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Santamarina-García M, Brea-Iglesias J, Bramsen JB, Fuentes-Losada M, Caneiro-Gómez FJ, Vázquez-Bueno JÁ, Lázare-Iglesias H, Fernández-Díaz N, Sánchez-Rivadulla L, Betancor YZ, Ferreiro-Pantín M, Conesa-Zamora P, Antúnez-López JR, Kawazu M, Esteller M, Andersen CL, Tubio JMC, López-López R, Ruiz-Bañobre J. MSIMEP: Predicting microsatellite instability from microarray DNA methylation tumor profiles. iScience 2023; 26:106127. [PMID: 36879816 PMCID: PMC9984554 DOI: 10.1016/j.isci.2023.106127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/15/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Deficiency in DNA MMR activity results in tumors with a hypermutator phenotype, termed microsatellite instability (MSI). Beyond its utility in Lynch syndrome screening algorithms, today MSI has gained importance as predictive biomarker for various anti-PD-1 therapies across many different tumor types. Over the past years, many computational methods have emerged to infer MSI using either DNA- or RNA-based approaches. Considering this together with the fact that MSI-high tumors frequently exhibit a hypermethylated phenotype, herein we developed and validated MSIMEP, a computational tool for predicting MSI status from microarray DNA methylation tumor profiles of colorectal cancer samples. We demonstrated that MSIMEP optimized and reduced models have high performance in predicting MSI in different colorectal cancer cohorts. Moreover, we tested its consistency in other tumor types with high prevalence of MSI such as gastric and endometrial cancers. Finally, we demonstrated better performance of both MSIMEP models vis-à-vis a MLH1 promoter methylation-based one in colorectal cancer.
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Affiliation(s)
- Martín Santamarina-García
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | - Jenifer Brea-Iglesias
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Translational Oncology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Álvaro Cunqueiro Hospital, 36213 Vigo, Spain
| | | | - Mar Fuentes-Losada
- Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | - Francisco Javier Caneiro-Gómez
- Department of Pathology, University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | | | - Héctor Lázare-Iglesias
- Department of Pathology, University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | - Natalia Fernández-Díaz
- Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | - Laura Sánchez-Rivadulla
- Department of Gynaecology and Obstetrics, Complejo Hospitalario Universitario de Ferrol, 15405 Ferrol, Spain
| | - Yoel Z Betancor
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | - Miriam Ferreiro-Pantín
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | - Pablo Conesa-Zamora
- Department of Clinical Analysis, Santa Lucía University Hospital, 30202 Cartagena, Spain
| | - José Ramón Antúnez-López
- Department of Pathology, University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | - Masahito Kawazu
- Chiba Cancer Center, Research Institute, 260-0801 Chiba, Japan.,Division of Cellular Signaling, National Cancer Center Research Institute, 104-0045 Tokyo, Japan
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08907 Barcelona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | | | - Jose M C Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain
| | - Rafael López-López
- Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Juan Ruiz-Bañobre
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), 15706 Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
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Mattesen TB, Andersen CL, Bramsen JB. MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples. Clin Epigenetics 2021; 13:20. [PMID: 33509261 PMCID: PMC7842045 DOI: 10.1186/s13148-021-01000-0] [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: 09/18/2020] [Accepted: 01/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Transcriptional analysis is widely used to study the molecular biology of cancer and hold great biomarker potential for clinical patient stratification. Yet, accurate transcriptional profiling requires RNA of a high quality, which often cannot be retrieved from formalin-fixed, paraffin-embedded (FFPE) tumor tissue that is routinely collected and archived in clinical departments. To overcome this roadblock to clinical testing, we previously developed MethCORR, a method that infers gene expression from DNA methylation data, which is robustly retrieved from FFPE tissue. MethCORR was originally developed for colorectal cancer and with this study, we aim to: (1) extend the MethCORR method to 10 additional cancer types and (2) to illustrate that the inferred gene expression is accurate and clinically informative. Results Regression models to infer gene expression information