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Jodal HC, Akwiwu EU, Lemmens M, Delis-van Diemen PM, Klotz D, Leon LG, Lakbir S, de Wit M, Fijneman RJ, van Leerdam ME, Dekker E, Spaander MC, Meijer GA, Løberg M, Coupé VM, Kalager M, Carvalho B. Risk Prediction of Metachronous Colorectal Cancer from Molecular Features of Adenomas: A Nested Case-Control Study. Cancer Res Commun 2023; 3:2292-2301. [PMID: 37921412 PMCID: PMC10642372 DOI: 10.1158/2767-9764.crc-23-0186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/22/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Current morphologic features defining advanced adenomas (size ≥10 mm, high-grade dysplasia or ≥25% villous component) cannot optimally distinguish individuals at high risk or low risk of metachronous colorectal cancer (me-CRC), which may result in suboptimal surveillance. Certain DNA copy-number alterations (CNAs) are associated with adenoma-to-carcinoma progression. We aimed to evaluate whether these molecular features can better predict an individual's risk of me-CRC than the morphologic advanced adenoma features.In this nested case-control study, 529 individuals with a single adenoma at first colonoscopy were selected from a Norwegian adenoma cohort. DNA copy-number profiles were determined, by low-coverage whole-genome sequencing. Prevalence of CNAs in advanced and non-advanced adenomas and its association (OR) with me-CRC was assessed. For the latter, cases (with me-CRC) were matched to controls (without me-CRC) on follow-up, age and sex.CNAs associated with adenoma-to-carcinoma progression were observed in 85/267 (32%) of advanced adenomas and in 27/262 (10%) of non-advanced adenomas. me-CRC was statistically significantly associated, also after adjustment for other variables, with age at baseline [OR, 1.14; 95% confidence interval CI), 1.03-1.26; P = 0.012], advanced adenomas (OR, 2.46; 95% CI, 1.50-4.01; P < 0.001) and with the presence of ≥3 DNA copy-number losses (OR, 1.90; 95% CI. 1.02-3.54; P = 0.043).Molecularly-defined high-risk adenomas were associated with me-CRC, but the association of advanced adenoma with me-CRC was stronger. SIGNIFICANCE Identifying new biomarkers may improve prediction of me-CRC for individuals with adenomas and optimize surveillance intervals to reduce risk of colorectal cancer and reduce oversurveillance of patients with low risk of colorectal cancer. Use of DNA CNAs alone does not improve prediction of me-CRC. Further research to improve risk classification is required.
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Affiliation(s)
- Henriette C. Jodal
- Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
- Clinical Effectiveness Research Group, Oslo University Hospital, Oslo, Norway
- Section of Oncology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Eddymurphy U. Akwiwu
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Group, Amsterdam University Medical Centers, Location VU Medical Center, Amsterdam, the Netherlands
| | - Margriet Lemmens
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Dagmar Klotz
- Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Leticia G. Leon
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Soufyan Lakbir
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Meike de Wit
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Remond J.A. Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Monique E. van Leerdam
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Location Academic Medical Center, Amsterdam, the Netherlands
| | - Manon C.W. Spaander
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Magnus Løberg
- Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
- Clinical Effectiveness Research Group, Oslo University Hospital, Oslo, Norway
| | - Veerle M.H. Coupé
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Group, Amsterdam University Medical Centers, Location VU Medical Center, Amsterdam, the Netherlands
| | - Mette Kalager
- Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
- Clinical Effectiveness Research Group, Oslo University Hospital, Oslo, Norway
| | - Beatriz Carvalho
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
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Lakbir S, Lahoz S, Cuatrecasas M, Camps J, Glas RA, Heringa J, Meijer GA, Abeln S, Fijneman RJA. Tumour break load is a biologically relevant feature of genomic instability with prognostic value in colorectal cancer. Eur J Cancer 2022; 177:94-102. [PMID: 36334560 DOI: 10.1016/j.ejca.2022.09.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND Clinically implemented prognostic biomarkers are lacking for the 80% of colorectal cancers (CRCs) that exhibit chromosomal instability (CIN). CIN is characterised by chromosome segregation errors and double-strand break repair defects that lead to somatic copy number aberrations (SCNAs) and chromosomal rearrangement-associated structural variants (SVs), respectively. We hypothesise that the number of SVs is a distinct feature of genomic instability and defined a new measure to quantify SVs: the tumour break load (TBL). The present study aimed to characterise the biological impact and clinical relevance of TBL in CRC. METHODS Disease-free survival and SCNA data were obtained from The Cancer Genome Atlas and two independent CRC studies. TBL was defined as the sum of SCNA-associated SVs. RNA gene expression data of microsatellite stable (MSS) CRC samples were used to train an RNA-based TBL classifier. Dichotomised DNA-based TBL data were used for survival analysis. RESULTS TBL shows large variation in CRC with poor correlation to tumour mutational burden and fraction of genome altered. TBL impact on tumour biology was illustrated by the high accuracy of classifying cancers in TBL-high and TBL-low (area under the receiver operating characteristic curve [AUC]: 0.88; p < 0.01). High TBL was associated with disease recurrence in 85 stages II-III MSS CRCs from The Cancer Genome Atlas (hazard ratio [HR]: 6.1; p = 0.007) and in two independent validation series of 57 untreated stages II-III (HR: 4.1; p = 0.012) and 74 untreated stage II MSS CRCs (HR: 2.4; p = 0.01). CONCLUSION TBL is a prognostic biomarker in patients with non-metastatic MSS CRC with great potential to be implemented in routine molecular diagnostics.
