Determine the Aggressive Biology of Tumor-Initiating Cells and Tumor Heterogeneity. Cancer Control 2022; 29:10732748221078160. [PMID: 35213254 PMCID: PMC8891845 DOI: 10.1177/10732748221078160] [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] [Indexed: 12/03/2022] Open
Abstract
The acquisition of genetic- and epigenetic-abnormalities during transformation has been recognized as the two fundamental factors that lead to tumorigenesis and determine the aggressive biology of tumor cells. However, there is a regularity that tumors derived from less-differentiated normal origin cells (NOCs) usually have a higher risk of vascular involvement, lymphatic and distant metastasis, which can be observed in both lymphohematopoietic malignancies and somatic cancers. Obviously, the hypothesis of genetic- and epigenetic-abnormalities is not sufficient to explain how the linear relationship between the cellular origin and the biological behavior of tumors is formed, because the cell origin of tumor is an independent factor related to tumor biology. In a given system, tumors can originate from multiple cell types, and tumor-initiating cells (TICs) can be mapped to different differentiation hierarchies of normal stem cells, suggesting that the heterogeneity of the origin of TICs is not completely chaotic. TIC’s epigenome includes not only genetic- and epigenetic-abnormalities, but also established epigenetic status of genes inherited from NOCs. In reviewing previous studies, we found much evidence supporting that the status of many tumor-related “epigenetic abnormalities” in TICs is consistent with that of the corresponding NOC of the same differentiation hierarchy, suggesting that they may not be true epigenetic abnormalities. So, we speculate that the established statuses of genes that control NOC’s migration, adhesion and colonization capabilities, cell-cycle quiescence, expression of drug transporters, induction of mesenchymal formation, overexpression of telomerase, and preference for glycolysis can be inherited to TICs through epigenetic memory and be manifested as their aggressive biology. TICs of different origins can maintain different degrees of innate stemness from NOC, which may explain why malignancies with stem cell phenotypes are usually more aggressive.
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Affiliation(s)
- Jiliang Feng
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Dawei Zhao
- Medical Imaging Department, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Fudong Lv
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Zhongyu Yuan
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
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22
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The Transcriptome and Methylome of the Developing and Aging Brain and Their Relations to Gliomas and Psychological Disorders. Cells 2022; 11:cells11030362. [PMID: 35159171 PMCID: PMC8834030 DOI: 10.3390/cells11030362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 02/01/2023] Open
Abstract
Mutually linked expression and methylation dynamics in the brain govern genome regulation over the whole lifetime with an impact on cognition, psychological disorders, and cancer. We performed a joint study of gene expression and DNA methylation of brain tissue originating from the human prefrontal cortex of individuals across the lifespan to describe changes in cellular programs and their regulation by epigenetic mechanisms. The analysis considers previous knowledge in terms of functional gene signatures and chromatin states derived from independent studies, aging profiles of a battery of chromatin modifying enzymes, and data of gliomas and neuropsychological disorders for a holistic view on the development and aging of the brain. Expression and methylation changes from babies to elderly adults decompose into different modes associated with the serial activation of (brain) developmental, learning, metabolic and inflammatory functions, where methylation in gene promoters mostly represses transcription. Expression of genes encoding methylome modifying enzymes is very diverse reflecting complex regulations during lifetime which also associates with the marked remodeling of chromatin between permissive and restrictive states. Data of brain cancer and psychotic disorders reveal footprints of pathophysiologies related to brain development and aging. Comparison of aging brains with gliomas supports the view that glioblastoma-like and astrocytoma-like tumors exhibit higher cellular plasticity activated in the developing healthy brain while oligodendrogliomas have a more stable differentiation hierarchy more resembling the aged brain. The balance and specific shifts between volatile and stable and between more irreversible and more plastic epigenomic networks govern the development and aging of healthy and diseased brain.
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23
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Cao LJ, Peng XL, Xue WQ, Zhang R, Zhang JB, Zhou T, Wu ZY, Li GR, Wang TM, He YQ, Yang DW, Liao Y, Tong XT, Wang F, Chen KX, Zhang SH, Zhu LQ, Ding PR, Jia WH. A fecal-based test for the detection of advanced adenoma and colorectal cancer: a case-control and screening cohort study. BMC Med 2021; 19:250. [PMID: 34689777 PMCID: PMC8543798 DOI: 10.1186/s12916-021-02123-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/13/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the leading cause of cancer death worldwide. Screening is a confirmed way to reduce the incidence and mortality rates of CRC. This study aimed to identify a fecal-based, noninvasive, and accurate method for detection of colorectal cancer (CRC) and advanced adenoma (AA). METHODS Through detection in tissue (n = 96) and fecal samples (n = 88) and tested in an independent group of fecal samples (n = 294), the methylated DNA marker ITGA4 and bacterial markers Fusobacterium nucleatum (Fn) and Pepetostreptococcusanaerobius (Pa) were identified from the candidate biomarkers for CRC and AA detection. A prediction score (pd-score) was constructed using the selected markers and fecal immunochemical test (FIT) for distinguishing AA and CRC from healthy subjects by logistic regression method. The diagnostic performance of the pd-score was compared with FIT and validated in the external validation cohort (n = 117) and in a large CRC screening cohort. RESULTS The pd-score accurately identified AA and CRC from healthy subjects with an area under the curve (AUC) of 0.958, at a specificity of 91.37%; the pd-score showed sensitivities of 95.38% for CRC and 70.83% for AA, respectively. In the external validation cohort, the sensitivities of the pd-score for CRC and AA detection were 94.03% and 80.00%, respectively. When applied in screening, the pd-score identified 100% (11/11) of CRC and 70.83% (17/24) of AA in participants with both colonoscopy results and qualified fecal samples, showing an improvement by 41.19% compared to FIT. CONCLUSIONS The current study developed a noninvasive and well-validated approach for AA and CRC detection, which could be applied widely as a diagnostic and screening test.
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Affiliation(s)
- Lian-Jing Cao
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Xiao-Lin Peng
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, People's Republic of China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Rong Zhang
- Department of Endoscopy and Laser, Sun Yat-Sen University Cancer Center, Guangzhou, People's Republic of China
| | - Jiang-Bo Zhang
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China.,Biobank of Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Zi-Yi Wu
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Gai-Rui Li
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, People's Republic of China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Ying Liao
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Xia-Ting Tong
- School of Public Health, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Fang Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Ke-Xin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Shi-Hong Zhang
- Department of Laboratory Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Li-Qing Zhu
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, People's Republic of China
| | - Pei-Rong Ding
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China. .,Biobank of Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China. .,School of Public Health, Sun Yat-Sen University, Guangzhou, People's Republic of China.
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24
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Jurmeister P, Weber K, Villegas S, Karn T, Untch M, Thieme A, Müller V, Taube E, Fasching P, Schmitt WD, Marmé F, Stickeler E, Sinn BV, Jank P, Schem C, Klauschen F, van Mackelenbergh M, Denkert C, Loibl S, Capper D. DNA methylation profiling identifies two distinct subgroups in breast cancers with low hormone receptor expression, mainly associated with HER2 amplification status. Clin Epigenetics 2021; 13:184. [PMID: 34602069 PMCID: PMC8489064 DOI: 10.1186/s13148-021-01176-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 09/22/2021] [Indexed: 11/25/2022] Open
Abstract
Background Current clinical guidelines suggest that breast cancers with low hormone receptor expression (LowHR) in 1–10% of tumor cells should be regarded as hormone receptor positive. However, clinical data show that these patients have worse outcome compared to patients with hormone receptor expression above 10%. We performed DNA methylation profiling on 23 LowHR breast cancer specimens, including 13 samples with HER2 amplification and compared our results with a reference breast cancer cohort from The Cancer Genome Atlas to clarify the status for this infrequent but important patient subgroup. Results In unsupervised clustering and dimensionality reduction, breast cancers with low hormone receptor expression that lacked HER2 amplification usually clustered with triple negative breast cancer (TNBC) reference samples (8/10; “LowHR TNBC-like”). In contrast, most specimens with low hormone receptor expression and HER2 amplification grouped with hormone receptor positive cancers (11/13; “LowHR HRpos-like”). We observed highly similar DNA methylation patterns of LowHR TNBC-like samples and true TNBCs. Furthermore, the Ki67 proliferation index of LowHR TNBC-like samples and clinical outcome parameters were more similar to TNBCs and differed from LowHR HRpos-like cases.