from DNA methylation were developed for ten common cancer types using matched RNA sequencing and DNA methylation profiles (HumanMethylation450 BeadChip) from The Cancer Genome Atlas Project. Robust and accurate gene expression profiles were inferred for all cancer types: on average, the expression of 11,000 genes was modeled with good accuracy and an intra-sample correlation of R2 = 0.90 between inferred and measured gene expression was observed. Molecular pathway analysis and transcriptional subtyping were performed for breast, prostate, and lung cancer samples to illustrate the general usability of the inferred gene expression profiles: overall, a high correlation of r = 0.96 (Pearson) in pathway enrichment scores and a 76% correspondence in molecular subtype calls were observed when using measured and inferred gene expression as input. Finally, inferred expression from FFPE tissue correlated better with RNA sequencing data from matched fresh-frozen tissue than did RNA sequencing data from FFPE tissue (P < 0.0001; Wilcoxon rank-sum test). Conclusions In all cancers investigated, MethCORR enabled DNA methylation-based transcriptional analysis, thus enabling future analysis of cancer in situations where high-quality DNA, but not RNA, is available. Here, we provide the framework and resources for MethCORR modeling of ten common cancer types, thereby widely expanding the possibilities for transcriptional studies of archival FFPE material.
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Affiliation(s)
- Trine B Mattesen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
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Ili C, Buchegger K, Demond H, Castillo-Fernandez J, Kelsey G, Zanella L, Abanto M, Riquelme I, López J, Viscarra T, García P, Bellolio E, Saavedra D, Brebi P. Landscape of Genome-Wide DNA Methylation of Colorectal Cancer Metastasis. Cancers (Basel) 2020; 12:E2710. [PMID: 32971738 PMCID: PMC7564781 DOI: 10.3390/cancers12092710] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer is a heterogeneous disease caused by both genetic and epigenetics factors. Analysing DNA methylation changes occurring during colorectal cancer progression and metastasis formation is crucial for the identification of novel epigenetic markers of patient prognosis. Genome-wide methylation sequencing of paired samples of colon (normal adjacent, primary tumour and lymph node metastasis) showed global hypomethylation and CpG island (CGI) hypermethylation of primary tumours compared to normal. In metastasis we observed high global and non-CGI regions methylation, but lower CGI methylation, compared to primary tumours. Gene ontology analysis showed shared biological processes between hypermethylated CGIs in metastasis and primary tumours. After complementary analysis with The Cancer Genome Atlas (TCGA) cohort, FIGN, HTRA3, BDNF, HCN4 and STAC2 genes were found associated with poor survival. We mapped the methylation landscape of colon normal tissues, primary tumours and lymph node metastasis, being capable of identified methylation changes throughout the genome. Furthermore, we found five genes with potential for methylation biomarkers of poor prognosis in colorectal cancer patients.
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Affiliation(s)
- Carmen Ili
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
| | - Kurt Buchegger
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
- Departamento Ciencias Básicas, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile
| | - Hannah Demond
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; (J.C.-F.); (G.K.)
| | - Juan Castillo-Fernandez
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; (J.C.-F.); (G.K.)
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; (J.C.-F.); (G.K.)
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 1TN, UK
| | - Louise Zanella
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
| | - Michel Abanto
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile;
| | - Ismael Riquelme
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco 4810101, Chile;
| | - Jaime López
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
| | - Tamara Viscarra
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
| | - Patricia García
- Department of Pathology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330034, Chile;
| | - Enrique Bellolio
- Departamento Anatomía Patológica, Facultad de Medicina, Universidad de La Frontera, Temuco 4781180, Chile;
- Departamento de Medicina Interna, Hospital Hernán Henríquez Aravena, Temuco 4781151, Chile;
| | - David Saavedra
- Departamento de Medicina Interna, Hospital Hernán Henríquez Aravena, Temuco 4781151, Chile;
- Clínica Alemana de Temuco, Temuco 4810297, Chile
| | - Priscilla Brebi
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
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