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Park JE, Smith MA, Van Alsten SC, Walens A, Wu D, Hoadley KA, Troester MA, Love MI. Diffsig: Associating Risk Factors with Mutational Signatures. Cancer Epidemiol Biomarkers Prev 2024; 33:721-730. [PMID: 38426904 PMCID: PMC11062813 DOI: 10.1158/1055-9965.epi-23-0728] [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: 07/03/2023] [Revised: 10/12/2023] [Accepted: 02/28/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Somatic mutational signatures elucidate molecular vulnerabilities to therapy, and therefore detecting signatures and classifying tumors with respect to signatures has clinical value. However, identifying the etiology of the mutational signatures remains a statistical challenge, with both small sample sizes and high variability in classification algorithms posing barriers. As a result, few signatures have been strongly linked to particular risk factors. METHODS Here, we develop a statistical model, Diffsig, for estimating the association of one or more continuous or categorical risk factors with DNA mutational signatures. Diffsig takes into account the uncertainty associated with assigning signatures to samples as well as multiple risk factors' simultaneous effect on observed DNA mutations. RESULTS We applied Diffsig to breast cancer data to assess relationships between five established breast-relevant mutational signatures and etiologic variables, confirming known mechanisms of cancer development. In simulation, our model was capable of accurately estimating expected associations in a variety of contexts. CONCLUSIONS Diffsig allows researchers to quantify and perform inference on the associations of risk factors with mutational signatures. IMPACT We expect Diffsig to provide more robust associations of risk factors with signatures to lead to better understanding of the tumor development process and improved models of tumorigenesis.
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Affiliation(s)
- Ji-Eun Park
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Andrea Walens
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa A. Troester
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Michael I. Love
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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2
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George J, Maas L, Abedpour N, Cartolano M, Kaiser L, Fischer RN, Scheel AH, Weber JP, Hellmich M, Bosco G, Volz C, Mueller C, Dahmen I, John F, Alves CP, Werr L, Panse JP, Kirschner M, Engel-Riedel W, Jürgens J, Stoelben E, Brockmann M, Grau S, Sebastian M, Stratmann JA, Kern J, Hummel HD, Hegedüs B, Schuler M, Plönes T, Aigner C, Elter T, Toepelt K, Ko YD, Kurz S, Grohé C, Serke M, Höpker K, Hagmeyer L, Doerr F, Hekmath K, Strapatsas J, Kambartel KO, Chakupurakal G, Busch A, Bauernfeind FG, Griesinger F, Luers A, Dirks W, Wiewrodt R, Luecke A, Rodermann E, Diel A, Hagen V, Severin K, Ullrich RT, Reinhardt HC, Quaas A, Bogus M, Courts C, Nürnberg P, Becker K, Achter V, Büttner R, Wolf J, Peifer M, Thomas RK. Evolutionary trajectories of small cell lung cancer under therapy. Nature 2024; 627:880-889. [PMID: 38480884 PMCID: PMC10972747 DOI: 10.1038/s41586-024-07177-7] [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: 01/25/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024]
Abstract
The evolutionary processes that underlie the marked sensitivity of small cell lung cancer (SCLC) to chemotherapy and rapid relapse are unknown1-3. Here we determined tumour phylogenies at diagnosis and throughout chemotherapy and immunotherapy by multiregion sequencing of 160 tumours from 65 patients. Treatment-naive SCLC exhibited clonal homogeneity at distinct tumour sites, whereas first-line platinum-based chemotherapy led to a burst in genomic intratumour heterogeneity and spatial clonal diversity. We observed branched evolution and a shift to ancestral clones underlying tumour relapse. Effective radio- or immunotherapy induced a re-expansion of founder clones with acquired genomic damage from first-line chemotherapy. Whereas TP53 and RB1 alterations were exclusively part of the common ancestor, MYC family amplifications were frequently not constituents of the founder clone. At relapse, emerging subclonal mutations affected key genes associated with SCLC biology, and tumours harbouring clonal CREBBP/EP300 alterations underwent genome duplications. Gene-damaging TP53 alterations and co-alterations of TP53 missense mutations with TP73, CREBBP/EP300 or FMN2 were significantly associated with shorter disease relapse following chemotherapy. In summary, we uncover key processes of the genomic evolution of SCLC under therapy, identify the common ancestor as the source of clonal diversity at relapse and show central genomic patterns associated with sensitivity and resistance to chemotherapy.