Conclusions We here demonstrate that LowHR breast cancer comprises two epigenetically distinct groups. Our data strongly suggest that LowHR TNBC-like samples are molecularly, histologically and clinically closely related to TNBC, while LowHR HRpos-like specimens are closely related to hormone receptor positive tumors. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01176-5.
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Affiliation(s)
- Philipp Jurmeister
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), 69210, Heidelberg, Germany. .,Berlin Institute of Health, Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany. .,Institute of Pathology, Ludwig Maximilians University Hospital Munich, Thalkirchner Str. 36, 80337, Munich, Germany.
| | | | - Sonia Villegas
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
| | - Thomas Karn
- Department of Gynecology and Obstetrics, Goethe University, Frankfurt, Germany
| | - Michael Untch
- Department of Gynecology and Obstetrics, Breast Cancer Center, Helios-Klinikum Berlin, Buch, Germany
| | - Anne Thieme
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), 69210, Heidelberg, Germany
| | - Volkmar Müller
- Department of Obstetrics and Gynecology, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Hamburg, Germany
| | - Eliane Taube
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
| | - Peter Fasching
- Brustzentrum, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Wolfgang D Schmitt
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
| | - Frederik Marmé
- Department of Obstetrics and Gynecology, University Hospital Heidelberg, Heidelberg, Germany
| | - Elmar Stickeler
- Klinik für Gynäkologie und Geburtsmedizin, Universitätsklinikum Aachen, Aachen, Germany
| | - Bruno V Sinn
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
| | - Paul Jank
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | | | - Frederick Klauschen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), 69210, Heidelberg, Germany.,Berlin Institute of Health, Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | | | - Carsten Denkert
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | | | - David Capper
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), 69210, Heidelberg, Germany.,Berlin Institute of Health, Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany.,Department of Neuropathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117, Berlin, Germany
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25
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Hu H, Wu D, Liu X, Yu H, Xu J, Cai W, Huang Y, Bai R, Zhang J, Gu Y, Zheng S, Ge W. SPARCL1 exhibits different expressions in left- and right-sided colon cancer and is downregulated via DNA methylation. Epigenomics 2021; 13:1269-1282. [PMID: 34435512 DOI: 10.2217/epi-2021-0231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: The authors previously found that SPARCL1 functions to suppress colorectal cancer metastasis. Here, the epigenetic mechanism of SPARCL1 regulation and its relationship with clinicopathological features in colon cancer were investigated. Materials & methods: SPARCL1 expression was evaluated by immunohistochemistry staining in a tissue array containing 271 left-sided colon cancer samples and 257 right-sided colon cancer samples. In vivo and in vitro DNA methylation states were measured by biochemical sulfide potential assay. The transcription and DNA methylation states in cells were altered by siRNA or decitabine treatment, respectively. Cellular motility properties were compared through transwell assay. Results & conclusion: SPARCL1, mediated by its DNA methylation, may arrest colorectal carcinoma motility. Furthermore, SPARCL1 expression is higher and may have a specific prognostic value in left-sided colon cancer.
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Affiliation(s)
- Hanguang Hu
- Cancer Institute, Key Laboratory of Cancer Prevention & Intervention, China National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences; the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou 310009, Zhejiang Province, China.,Department of Oncology, the Second Affiliated Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang Province, China
| | - Dehao Wu
- Cancer Institute, Key Laboratory of Cancer Prevention & Intervention, China National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences; the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou 310009, Zhejiang Province, China
| | - Xibo Liu
- Department of Pathology, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China
| | - Haifeng Yu
- Department of Oncology, the Second Affiliated Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang Province, China.,Department of Lymphatic Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310005, Zhejiang Province, China.,Institute of Cancer & Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang Province, China
| | - Junxi Xu
- Department of Gastroenterology, the Second Affiliated Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang Province, China
| | - Wen Cai
- Cancer Institute, Key Laboratory of Cancer Prevention & Intervention, China National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences; the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou 310009, Zhejiang Province, China.,Department of Gastroenterology, the Second Affiliated Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, Zhejiang Province, China
| | - Yanqin Huang
- Cancer Institute, Key Laboratory of Cancer Prevention & Intervention, China National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences; the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou 310009, Zhejiang Province, China
| | - Rui Bai
- Cancer Institute, Key Laboratory of Cancer Prevention & Intervention, China National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences; the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou 310009, Zhejiang Province, China
| | - Jiawei Zhang
- Cancer Institute, Key Laboratory of Cancer Prevention & Intervention, China National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences; the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou 310009, Zhejiang Province, China
| | - Ying Gu
- Institute of genetics, Zhejiang University, Zijingang Campus of Zhejiang University, Yuhangtang Road No.388, Hangzhou, 310058, Zhejiang Province, China
| | - Shu Zheng
- Cancer Institute, Key Laboratory of Cancer Prevention & Intervention, China National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences; the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou 310009, Zhejiang Province, China
| | - Weiting Ge
- Cancer Institute, Key Laboratory of Cancer Prevention & Intervention, China National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences; the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou 310009, Zhejiang Province, China.,Cancer Center, Zhejiang University, Hangzhou, 310000, Zhejiang Province, China
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26
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Mosella MS, Sabedot TS, Silva TC, Malta TM, Dezem FS, Asmaro KP, Wells M, Mukherjee A, Poisson LM, Snyder J, deCarvalho AC, Walbert T, Aho T, Kalkanis S, Elias PC, Antonini SR, Rock J, Noushmehr H, Castro M, Castro AV. DNA methylation-based signatures classify sporadic pituitary tumors according to clinicopathological features. Neuro Oncol 2021; 23:1292-1303. [PMID: 33631002 DOI: 10.1093/neuonc/noab044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Distinct genome-wide methylation patterns cluster pituitary neuroendocrine tumors (PitNETs) into molecular groups associated with specific clinicopathological features. Here we aim to identify, characterize, and validate methylation signatures that objectively classify PitNET into clinicopathological groups. METHODS Combining in-house and publicly available data, we conducted an analysis of the methylome profile of a comprehensive cohort of 177 tumors (Panpit cohort) and 20 nontumor specimens from the pituitary gland. We also retrieved methylome data from an independent PitNET cohort (N = 86) to validate our findings. RESULTS We identified three methylation clusters associated with adenohypophyseal cell lineages and functional status using an unsupervised approach. Differentially methylated probes (DMP) significantly distinguished the Panpit clusters and accurately assigned the samples of the validation cohort to their corresponding lineage and functional subtypes memberships. The DMPs were annotated in regulatory regions enriched with enhancer elements, associated with pathways and genes involved in pituitary cell identity, function, tumorigenesis, and invasiveness. Some DMPs correlated with genes with prognostic and therapeutic values in other intra- or extracranial tumors. CONCLUSIONS We identified and validated methylation signatures, mainly annotated in enhancer regions that distinguished PitNETs by distinct adenohypophyseal cell lineages and functional status. These signatures provide the groundwork to develop an unbiased approach to classifying PitNETs according to the most recent classification recommended by the 2017 WHO and to explore their biological and clinical relevance in these tumors.
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Affiliation(s)
- Maritza S Mosella
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA.,Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Thais S Sabedot
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Tiago C Silva
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Tathiane M Malta
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Felipe Segato Dezem
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Karam P Asmaro
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Michael Wells
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Abir Mukherjee
- Department of Pathology, Henry Ford Health System, Detroit, Michigan, USA
| | - Laila M Poisson
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA.,Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - James Snyder
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Ana C deCarvalho
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Tobias Walbert
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Todd Aho
- Department of Radiology, Henry Ford Health System, Detroit, Michigan, USA
| | - Steven Kalkanis
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Paula C Elias
- Internal Medicine Department, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Sonir R Antonini
- Department of Pediatrics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Jack Rock
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA.,Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Margaret Castro
- Internal Medicine Department, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Ana Valeria Castro
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
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27
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Dieter SM, Siegl C, Codó PL, Huerta M, Ostermann-Parucha AL, Schulz E, Zowada MK, Martin S, Laaber K, Nowrouzi A, Blatter M, Kreth S, Westermann F, Benner A, Uhrig U, Putzker K, Lewis J, Haegebarth A, Mumberg D, Holton SJ, Weiske J, Toepper LM, Scheib U, Siemeister G, Ball CR, Kuster B, Stoehr G, Hahne H, Johannes S, Lange M, Herbst F, Glimm H. Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer. Cell Rep 2021; 36:109394. [PMID: 34289372 DOI: 10.1016/j.celrep.2021.109394] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/08/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Novel treatment options for metastatic colorectal cancer (CRC) are urgently needed to improve patient outcome. Here, we screen a library of non-characterized small molecules against a heterogeneous collection of patient-derived CRC spheroids. By prioritizing compounds with inhibitory activity in a subset of-but not all-spheroid cultures, NCT02 is identified as a candidate with minimal risk of non-specific toxicity. Mechanistically, we show that NCT02 acts as molecular glue that induces ubiquitination of cyclin K (CCNK) and proteasomal degradation of CCNK and its complex partner CDK12. Knockout of CCNK or CDK12 decreases proliferation of CRC cells in vitro and tumor growth in vivo. Interestingly, sensitivity to pharmacological CCNK/CDK12 degradation is associated with TP53 deficiency and consensus molecular subtype 4 in vitro and in patient-derived xenografts. We thus demonstrate the efficacy of targeted CCNK/CDK12 degradation for a CRC subset, highlighting the potential of drug-induced proteolysis for difficult-to-treat types of cancer.