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Affiliation(s)
- Soufyan Lakbir
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands; Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
| | - Sara Lahoz
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, 08036, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Biomedical Diagnostic Center (CDB), Hospital Clínic de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de Barcelona (UB), Barcelona, 08036, Spain
| | - Jordi Camps
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, 08036, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Medicine, Autonomous University of Barcelona, Bellaterra, 08193, Spain
| | - Roel A Glas
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands; Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
| | - Jaap Heringa
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands; AIMMS - Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
| | - Sanne Abeln
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands; Life Sciences and Health Research Group, Centrum Wiskunde & Informatica (CWI), Science Park 123, Amsterdam 1098 XG, the Netherlands.
| | - Remond J A Fijneman
- Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands.
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3
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van Bree E, Alarcón CR, Lakbir S, Stelloo E, Buranelli C, Hondema A, van 't Erve I, Vessies D, Delis-van Diemen P, Tijssen M, Bolijn A, Lanfermeijer M, Linders D, Swennenhuis J, van den Broek D, Heringa J, Meijer G, Carvalho B, Feitsma H, Abeln S, Fijneman RJA. Abstract A020: Structural variants in the pathogenesis of colorectal cancer: The elephant in the room. Cancer Res 2022. [DOI: 10.1158/1538-7445.crc22-a020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Abstract
Background: Cancer is caused by somatic DNA alterations, comprising single/small nucleotide variants (SNVs), somatic copy number alterations (SCNAs) and chromosomal rearrangement structural variants (SVs). We previously demonstrated that SVs are recurrently identified in hundreds of genes and are highly prevalent in common fragile site genes, e.g., in MACROD2 in >40% of colorectal cancers (CRCs). However, computational methods that discriminate SV-driver from SV-passenger events are lacking and laboratory methods to detect SVs at nucleotide resolution from routinely obtained formalin-fixed paraffin-embedded (FFPE) tumor tissue material are underdeveloped. Therefore, despite the abundant presence of SVs, knowledge about their biological and clinical impact is limited. Aim: The aim of our studies is to identify genes of which the function is frequently affected by SV, to understand how these genes contribute to CRC pathogenesis, and to translate these SVs into clinically relevant biomarkers. Methods: We made use of publicly available deep whole genome DNA sequencing data and tumor-matched RNA sequencing data from the Hartwig Medical Foundation to develop the algorithm ‘CoBRA’: Computation of Biologically Relevant Alterations. Adenoma-derived organoids were used for CRISPR/Cas9-mediated gene modulation for functional analysis of SV-driver events. Cergentis’ targeted locus capture (FFPE-TLC) technology was used to detect SVs at nucleotide resolution from FFPE material, which were translated into droplet digital PCR (ddPCR) assays for the detection of SVs in cell-free circulating tumor DNA (ctDNA) in liquid biopsies. Results: The CoBRA algorithm associated the presence of SV-events in frequently affected genes to the extent in which genome-wide RNA sequencing data were altered. In this way, CoBRA ranked SV-events in genes according to their putative impact on tumor biology. SVs in MACROD2 ranked among those with the highest impact on tumor biology. Therefore, we generated focal deletions in MACROD2 in adenoma-derived organoids for functional analyses. Moreover, using FFPE tumor tissue material we detected SVs at nucleotide resolution in MACROD2 and three other genes in 21 out of 29 patients. SVs were verified by PCR on tumor tissue and subsequently translated into ddPCR biomarker assays for detection of SVs in ctDNA in blood from the same patients. Conclusions: We developed the computational method CoBRA and succeeded to detect SVs with high impact on tumor biology. These SVs are prioritized for functional analysis in pre-malignant adenoma-derived organoids; for targeted detection in routinely obtained FFPE tumor tissue material; and for translation into liquid biopsy ctDNA assays. Proof of concept was delivered for MACROD2. Our novel computational and laboratory methodologies provide valuable tools to effectively explore the biological and clinical impact of SVs, which will contribute to our understanding of these common recurrent somatic alterations in CRC and their translation into clinically relevant biomarker applications.