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Affiliation(s)
- Julie George
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine and University Hospital Cologne, University Hospital of Cologne, Cologne, Germany.
| | - Lukas Maas
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Nima Abedpour
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
- Cancer Research Centre Cologne Essen, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maria Cartolano
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Centre for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Laura Kaiser
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Rieke N Fischer
- Department I of Internal Medicine, Lung Cancer Group Cologne, University Hospital Cologne, Cologne, Germany
| | - Andreas H Scheel
- Institute of Pathology, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jan-Philipp Weber
- Department I of Internal Medicine, Lung Cancer Group Cologne, University Hospital Cologne, Cologne, Germany
| | - Martin Hellmich
- Institute of Medical Statistics, and Computational Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Graziella Bosco
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Caroline Volz
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
- Centre for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Christian Mueller
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine and University Hospital Cologne, University Hospital of Cologne, Cologne, Germany
| | - Ilona Dahmen
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Felix John
- Department I of Internal Medicine, Lung Cancer Group Cologne, University Hospital Cologne, Cologne, Germany
| | - Cleidson Padua Alves
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lisa Werr
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jens Peter Panse
- Department of Haematology, Oncology, Haemostaseology and Stem Cell Transplantation, University Hospital RWTH Aachen, Aachen, Germany
- Centre for Integrated Oncology, Aachen Bonn Cologne Düsseldorf, Aachen, Germany
| | - Martin Kirschner
- Department of Haematology, Oncology, Haemostaseology and Stem Cell Transplantation, University Hospital RWTH Aachen, Aachen, Germany
- Centre for Integrated Oncology, Aachen Bonn Cologne Düsseldorf, Aachen, Germany
| | - Walburga Engel-Riedel
- Department of Pneumology, City of Cologne Municipal Hospitals, Lung Hospital Cologne Merheim, Cologne, Germany
| | - Jessica Jürgens
- Department of Pneumology, City of Cologne Municipal Hospitals, Lung Hospital Cologne Merheim, Cologne, Germany
| | - Erich Stoelben
- Thoraxclinic Cologne, Thoracic Surgery, St. Hildegardis-Krankenhaus, Cologne, Germany
| | - Michael Brockmann
- Department of Pathology, City of Cologne Municipal Hospitals, Witten/Herdecke University, Cologne, Germany
| | - Stefan Grau
- Department of General Neurosurgery, Centre of Neurosurgery, University Hospital Cologne, Cologne, Germany
- University Medicine Marburg - Campus Fulda, Department of Neurosurgery, Fulda, Germany
| | - Martin Sebastian
- Department of Medicine II, Haematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
- DKFZ, German Cancer Research Centre, German Cancer Consortium, Heidelberg, Germany
| | - Jan A Stratmann
- Department of Medicine II, Haematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Jens Kern
- Klinikum Würzburg Mitte - Missioklinik site, Pneumology and Respiratory Medicine, Würzburg, Germany
| | - Horst-Dieter Hummel
- Translational Oncology/Early Clinical Trial Unit, Comprehensive Cancer Centre Mainfranken, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Balazs Hegedüs
- Department of Thoracic Surgery, University Medicine Essen - Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
| | - Martin Schuler
- DKFZ, German Cancer Research Centre, German Cancer Consortium, Heidelberg, Germany
- Department of Medical Oncology, West German Cancer Centre Essen, University Duisburg-Essen, Essen, Germany
| | - Till Plönes
- Department of Medical Oncology, West German Cancer Centre Essen, University Duisburg-Essen, Essen, Germany
- Division of Thoracic Surgery, Department of General, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Clemens Aigner
- Department of Thoracic Surgery, University Medicine Essen - Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
- Department of Thoracic Surgery, Medical University of Vienna, Vienna General Hospital, Vienna, Austria
| | - Thomas Elter
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
| | - Karin Toepelt
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
| | | | - Sylke Kurz
- Department of Respiratory Diseases, Evangelische Lungenklinik, Berlin, Germany
| | - Christian Grohé
- Department of Respiratory Diseases, Evangelische Lungenklinik, Berlin, Germany
| | - Monika Serke
- DGD Lungenklinik Hemer, Internal Medicine, Pneumology and Oncology, Hemer, Germany
| | - Katja Höpker
- Clinic III for Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lars Hagmeyer
- Clinic of Pneumology and Allergology, Centre for Sleep Medicine and Respiratory Care, Bethanien Hospital Solingen, Solingen, Germany
| | - Fabian Doerr
- Department of Thoracic Surgery, University Medicine Essen - Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
- Department of Cardiothoracic Surgery, University Hospital of Cologne, Cologne, Germany
| | - Khosro Hekmath
- Department of Cardiothoracic Surgery, University Hospital of Cologne, Cologne, Germany
| | - Judith Strapatsas
- Department of Haematology, Oncology and Clinical Immunology, University Hospital of Duesseldorf, Düsseldorf, Germany
| | | | | | - Annette Busch
- Medical Clinic III for Oncology, Haematology, Immune-Oncology and Rheumatology, Centre for Integrative Medicine, University Hospital Bonn, Bonn, Germany
| | - Franz-Georg Bauernfeind
- Medical Clinic III for Oncology, Haematology, Immune-Oncology and Rheumatology, Centre for Integrative Medicine, University Hospital Bonn, Bonn, Germany
| | - Frank Griesinger