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Affiliation(s)
- Sebastian M Dieter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany.
| | | | - Paula L Codó
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; CureVac AG, 60325 Frankfurt am Main, Germany
| | - Mario Huerta
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Anna L Ostermann-Parucha
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Erik Schulz
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Martina K Zowada
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Sylvia Martin
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Karin Laaber
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Ali Nowrouzi
- Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Mona Blatter
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Sina Kreth
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Kerstin Putzker
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Andrea Haegebarth
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Dominik Mumberg
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Simon J Holton
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Joerg Weiske
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Lena-Marit Toepper
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Ulrike Scheib
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Gerhard Siemeister
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 01307 Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | | | | | - Sarah Johannes
- Bayer AG, Research & Development, Pharmaceuticals, 42117 Wuppertal, Germany
| | - Martin Lange
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Friederike Herbst
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 01307 Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany.
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Exploration of the Key Proteins in the Normal-Adenoma-Carcinoma Sequence of Colorectal Cancer Evolution Using In-Depth Quantitative Proteomics. JOURNAL OF ONCOLOGY 2021; 2021:5570058. [PMID: 34194496 PMCID: PMC8214504 DOI: 10.1155/2021/5570058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 12/30/2022]
Abstract
Purpose In most cases, the carcinogenesis of colorectal cancer (CRC) follows the normal-adenoma-carcinoma (N-A-C) sequence. In this study, we aimed to identify the key proteins in the N-A-C sequence. Methods Differentially expressed proteins (DEPs) in normal, adenoma, and carcinoma tissues were identified using the Tandem Mass Tag- (TMT-) based quantitative proteomics approach. The landscape of proteomic variation in the N-A-C sequence was explored using gene set enrichment analysis (GSEA) and Proteomaps. Key proteins in the N-A-C sequence were identified, verified, and validated based on our proteomic data, external proteomic data, and external transcriptomic data in the ProteomeXchange, CPTAC, GEO, and TCGA databases. The prognostic value of the key proteins in our database was evaluated by univariate and multivariate Cox regression analysis. The effects of the key proteins on adenoma organoids and colorectal cancer cells were explored in functional studies. Results Based on our proteomic profiles, we identified 1,294 DEPs between the carcinoma (CG) and normal (NG) groups, 919 DEPs between the adenoma group (AG) and NG, and 1,030 DEPs between the CG and AG. Ribosome- and spliceosome-related pathways were mainly enriched in the N-A process. Extracellular matrix- and epithelial-mesenchymal transition- (EMT-) related pathways were mainly enriched in the A-C process. RRP12 and SERPINH1 were identified, verified, and validated as candidate key proteins in the N-A and A-C processes, respectively. Furthermore, RRP12 and SERPINH1 knockdown impeded the viability and proliferation of adenoma organoids. SERPINH1 was validated as a risk factor for disease-free survival (DFS) based on the TCGA and our database, whereas RRP12 did not show prognostic value. SERPINH1 knockdown was accompanied by EMT-related protein variation, increased apoptosis, and reduced proliferation, invasion, and migration of CRC cells in vitro. Conclusions RRP12 and SERPINH1 may play an important role in the N-A and A-C processes, respectively. Furthermore, SERPINH1 showed favorable prognostic value for DFS in CRC patients. We speculate that SERPINH1 might promote not only the A-C process but also the development of CRC.
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29
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Kannan S, Lock I, Ozenberger BB, Jones KB. Genetic drivers and cells of origin in sarcomagenesis. J Pathol 2021; 254:474-493. [DOI: 10.1002/path.5617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/01/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Sarmishta Kannan
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Ian Lock
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Benjamin B Ozenberger
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Kevin B Jones
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
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30
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Liu G, Liu Z, Sun X, Xia X, Liu Y, Liu L. Pan-Cancer Genome-Wide DNA Methylation Analyses Revealed That Hypermethylation Influences 3D Architecture and Gene Expression Dysregulation in HOXA Locus During Carcinogenesis of Cancers. Front Cell Dev Biol 2021; 9:649168. [PMID: 33816499 PMCID: PMC8012915 DOI: 10.3389/fcell.2021.649168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/01/2021] [Indexed: 01/22/2023] Open
Abstract
DNA methylation dysregulation during carcinogenesis has been widely discussed in recent years. However, the pan-cancer DNA methylation biomarkers and corresponding biological mechanisms were seldom investigated. We identified differentially methylated sites and regions from 5,056 The Cancer Genome Atlas (TCGA) samples across 10 cancer types and then validated the findings using 48 manually annotated datasets consisting of 3,394 samples across nine cancer types from Gene Expression Omnibus (GEO). All samples’ DNA methylation profile was evaluated with Illumina 450K microarray to narrow down the batch effect. Nine regions were identified as commonly differentially methylated regions across cancers in TCGA and GEO cohorts. Among these regions, a DNA fragment consisting of ∼1,400 bp detected inside the HOXA locus instead of the boundary may relate to the co-expression attenuation of genes inside the locus during carcinogenesis. We further analyzed the 3D DNA interaction profile by the publicly accessible Hi-C database. Consistently, the HOXA locus in normal cell lines compromised isolated topological domains while merging to the domain nearby in cancer cell lines. In conclusion, the dysregulation of the HOXA locus provides a novel insight into pan-cancer carcinogenesis.
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Affiliation(s)
- Gang Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhenhao Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, National Health and Family Planning Commission, Xiangya Hospital, Central South University, Changsha, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Xiaomeng Sun
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiaoqiong Xia
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yunhe Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lei Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
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31
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Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13051097. [PMID: 33806447 PMCID: PMC7961698 DOI: 10.3390/cancers13051097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/28/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Different types of cells with tumor-initiating cell (TIC) activity contribute to colorectal cancer (CRC) progression and resistance to anti-cancer treatment. In this study, we aimed to understand whether different cell types exist within a patient-derived tumor culture, distinguishable by different patterns of their gene expression. By mRNA sequencing of patient-derived CRC cultures at the single-cell level, we defined expression programs that closely resemble differentiated cell populations of the normal intestine. Here, cell type-associated subpopulations showed differences in functional properties such as cell growth and energy metabolism. Subsequent functional analyses in vitro and in vivo demonstrated that metabolic states are linked to TIC activity in primary CRC cultures. We also show that TIC activity is dependent on oxidative phosphorylation, which may therefore represent a target for novel therapies. Abstract Intra-tumor heterogeneity of tumor-initiating cell (TIC) activity drives colorectal cancer (CRC) progression and therapy resistance. Here, we used single-cell RNA-sequencing of patient-derived CRC models to decipher distinct cell subpopulations based on their transcriptional profiles. Cell type-specific expression modules of stem-like, transit amplifying-like, and differentiated CRC cells resemble differentiation states of normal intestinal epithelial cells. Strikingly, identified subpopulations differ in proliferative activity and metabolic state. In summary, we here show at single-cell resolution that transcriptional heterogeneity identifies functional states during TIC differentiation. Furthermore, identified expression signatures are linked to patient prognosis. Targeting transcriptional states associated to cancer cell differentiation might unravel novel vulnerabilities in human CRC.