Citation Format: Elise van Bree, Carmen Rubio Alarcón, Soufyan Lakbir, Ellen Stelloo, Caterina Buranelli, Amber Hondema, Iris van 't Erve, Daan Vessies, Pien Delis-van Diemen, Marianne Tijssen, Anne Bolijn, Mirthe Lanfermeijer, Dorothe Linders, Joost Swennenhuis, Daan van den Broek, Jaap Heringa, Gerrit Meijer, Beatriz Carvalho, Harma Feitsma, Sanne Abeln, Remond J. A. Fijneman. Structural variants in the pathogenesis of colorectal cancer: The elephant in the room [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr A020.
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Affiliation(s)
| | | | - Soufyan Lakbir
- 2Netherlands Cancer Institute & VU University, Amsterdam, Netherlands,
| | | | | | - Amber Hondema
- 1Netherlands Cancer Institute, Amsterdam, Netherlands,
| | | | - Daan Vessies
- 1Netherlands Cancer Institute, Amsterdam, Netherlands,
| | | | | | - Anne Bolijn
- 1Netherlands Cancer Institute, Amsterdam, Netherlands,
| | | | | | | | | | | | - Gerrit Meijer
- 1Netherlands Cancer Institute, Amsterdam, Netherlands,
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4
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Baardman J, Verberk SGS, van der Velden S, Gijbels MJJ, van Roomen CPPA, Sluimer JC, Broos JY, Griffith GR, Prange KHM, van Weeghel M, Lakbir S, Molenaar D, Meinster E, Neele AE, Kooij G, de Vries HE, Lutgens E, Wellen KE, de Winther MPJ, Van den Bossche J. Macrophage ATP citrate lyase deficiency stabilizes atherosclerotic plaques. Nat Commun 2020; 11:6296. [PMID: 33293558 PMCID: PMC7722882 DOI: 10.1038/s41467-020-20141-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
Macrophages represent a major immune cell population in atherosclerotic plaques and play central role in the progression of this lipid-driven chronic inflammatory disease. Targeting immunometabolism is proposed as a strategy to revert aberrant macrophage activation to improve disease outcome. Here, we show ATP citrate lyase (Acly) to be activated in inflammatory macrophages and human atherosclerotic plaques. We demonstrate that myeloid Acly deficiency induces a stable plaque phenotype characterized by increased collagen deposition and fibrous cap thickness, along with a smaller necrotic core. In-depth functional, lipidomic, and transcriptional characterization indicate deregulated fatty acid and cholesterol biosynthesis and reduced liver X receptor activation within the macrophages in vitro. This results in macrophages that are more prone to undergo apoptosis, whilst maintaining their capacity to phagocytose apoptotic cells. Together, our results indicate that targeting macrophage metabolism improves atherosclerosis outcome and we reveal Acly as a promising therapeutic target to stabilize atherosclerotic plaques.
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Affiliation(s)
- Jeroen Baardman
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sanne G S Verberk
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Saskia van der Velden
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marion J J Gijbels
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Department of Pathology and Molecular Genetics, CARIM, Maastricht University, Maastricht, Netherlands
| | - Cindy P P A van Roomen
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Judith C Sluimer
- Department of Pathology and Molecular Genetics, CARIM, Maastricht University, Maastricht, Netherlands.,BHF Centre for Cardiovascular Sciences (CVS), University of Edinburgh, Edinburgh, UK
| | - Jelle Y Broos
- Department of Molecular Cell Biology and Immunology, Amsterdam Neuroscience, MS Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Leiden University Medical Center, Center for Proteomics & Metabolomics, Leiden, Netherlands
| | - Guillermo R Griffith
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Koen H M Prange
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam Cardiovascular sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Soufyan Lakbir
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Douwe Molenaar
- Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Elisa Meinster
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Annette E Neele
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Gijs Kooij
- Department of Molecular Cell Biology and Immunology, Amsterdam Neuroscience, MS Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Helga E de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam Neuroscience, MS Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Esther Lutgens
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilians University, Munich, Germany
| | - Kathryn E Wellen
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Menno P J de Winther
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands. .,Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilians University, Munich, Germany.
| | - Jan Van den Bossche
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands. .,Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.
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