- Pius-Hospital Oldenburg, Department of Haematology and Oncology, University Department Internal Medicine-Oncology, University Medicine Oldenburg, Oldenburg, Germany
| | - Anne Luers
- Pius-Hospital Oldenburg, Department of Haematology and Oncology, University Department Internal Medicine-Oncology, University Medicine Oldenburg, Oldenburg, Germany
| | - Wiebke Dirks
- Pius-Hospital Oldenburg, Department of Haematology and Oncology, University Department Internal Medicine-Oncology, University Medicine Oldenburg, Oldenburg, Germany
| | - Rainer Wiewrodt
- Pulmonary Division, Department of Medicine A, Münster University Hospital, Münster, Germany
| | - Andrea Luecke
- Pulmonary Division, Department of Medicine A, Münster University Hospital, Münster, Germany
| | - Ernst Rodermann
- Onkologie Rheinsieg, Praxisnetzwerk Hämatologie und Internistische Onkologie, Troisdorf, Germany
| | - Andreas Diel
- Onkologie Rheinsieg, Praxisnetzwerk Hämatologie und Internistische Onkologie, Troisdorf, Germany
| | - Volker Hagen
- Clinic II for Internal Medicine, St.-Johannes-Hospital Dortmund, Dortmund, Germany
| | - Kai Severin
- Haematologie und Onkologie Köln MV-Zentrum, Cologne, Germany
| | - Roland T Ullrich
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
- Centre for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Haematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
- West German Cancer Centre, University Hospital Essen, Essen, Germany
| | - Alexander Quaas
- Institute of Pathology, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Magdalena Bogus
- Institute of Legal Medicine, University of Cologne, Cologne, Germany
| | - Cornelius Courts
- Institute of Legal Medicine, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Centre for Genomics, West German Genome Centre, University of Cologne, Cologne, Germany
| | - Kerstin Becker
- Cologne Centre for Genomics, West German Genome Centre, University of Cologne, Cologne, Germany
| | - Viktor Achter
- Computing Centre, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jürgen Wolf
- Department I of Internal Medicine, Lung Cancer Group Cologne, University Hospital Cologne, Cologne, Germany
| | - Martin Peifer
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Centre for Molecular Medicine, University of Cologne, Cologne, Germany.
| | - Roman K Thomas
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Institute of Pathology, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, Germany.
- DKFZ, German Cancer Research Centre, German Cancer Consortium, Heidelberg, Germany.
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5
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Perne C, Peters S, Cartolano M, Horpaopan S, Grimm C, Altmüller J, Sommer AK, Hillmer AM, Thiele H, Odenthal M, Möslein G, Adam R, Sivalingam S, Kirfel J, Schweiger MR, Peifer M, Spier I, Aretz S. Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis. PLoS One 2021; 16:e0259185. [PMID: 34843512 PMCID: PMC8629245 DOI: 10.1371/journal.pone.0259185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
The spectrum of somatic genetic variation in colorectal adenomas caused by biallelic pathogenic germline variants in the MSH3 gene, was comprehensively analysed to characterise mutational signatures and identify potential driver genes and pathways of MSH3-related tumourigenesis. Three patients from two families with MSH3-associated polyposis were included. Whole exome sequencing of nine adenomas and matched normal tissue was performed. The amount of somatic variants in the MSH3-deficient adenomas and the pattern of single nucleotide variants (SNVs) was similar to sporadic adenomas, whereas the fraction of small insertions/deletions (indels) (21-42% of all small variants) was significantly higher. Interestingly, pathogenic somatic APC variants were found in all but one adenoma. The vast majority (12/13) of these were di-, tetra-, or penta-base pair (bp) deletions. The fraction of APC indels was significantly higher than that reported in patients with familial adenomatous polyposis (FAP) (p < 0.01) or in sporadic adenomas (p < 0.0001). In MSH3-deficient adenomas, the occurrence of APC indels in a repetitive sequence context was significantly higher than in FAP patients (p < 0.01). In addition, the MSH3-deficient adenomas harboured one to five (recurrent) somatic variants in 13 established or candidate driver genes for early colorectal carcinogenesis, including ACVR2A and ARID genes. Our data suggest that MSH3-related colorectal carcinogenesis seems to follow the classical APC-driven pathway. In line with the specific function of MSH3 in the mismatch repair (MMR) system, we identified a characteristic APC mutational pattern in MSH3-deficient adenomas, and confirmed further driver genes for colorectal tumourigenesis.
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Affiliation(s)
- Claudia Perne
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Maria Cartolano
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sukanya Horpaopan
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Christina Grimm
- Institute for Translational Epigenetics, Medical Faculty and University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
- Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anna K. Sommer
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Axel M. Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Margarete Odenthal
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Gabriela Möslein
- Zentrum für Hereditäre Tumore, BETHESDA Khs. Duisburg, Duisburg, Germany
| | - Ronja Adam
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jutta Kirfel
- Institute of Pathology, University of Lübeck, Lübeck, Germany
| | - Michal R. Schweiger
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Translational Epigenetics, Medical Faculty and University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
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