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32
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Gravemeyer J, Lange A, Ritter C, Spassova I, Song L, Picard D, Remke M, Horny K, Sriram A, Gambichler T, Schadendorf D, Hoffmann D, Becker JC. Classical and Variant Merkel Cell Carcinoma Cell Lines Display Different Degrees of Neuroendocrine Differentiation and Epithelial-Mesenchymal Transition. J Invest Dermatol 2021; 141:1675-1686.e4. [PMID: 33600825 DOI: 10.1016/j.jid.2021.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 01/13/2021] [Accepted: 01/28/2021] [Indexed: 02/06/2023]
Abstract
Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer characterized by high invasiveness, early metastases, and high mortality. Because of the lack of suitable animal models, most functional studies are performed using cell lines, some of which lack classical neuroendocrine growth characteristics. Here, we scrutinized the molecular characteristics of classical MCC and variant MCC cell lines by differential gene expression and the respective epigenetic regulation by microRNAs and DNA methylation. Cutaneous squamous cell carcinoma cell lines were used for comparison. The most striking observation was a lower expression of epithelial-mesenchymal transition-related genes in classical MCCs, which was accompanied by higher expression of the epithelial-mesenchymal transition-regulating microRNA clusters miR-200c-141 and miR-183-96-182 and hypomethylation of the respective microRNA loci. Experimental expression of the MCC lineage factor ATOH1 in variant MCCs resulted in an increased expression of miR-200c-141 paralleled by a reduction of genes associated with epithelial-mesenchymal transition, thus demonstrating a connection between neuroendocrine characteristics and the lack of epithelial-mesenchymal transition. Together, our observations not only reinforce concerns about the use of variant MCCs as proper MCC representatives, but also suggest variant MCCs as cells locked in an intermediate state between neuroendocrine and epithelial differentiation.
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Affiliation(s)
- Jan Gravemeyer
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Lange
- Bioinformatics and Computational Biophysics, University Duisburg-Essen, Essen, Germany
| | - Cathrin Ritter
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivelina Spassova
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany
| | - Lina Song
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany
| | - Daniel Picard
- German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marc Remke
- German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Kai Horny
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ashwin Sriram
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thilo Gambichler
- Skin Cancer Center, Department for Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, University Duisburg-Essen, Essen, Germany
| | - Jürgen C Becker
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Dermatology, University Hospital Essen, Essen, Germany.
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33
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Traversi D, Pulliero A, Izzotti A, Franchitti E, Iacoviello L, Gianfagna F, Gialluisi A, Izzi B, Agodi A, Barchitta M, Calabrò GE, Hoxhaj I, Sassano M, Sbrogiò LG, Del Sole A, Marchiori F, Pitini E, Migliara G, Marzuillo C, De Vito C, Tamburro M, Sammarco ML, Ripabelli G, Villari P, Boccia S. Precision Medicine and Public Health: New Challenges for Effective and Sustainable Health. J Pers Med 2021; 11:135. [PMID: 33669364 PMCID: PMC7920275 DOI: 10.3390/jpm11020135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 02/06/2023] Open
Abstract
The development of high-throughput omics technologies represents an unmissable opportunity for evidence-based prevention of adverse effects on human health. However, the applicability and access to multi-omics tests are limited. In Italy, this is due to the rapid increase of knowledge and the high levels of skill and economic investment initially necessary. The fields of human genetics and public health have highlighted the relevance of an implementation strategy at a national level in Italy, including integration in sanitary regulations and governance instruments. In this review, the emerging field of public health genomics is discussed, including the polygenic scores approach, epigenetic modulation, nutrigenomics, and microbiomes implications. Moreover, the Italian state of implementation is presented. The omics sciences have important implications for the prevention of both communicable and noncommunicable diseases, especially because they can be used to assess the health status during the whole course of life. An effective population health gain is possible if omics tools are implemented for each person after a preliminary assessment of effectiveness in the medium to long term.
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Affiliation(s)
- Deborah Traversi
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Alessandra Pulliero
- Department of Health Sciences School of Medicine, University of Genoa, 16132 Genova, Italy;
| | - Alberto Izzotti
- Department of Experimental Medicine, University of Genoa, 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 161632 Genova, Italy
| | - Elena Franchitti
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Licia Iacoviello
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Francesco Gianfagna
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Mediterranea Cardiocentro, 80122 Napoli, Italy
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Martina Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Giovanna Elisa Calabrò
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Ilda Hoxhaj
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Michele Sassano
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Luca Gino Sbrogiò
- Dipartimento di Prevenzione, Az. ULSS3 Serenissima, 30174 Venezia, Italy;
| | | | | | - Erica Pitini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Manuela Tamburro
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Michela Lucia Sammarco
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Giancarlo Ripabelli
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
- Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
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Mancarella D, Plass C. Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation. Genome Med 2021; 13:23. [PMID: 33568205 PMCID: PMC7874645 DOI: 10.1186/s13073-021-00837-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 01/21/2021] [Indexed: 12/26/2022] Open
Abstract
Epigenetic alterations are associated with normal biological processes such as aging or differentiation. Changes in global epigenetic signatures, together with genetic alterations, are driving events in several diseases including cancer. Comparative studies of cancer and healthy tissues found alterations in patterns of DNA methylation, histone posttranslational modifications, and changes in chromatin accessibility. Driven by sophisticated, next-generation sequencing-based technologies, recent studies discovered cancer epigenomes to be dominated by epigenetic patterns already present in the cell-of-origin, which transformed into a neoplastic cell. Tumor-specific epigenetic changes therefore need to be redefined and factors influencing epigenetic patterns need to be studied to unmask truly disease-specific alterations. The underlying mechanisms inducing cancer-associated epigenetic alterations are poorly understood. Studies of mutated epigenetic modifiers, enzymes that write, read, or edit epigenetic patterns, or mutated chromatin components, for example oncohistones, help to provide functional insights on how cancer epigenomes arise. In this review, we highlight the importance and define challenges of proper control tissues and cell populations to exploit cancer epigenomes. We summarize recent advances describing mechanisms leading to epigenetic changes in tumorigenesis and briefly discuss advances in investigating their translational potential.
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Affiliation(s)
- Daniela Mancarella
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, 69120, Heidelberg, Germany.
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), 69120, Heidelberg, Germany
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35
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Raschdorf A, Sünderhauf A, Skibbe K, Ghebrehiwet B, Peerschke EI, Sina C, Derer S. Heterozygous P32/ C1QBP/ HABP1 Polymorphism rs56014026 Reduces Mitochondrial Oxidative Phosphorylation and Is Expressed in Low-grade Colorectal Carcinomas. Front Oncol 2021; 10:631592. [PMID: 33628739 PMCID: PMC7897657 DOI: 10.3389/fonc.2020.631592] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
Rapid proliferation of cancer cells is enabled by favoring aerobic glycolysis over mitochondrial oxidative phosphorylation (OXPHOS). P32 (C1QBP/gC1qR) is essential for mitochondrial protein translation and thus indispensable for OXPHOS activity. It is ubiquitously expressed and directed to the mitochondrial matrix in almost all cell types with an excessive up-regulation of p32 expression reported for tumor tissues. We recently demonstrated high levels of non-mitochondrial p32 to be associated with high-grade colorectal carcinoma. Mutations in human p32 are likely to disrupt proper mitochondrial function giving rise to various diseases including cancer. Hence, we aimed to investigate the impact of the most common single nucleotide polymorphism (SNP) rs56014026 in the coding sequence of p32 on tumor cell metabolism. In silico homology modeling of the resulting p.Thr130Met mutated p32 revealed that the single amino acid substitution potentially induces a strong conformational change in the protein, mainly affecting the mitochondrial targeting sequence (MTS). In vitro experiments confirmed an impaired mitochondrial import of mutated p32-T130M, resulting in reduced OXPHOS activity and a shift towards a low metabolic phenotype. Overexpression of p32-T130M maintained terminal differentiation of a goblet cell-like colorectal cancer cell line compared to p32-wt without affecting cell proliferation. Sanger sequencing of tumor samples from 128 CRC patients identified the heterozygous SNP rs56014026 in two well-differentiated, low proliferating adenocarcinomas, supporting our in vitro data. Together, the SNP rs56014026 reduces metabolic activity and proliferation while promoting differentiation in tumor cells.
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Affiliation(s)
- Annika Raschdorf
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Annika Sünderhauf
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Kerstin Skibbe
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Berhane Ghebrehiwet
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Ellinor I Peerschke
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Christian Sina
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.,1st Department of Medicine, Division of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Stefanie Derer
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
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36
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Kretzmer H, Biran A, Purroy N, Lemvigh CK, Clement K, Gruber M, Gu H, Rassenti L, Mohammad AW, Lesnick C, Slager SL, Braggio E, Shanafelt TD, Kay NE, Fernandes SM, Brown JR, Wang L, Li S, Livak KJ, Neuberg DS, Klages S, Timmermann B, Kipps TJ, Campo E, Gnirke A, Wu CJ, Meissner A. Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy. Blood Cancer Discov 2021; 2:54-69. [PMID: 33604581 PMCID: PMC7888194 DOI: 10.1158/2643-3230.bcd-19-0058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 10/28/2020] [Accepted: 11/18/2020] [Indexed: 01/09/2023] Open
Abstract
Most human cancers converge to a deregulated methylome with reduced global levels and elevated methylation at select CpG islands. To investigate the emergence and dynamics of the cancer methylome, we characterized genome-wide DNA methylation in pre-neoplastic monoclonal B cell lymphocytosis (MBL) and chronic lymphocytic leukemia (CLL), including serial samples collected across disease course. We detected the aberrant tumor-associated methylation landscape at CLL diagnosis and found no significantly differentially methylated regions in the high-count MBL-to-CLL transition. Patient methylomes showed remarkable stability with natural disease and post-therapy progression. Single CLL cells were consistently aberrantly methylated, indicating a homogeneous transition to the altered epigenetic state, and a distinct expression profile together with MBL cells compared to normal B cells. Our longitudinal analysis reveals the cancer methylome to emerge early, which may provide a platform for subsequent genetically-driven growth dynamics and together with its persistent presence suggests a central role in the normal-to-cancer transition.
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Affiliation(s)
- Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anat Biran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Noelia Purroy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Camilla K Lemvigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Michaela Gruber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Haematology and Haemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Laura Rassenti
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | | | - Connie Lesnick
- Mayo Clinic, Division of Hematology, Rochester, Minnesota
| | - Susan L Slager
- Mayo Clinic, Division of Hematology, Rochester, Minnesota
| | | | | | - Neil E Kay
- Mayo Clinic, Division of Hematology, Rochester, Minnesota
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Monrovia, California
| | - Shuqiang Li
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth J Livak
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Donna S Neuberg
- Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas J Kipps
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Elias Campo
- Lymphoid Neoplasm Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Section, Hospital Clínic; Departament d'Anatomia Patològica, Universitat de Barcelona, Barcelona, Spain
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
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37
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Di Domenico A, Pipinikas CP, Maire RS, Bräutigam K, Simillion C, Dettmer MS, Vassella E, Thirlwell C, Perren A, Marinoni I. Epigenetic landscape of pancreatic neuroendocrine tumours reveals distinct cells of origin and means of tumour progression. Commun Biol 2020; 3:740. [PMID: 33288854 PMCID: PMC7721725 DOI: 10.1038/s42003-020-01479-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023] Open
Abstract
Recent data suggest that Pancreatic Neuroendocrine Tumours (PanNETs) originate from α- or β-cells of the islets of Langerhans. The majority of PanNETs are non-functional and do not express cell-type specific hormones. In the current study we examine whether tumour DNA methylation (DNAme) profiling combined with genomic data is able to identify cell of origin and to reveal pathways involved in PanNET progression. We analyse genome-wide DNAme data of 125 PanNETs and sorted α- and β-cells. To confirm cell identity, we investigate ARX and PDX1 expression. Based on epigenetic similarities, PanNETs cluster in α-like, β-like and intermediate tumours. The epigenetic similarity to α-cells progressively decreases in the intermediate tumours, which present unclear differentiation. Specific transcription factor methylation and expression vary in the respective α/β-tumour groups. Depending on DNAme similarity to α/β-cells, PanNETs have different mutational spectra, stage of the disease and prognosis, indicating potential means of PanNET progression.
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Affiliation(s)
- Annunziata Di Domenico
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | | | - Renaud S Maire
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Konstantin Bräutigam
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Cedric Simillion
- Bioinformatics and Computational Biology, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Matthias S Dettmer
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Erik Vassella
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Chrissie Thirlwell
- UCL Cancer Institute, 72, Huntley Street, London, WC1E 6JD, UK
- University of Exeter, College of Medicine and Health, St Luke's Campus, Heavitree Road, Exeter, EX1 2LU, UK
| | - Aurel Perren
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Ilaria Marinoni
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland.
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38
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Bhol CS, Panigrahi DP, Praharaj PP, Mahapatra KK, Patra S, Mishra SR, Behera BP, Bhutia SK. Epigenetic modifications of autophagy in cancer and cancer therapeutics. Semin Cancer Biol 2020; 66:22-33. [DOI: 10.1016/j.semcancer.2019.05.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/09/2019] [Accepted: 05/30/2019] [Indexed: 12/30/2022]
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Dodgshun AJ, Fukuoka K, Edwards M, Bianchi VJ, Das A, Sexton-Oates A, Larouche V, Vanan MI, Lindhorst S, Yalon M, Mason G, Crooks B, Constantini S, Massimino M, Chiaravalli S, Ramdas J, Mason W, Ashraf S, Farah R, Van Damme A, Opocher E, Hamid SA, Ziegler DS, Samuel D, Cole KA, Tomboc P, Stearns D, Thomas GA, Lossos A, Sullivan M, Hansford JR, Mackay A, Jones C, Jones DTW, Ramaswamy V, Hawkins C, Bouffet E, Tabori U. Germline-driven replication repair-deficient high-grade gliomas exhibit unique hypomethylation patterns. Acta Neuropathol 2020; 140:765-776. [PMID: 32895736 DOI: 10.1007/s00401-020-02209-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 08/03/2020] [Indexed: 01/02/2023]
Abstract
Replication repair deficiency (RRD) leading to hypermutation is an important driving mechanism of high-grade glioma (HGG) occurring predominantly in the context of germline mutations in RRD-associated genes. Although HGG presents specific patterns of DNA methylation corresponding to oncogenic mutations, this has not been well studied in replication repair-deficient tumors. We analyzed 51 HGG arising in the background of gene mutations in RRD utilizing either 450 k or 850 k methylation arrays. These were compared with HGG not known to be from patients with RRD. RRD HGG harboring secondary mutations in glioma genes such as IDH1 and H3F3A displayed a methylation pattern corresponding to these methylation subgroups. Strikingly, RRD HGG lacking these known secondary mutations clustered together with an incompletely described group of HGG previously labeled "Wild type-C" or "Paediatric RTK 1". Independent analysis of two comparator HGG cohorts showed that other RRD/hypermutant tumors clustered within these subgroups, suggesting that undiagnosed RRD may be driving some HGG clustering in this location. RRD HGG displayed a unique CpG Island Demethylator Phenotype in contrast to the CpG Island Methylator Phenotype described in other cancers. Hypomethylation was enriched at gene promoters with prominent demethylation in genes and pathways critical to cellular survival including cell cycle, gene expression, cellular metabolism, and organization. These data suggest that methylation arrays may provide diagnostic information for the detection of RRD HGG. Furthermore, our findings highlight the unique natural selection pressures in these highly dysregulated, hypermutant cancers and provide the novel impact of hypermutation and RRD on the cancer epigenome.
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Affiliation(s)
- Andrew J Dodgshun
- Children's Haematology/Oncology Centre, Christchurch Hospital and University of Otago Christchurch, 2 Riccarton Ave, Christchurch, 8041, New Zealand.
| | - Kohei Fukuoka
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Melissa Edwards
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Vanessa J Bianchi
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Anirban Das
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Alexandra Sexton-Oates
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Valérie Larouche
- Université Laval, 2325 Rue de l'Université, Québec, QC, G1V 0A6, Canada
| | - Magimairajan I Vanan
- Cancer Care Manitoba and University of Manitoba, 675 McDermot Ave, Winnipeg, MB, R3E 0V9, Canada
| | - Scott Lindhorst
- Medical University of South Carolina, 171 Ashley Ave Suite 419, MSC 403, Charleston, SC, 29425, USA
| | - Michal Yalon
- Sheba Medical CenterSheba Medical Center, Derech Sheba 2, Tel Hashomer, Ramat Gan, Israel
| | - Gary Mason
- Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Bruce Crooks
- IWK Health Centre, 5850-5980 University Avenue, Halifax, NS, Canada
| | | | - Maura Massimino
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133, Milano, MI, Italy
| | - Stefano Chiaravalli
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133, Milano, MI, Italy
| | - Jagadeesh Ramdas
- Geisinger Medical Center, 100 N. Academy Ave, Danville, PA, 17822, USA
| | - Warren Mason
- Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON, M5G 2C1, Canada
| | | | - Roula Farah
- LAU Medical Center Rizk Hospital, Zahra Street, Achrafieh, Beirut, Lebanon
| | - An Van Damme
- St Luc University Hospital Université Catholique de Louvain, 10 Avenue Hippocrate, 1200, Brussels, Belgium
| | - Enrico Opocher
- Azienda Ospedaliera di Padova, via Giustiniani n.2, 35121, Padova, PD, Italy
| | | | - David S Ziegler
- Sydney Children's Hospital, High St, Randwick, NSW, 2031, Australia
| | - David Samuel
- Valley Children's Hospital, 9300 Valley Children's Pl, Madera, CA, 93636, USA
| | - Kristina A Cole
- Children's Hospital of Philadelphia and University of Pennsylvania, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Patrick Tomboc
- WVU Medicine Children's Hospital, 1 Medical Center Dr, Morgantown, WV, 26505, USA
| | - Duncan Stearns
- University Hospitals Cleveland, 2101 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Gregory A Thomas
- Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - Alexander Lossos
- Hadassah Medical Center and the Hebrew University, POB 12000, 91120, Jerusalem, Israel
| | - Michael Sullivan
- The Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Jordan R Hansford
- The Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Alan Mackay
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Chris Jones
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Cynthia Hawkins
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Eric Bouffet
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Uri Tabori
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada.
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40
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Espinet E, Gu Z, Imbusch CD, Giese NA, Büscher M, Safavi M, Weisenburger S, Klein C, Vogel V, Falcone M, Insua-Rodríguez J, Reitberger M, Thiel V, Kossi SO, Muckenhuber A, Sarai K, Lee AYL, Backx E, Zarei S, Gaida MM, Rodríguez-Paredes M, Donato E, Yen HY, Eils R, Schlesner M, Pfarr N, Hackert T, Plass C, Brors B, Steiger K, Weichenhan D, Arda HE, Rooman I, Kopp JL, Strobel O, Weichert W, Sprick MR, Trumpp A. Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin. Cancer Discov 2020; 11:638-659. [PMID: 33060108 DOI: 10.1158/2159-8290.cd-20-1202] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. Methylationlow tumors are characterized by higher expression of endogenous retroviral transcripts and double-stranded RNA sensors, which lead to a cell-intrinsic activation of an interferon signature (IFNsign). This results in a protumorigenic microenvironment and poor patient outcome. Methylationlow/IFNsignhigh and Methylationhigh/IFNsignlow PDAC cells preserve lineage traits, respective of normal ductal or acinar pancreatic cells. Moreover, ductal-derived Kras G12D/Trp53 -/- mouse PDACs show higher expression of IFNsign compared with acinar-derived counterparts. Collectively, our data point to two different origins and etiologies of human PDACs, with the aggressive Methylationlow/IFNsignhigh subtype potentially targetable by agents blocking intrinsic IFN signaling. SIGNIFICANCE: The mutational landscapes of PDAC alone cannot explain the observed interpatient heterogeneity. We identified two PDAC subtypes characterized by differential DNA methylation, preserving traits from normal ductal/acinar cells associated with IFN signaling. Our work suggests that epigenetic traits and the cell of origin contribute to PDAC heterogeneity.This article is highlighted in the In This Issue feature, p. 521.
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Affiliation(s)
- Elisa Espinet
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany. .,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Zuguang Gu
- Bioinformatics and Omics Data Analytics, DKFZ, Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, DKFZ and NCT, Heidelberg, Germany
| | - Nathalia A Giese
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Magdalena Büscher
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mariam Safavi
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Silke Weisenburger
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Corinna Klein
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | - Vanessa Vogel
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | - Mattia Falcone
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jacob Insua-Rodríguez
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Manuel Reitberger
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Vera Thiel
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Steffi O Kossi
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | | | - Karnjit Sarai
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alex Y L Lee
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elyne Backx
- Laboratory of Molecular and Medical Oncology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Soheila Zarei
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthias M Gaida
- Institute of Pathology, University Hospital of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center JGU Mainz, Mainz, Germany
| | | | - Elisa Donato
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hsi-Yu Yen
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Roland Eils
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany.,Digital Health Centre, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany.,Health Data Science Unit, University Hospital and University of Heidelberg, Heidelberg, Germany
| | | | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Thilo Hackert
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Benedikt Brors
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Applied Bioinformatics, DKFZ and NCT, Heidelberg, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Dieter Weichenhan
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - H Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center of Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Ilse Rooman
- Laboratory of Molecular and Medical Oncology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Janel L Kopp
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Oliver Strobel
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany.,National Center of Tumor Diseases, NCT, Heidelberg, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Martin R Sprick
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Andreas Trumpp
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany. .,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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41
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Lee K, Song YS, Shin Y, Wen X, Kim Y, Cho NY, Bae JM, Kang GH. Intrahepatic cholangiocarcinomas with IDH1/2 mutation-associated hypermethylation at selective genes and their clinicopathological features. Sci Rep 2020; 10:15820. [PMID: 32978444 PMCID: PMC7519101 DOI: 10.1038/s41598-020-72810-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a rare but fatal tumor. The isocitrate dehydrogenase 1 and 2 (IDH1/2) genes are known to be mutated in ICC. IDH1/2 mutations tend to be accompanied by enhanced hypermethylation at a subset of genomic loci. We sought to clarify the clinicopathological features, including prognostic value, of ICCs with IDH1/2 mutation-associated hypermethylation at a subset of genes. The mutation status of IDH1/2 and methylation status of 30 gene CpG island loci were analyzed in 172 cases of ICC using pyrosequencing and the MethyLight assay, respectively. The mutation status of IDH1/2 was correlated with clinicopathological features and the DNA methylation status at 30 gene loci. Then, the clinicopathological characteristics were analyzed regarding three-tiered methylation statuses in genes showing IDH1/2 mutation-associated methylation. IDH1/2 mutations were found in 9.3% of ICCs, and IDH1/2-mutated tumors were associated with the histological subtype, including the bile ductular type and small duct type, and poor differentiation. Eight DNA methylation markers showed associations with IDH1/2 mutations, and ICCs with > 5/8 methylated markers were associated with the bile ductular type or small duct type, absence of mucin production, absence of biliary intraepithelial neoplasia, and presence of chronic liver disease. > 5/8 methylated markers were an independent prognostic marker associated with better survival in both cancer-specific survival and recurrence-free survival. In summary, by analyzing the association between IDH1/2 mutations and DNA methylation in individual genes, we developed a panel of DNA methylation markers that were significantly associated with IDH1/2 mutations and were able to identify a subset of ICC with better clinical outcomes.
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Affiliation(s)
- Kyoungbun Lee
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Young Seok Song
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Yoonju Shin
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Xianyu Wen
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Younghoon Kim
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Nam-Yun Cho
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea. .,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.
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42
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Islam M, Chen B, Spraggins JM, Kelly RT, Lau KS. Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. Gastroenterology 2020; 159:453-466.e1. [PMID: 32417404 PMCID: PMC7484006 DOI: 10.1053/j.gastro.2020.04.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 02/29/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023]
Abstract
Single cells are the building blocks of tissue systems that determine organ phenotypes, behaviors, and functions. Understanding the differences between cell types and their activities might provide us with insights into normal tissue physiology, development of disease, and new therapeutic strategies. Although -omic level single-cell technologies are a relatively recent development that have been used only in research settings, these approaches might eventually be used in the clinic. We review the prospects of applying single-cell genome, transcriptome, epigenome, proteome, and metabolome analyses to gastroenterology and hepatology research. Combining data from multi-omic platforms coupled to rapid technological development could lead to new diagnostic, prognostic, and therapeutic approaches.
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Affiliation(s)
- Mirazul Islam
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bob Chen
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Departments of Biochemistry and Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee.
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43
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Non-invasive early detection of cancer four years before conventional diagnosis using a blood test. Nat Commun 2020; 11:3475. [PMID: 32694610 PMCID: PMC7374162 DOI: 10.1038/s41467-020-17316-z] [Citation(s) in RCA: 287] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/24/2020] [Indexed: 02/06/2023] Open
Abstract
Early detection has the potential to reduce cancer mortality, but an effective screening test must demonstrate asymptomatic cancer detection years before conventional diagnosis in a longitudinal study. In the Taizhou Longitudinal Study (TZL), 123,115 healthy subjects provided plasma samples for long-term storage and were then monitored for cancer occurrence. Here we report the preliminary results of PanSeer, a noninvasive blood test based on circulating tumor DNA methylation, on TZL plasma samples from 605 asymptomatic individuals, 191 of whom were later diagnosed with stomach, esophageal, colorectal, lung or liver cancer within four years of blood draw. We also assay plasma samples from an additional 223 cancer patients, plus 200 primary tumor and normal tissues. We show that PanSeer detects five common types of cancer in 88% (95% CI: 80-93%) of post-diagnosis patients with a specificity of 96% (95% CI: 93-98%), We also demonstrate that PanSeer detects cancer in 95% (95% CI: 89-98%) of asymptomatic individuals who were later diagnosed, though future longitudinal studies are required to confirm this result. These results demonstrate that cancer can be non-invasively detected up to four years before current standard of care.
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44
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Teschendorff AE. A comparison of epigenetic mitotic-like clocks for cancer risk prediction. Genome Med 2020; 12:56. [PMID: 32580750 PMCID: PMC7315560 DOI: 10.1186/s13073-020-00752-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Background DNA methylation changes that accrue in the stem cell pool of an adult tissue in line with the cumulative number of cell divisions may contribute to the observed variation in cancer risk among tissues and individuals. Thus, the construction of epigenetic “mitotic” clocks that can measure the lifetime number of stem cell divisions is of paramount interest. Methods Building upon a dynamic model of DNA methylation gain in unmethylated CpG-rich regions, we here derive a novel mitotic clock (“epiTOC2”) that can directly estimate the cumulative number of stem cell divisions in a tissue. We compare epiTOC2 to a different mitotic model, based on hypomethylation at solo-WCGW sites (“HypoClock”), in terms of their ability to measure mitotic age of normal adult tissues and predict cancer risk. Results Using epiTOC2, we estimate the intrinsic stem cell division rate for different normal tissue types, demonstrating excellent agreement (Pearson correlation = 0.92, R2 = 0.85, P = 3e−6) with those derived from experiment. In contrast, HypoClock’s estimates do not (Pearson correlation = 0.30, R2 = 0.09, P = 0.29). We validate these results in independent datasets profiling normal adult tissue types. While both epiTOC2 and HypoClock correctly predict an increased mitotic rate in cancer, epiTOC2 is more robust and significantly better at discriminating preneoplastic lesions characterized by chronic inflammation, a major driver of tissue turnover and cancer risk. Our data suggest that DNA methylation loss at solo-WCGWs is significant only when cells are under high replicative stress and that epiTOC2 is a better mitotic age and cancer risk prediction model for normal adult tissues. Conclusions These results have profound implications for our understanding of epigenetic clocks and for developing cancer risk prediction or early detection assays. We propose that measurement of DNAm at the 163 epiTOC2 CpGs in adult pre-neoplastic lesions, and potentially in serum cell-free DNA, could provide the basis for building feasible pre-diagnostic or cancer risk assays. epiTOC2 is freely available from 10.5281/zenodo.2632938
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China. .,UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
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45
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Fennell LJ, Kane A, Liu C, McKeone D, Fernando W, Su C, Bond C, Jamieson S, Dumenil T, Patch AM, Kazakoff SH, Pearson JV, Waddell N, Leggett B, Whitehall VLJ. APC Mutation Marks an Aggressive Subtype of BRAF Mutant Colorectal Cancers. Cancers (Basel) 2020; 12:E1171. [PMID: 32384699 PMCID: PMC7281581 DOI: 10.3390/cancers12051171] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND WNT activation is a hallmark of colorectal cancer. BRAF mutation is present in 15% of colorectal cancers, and the role of mutations in WNT signaling regulators in this context is unclear. Here, we evaluate the mutational landscape of WNT signaling regulators in BRAF mutant cancers. METHODS we performed exome-sequencing on 24 BRAF mutant colorectal cancers and analyzed these data in combination with 175 publicly available BRAF mutant colorectal cancer exomes. We assessed the somatic mutational landscape of WNT signaling regulators, and performed hotspot and driver mutation analyses to identify potential drivers of WNT signaling. The effects of Apc and Braf mutation were modelled, in vivo, using the Apcmin/+ and BrafV637/Villin-CreERT2/+ mouse, respectively. RESULTS RNF43 was the most frequently mutated WNT signaling regulator (41%). Mutations in the beta-catenin destruction complex occurred in 48% of cancers. Hotspot analyses identified potential cancer driver genes in the WNT signaling cascade, including MEN1, GNG12 and WNT16. Truncating APC mutation was identified in 20.8% of cancers. Truncating APC mutation was associated with early age at diagnosis (p < 2 × 10-5), advanced stage (p < 0.01), and poor survival (p = 0.026). Apcmin/+/BrafV637 animals had more numerous and larger SI and colonic lesions (p < 0.0001 and p < 0.05, respectively), and a markedly reduced survival (median survival: 3.2 months, p = 8.8 × 10-21), compared to animals with Apc or Braf mutation alone. CONCLUSIONS the WNT signaling axis is frequently mutated in BRAF mutant colorectal cancers. WNT16 and MEN1 may be novel drivers of aberrant WNT signaling in colorectal cancer. Co-mutation of BRAF and APC generates an extremely aggressive neoplastic phenotype that is associated with poor patient outcome.
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Affiliation(s)
- Lochlan J. Fennell
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
- School of Medicine, The University of Queensland, Queensland 4072, Australia
| | - Alexandra Kane
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
- School of Medicine, The University of Queensland, Queensland 4072, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Herston 4006, Australia
| | - Cheng Liu
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
- School of Medicine, The University of Queensland, Queensland 4072, Australia
- Envoi Specialist Pathologists, Queensland 4059, Australia
| | - Diane McKeone
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
| | - Winnie Fernando
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
| | - Chang Su
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
- School of Medicine, The University of Queensland, Queensland 4072, Australia
| | - Catherine Bond
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
| | - Saara Jamieson
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
| | - Troy Dumenil
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
| | - Stephen H. Kazakoff
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
- School of Medicine, The University of Queensland, Queensland 4072, Australia
| | - Barbara Leggett
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
- School of Medicine, The University of Queensland, Queensland 4072, Australia
- Department of Gastroenterology and Hepatology, The Royal Brisbane and Women’s Hospital, Queensland 4006, Australia
| | - Vicki L. J. Whitehall
- QIMR Berghofer Medical Research Institute, Queensland 4006, Australia; (A.K.); (C.L.); (D.M.); (W.F.); (C.S.); (C.B.); (S.J.); (T.D.); (A.-M.P.); (S.H.K.); (J.V.P.); (N.W.); (B.L.); (V.L.J.W.)
- School of Medicine, The University of Queensland, Queensland 4072, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Herston 4006, Australia
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Wenzel J, Rose K, Haghighi EB, Lamprecht C, Rauen G, Freihen V, Kesselring R, Boerries M, Hecht A. Loss of the nuclear Wnt pathway effector TCF7L2 promotes migration and invasion of human colorectal cancer cells. Oncogene 2020; 39:3893-3909. [PMID: 32203164 PMCID: PMC7203011 DOI: 10.1038/s41388-020-1259-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/25/2022]
Abstract
The transcription factor TCF7L2 is indispensable for intestinal tissue homeostasis where it transmits mitogenic Wnt/β-Catenin signals in stem and progenitor cells, from which intestinal tumors arise. Yet, TCF7L2 belongs to the most frequently mutated genes in colorectal cancer (CRC), and tumor-suppressive functions of TCF7L2 were proposed. This apparent paradox warrants to clarify the role of TCF7L2 in colorectal carcinogenesis. Here, we investigated TCF7L2 dependence/independence of CRC cells and the cellular and molecular consequences of TCF7L2 loss-of-function. By genome editing we achieved complete TCF7L2 inactivation in several CRC cell lines without loss of viability, showing that CRC cells have widely lost the strict requirement for TCF7L2. TCF7L2 deficiency impaired G1/S progression, reminiscent of the physiological role of TCF7L2. In addition, TCF7L2-negative cells exhibited morphological changes, enhanced migration, invasion, and collagen adhesion, albeit the severity of the phenotypic alterations manifested in a cell-line-specific fashion. To provide a molecular framework for the observed cellular changes, we performed global transcriptome profiling and identified gene-regulatory networks in which TCF7L2 positively regulates the proto-oncogene MYC, while repressing the cell cycle inhibitors CDKN2C/CDKN2D. Consistent with its function in curbing cell motility and invasion, TCF7L2 directly suppresses the pro-metastatic transcription factor RUNX2 and impinges on the expression of cell adhesion molecules. Altogether, we conclude that the proliferation-stimulating activity of TCF7L2 persists in CRC cells. In addition, TCF7L2 acts as invasion suppressor. Despite its negative impact on cell cycle progression, TCF7L2 loss-of-function may thereby increase malignancy, which could explain why TCF7L2 is mutated in a sizeable fraction of colorectal tumors.
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Affiliation(s)
- Janna Wenzel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Katja Rose
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Elham Bavafaye Haghighi
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79104, Freiburg, Germany
| | - Constanze Lamprecht
- Institute of Physics, University of Freiburg, Hermann-Herder-Str. 3a, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technology (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
| | - Gilles Rauen
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Vivien Freihen
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Rebecca Kesselring
- Department of General and Visceral Surgery, Center for Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79104, Freiburg, Germany
- German Cancer Consortium (DKTK), Hugstetter Straße 55, 79106, Freiburg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Andreas Hecht
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany.
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany.
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Mattesen TB, Rasmussen MH, Sandoval J, Ongen H, Árnadóttir SS, Gladov J, Martinez-Cardus A, Castro de Moura M, Madsen AH, Laurberg S, Dermitzakis ET, Esteller M, Andersen CL, Bramsen JB. MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer. Nat Commun 2020; 11:2025. [PMID: 32332866 PMCID: PMC7181739 DOI: 10.1038/s41467-020-16000-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/02/2020] [Indexed: 12/29/2022] Open
Abstract
Transcriptional characterization and classification has potential to resolve the inter-tumor heterogeneity of colorectal cancer and improve patient management. Yet, robust transcriptional profiling is difficult using formalin-fixed, paraffin-embedded (FFPE) samples, which complicates testing in clinical and archival material. We present MethCORR, an approach that allows uniform molecular characterization and classification of fresh-frozen and FFPE samples. MethCORR identifies genome-wide correlations between RNA expression and DNA methylation in fresh-frozen samples. This information is used to infer gene expression information in FFPE samples from their methylation profiles. MethCORR is here applied to methylation profiles from 877 fresh-frozen/FFPE samples and comparative analysis identifies the same two subtypes in four independent cohorts. Furthermore, subtype-specific prognostic biomarkers that better predicts relapse-free survival (HR = 2.66, 95%CI [1.67-4.22], P value < 0.001 (log-rank test)) than UICC tumor, node, metastasis (TNM) staging and microsatellite instability status are identified and validated using DNA methylation-specific PCR. The MethCORR approach is general, and may be similarly successful for other cancer types.
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Grants
- R01 CA207467 NCI NIH HHS
- This research is supported by grants from the European Commission FP7 project SYSCOL (UE7-SYSCOL-258236), the Novo Nordisk Foundation (NNF16OC0023182), the Danish National Advanced Technology Foundation (056-2010-1), the John and Birthe Meyer Foundation, the Danish Council for Independent Research (Medical Sciences) (DFF - 0602-02128B, DFF – 4183-00619, DFF - 7016-00332B), the Danish Council for Strategic Research (1309-00006B), the Danish Cancer Society (R40-A1965_11_S2, R56-A3110-12-S2, R107-A7035, R133-A8520), the National Cancer Institute of the National Institutes of Health (R01 CA207467), the Aage and Johanne Louis-Hansen’s Foundation (17-2-0457), the Knud and Edith Eriksen’s Memorial Foundation, the Neye Foundation and the Manufacturer Einar Willumsen’s Memorial Foundation (6000073)
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Affiliation(s)
- Trine B Mattesen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Juan Sandoval
- Epigenomic Unit, Health Research Institute La Fe (ISSLaFe), Valencia, Spain
- Biomarker and precision medicine Unit, Health Research Institute La Fe (ISSLaFe), Valencia, Spain
| | - Halit Ongen
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Sigrid S Árnadóttir
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Josephine Gladov
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Anna Martinez-Cardus
- Badalona Applied Research Group in Oncology (B-ARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Catalonia, Spain
- Medical Oncology Service, Institute Catalan of Oncology (ICO), Badalona, Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Anders H Madsen
- Department of Surgery, Hospitalsenheden Vest, 7400, Herning, Denmark
| | - Søren Laurberg
- Colorectal Surgical Unit, Department of Surgery, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Emmanouil T Dermitzakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark.
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark.
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48
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Fan J, Li J, Guo S, Tao C, Zhang H, Wang W, Zhang Y, Zhang D, Ding S, Zeng C. Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma. Clin Epigenetics 2020; 12:56. [PMID: 32317010 PMCID: PMC7175491 DOI: 10.1186/s13148-020-00851-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
Background Abnormal DNA methylation is a hallmark of human cancers and may be a promising biomarker for early diagnosis of human cancers. However, the majority of DNA methylation biomarkers that have been identified are based on the hypothesis that early differential methylation regions (DMRs) are maintained throughout carcinogenesis and could be detected at all stages of cancer. Methods In this study, we identified potential early biomarkers of colorectal cancer (CRC) development by genome-wide DNA methylation assay (Illumina infinium450, 450 K) of normal (N = 20) and pre-colorectal cancer samples including 18 low-grade adenoma (LGA) and 22 high-grade adenoma (HGA), integrated with GEO and ArrayExpress datasets (N = 833). Results We identified 209 and 8692 CpG sites that were significantly hyper-methylated in LGA and HGA, respectively. Pathway analysis identified nervous system-related methylation changes that are significantly associated with early adenoma development. Integration analysis revealed that DNA methylation in the promoter region of ADHFE1 has the most potential for being an early diagnostic biomarker for colorectal adenoma and cancer (sensitivity = 0.96, specificity = 0.95, area under the curve = 0.97). Conclusions Overall, we demonstrated that DNA methylation have been shown significant changes in the stage of LGA and HGA in the development of colon cancer. Genome-wide DNA methylation to LGA and HGA provided an important proxy to identify promising early diagnosis biomarkers for colorectal cancer.
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Affiliation(s)
- Jian Fan
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53726, USA.,Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Chengcheng Tao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haikun Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjing Wang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, China
| | - Ying Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dake Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, China.
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
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49
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Köhler F, Rodríguez-Paredes M. DNA Methylation in Epidermal Differentiation, Aging, and Cancer. J Invest Dermatol 2019; 140:38-47. [PMID: 31427190 DOI: 10.1016/j.jid.2019.05.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/24/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022]
Abstract
The formation and maintenance of the epidermis depend on epidermal stem cell differentiation and must be tightly regulated. Epigenetic mechanisms such as DNA methylation allow the precise gene expression cascade needed during cellular differentiation. However, these mechanisms become deregulated during aging and tumorigenesis, where cellular function and identity become compromised. Here we provide a review of this rapidly developing field. We discuss recent discoveries related to epidermal homeostasis, aging, and cancer, including the functional role of DNA methyltransferases, the methylation clock, and the determination of tumor cells-of-origin. Finally, we focus on future advances, greatly influenced by single-cell sequencing technologies.
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Affiliation(s)
- Florian Köhler
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
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50
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Abstract
Biomarker discovery and validation are necessary for improving the prediction of clinical outcomes and patient monitoring. Despite considerable interest in biomarker discovery and development, improvements in the range and quality of biomarkers are still needed. The main challenge is how to integrate preclinical data to obtain a reliable biomarker that can be measured with acceptable costs in routine clinical practice. Epigenetic alterations are already being incorporated as valuable candidates in the biomarker field. Furthermore, their reversible nature offers a promising opportunity to ameliorate disease symptoms by using epigenetic-based therapy. Thus, beyond helping to understand disease biology, clinical epigenetics is being incorporated into patient management in oncology, as well as being explored for clinical applicability for other human pathologies such as neurological and infectious diseases and immune system disorders.
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