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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Vijayraghavan S, Blouin T, McCollum J, Porcher L, Virard F, Zavadil J, Feghali-Bostwick C, Saini N. Widespread mutagenesis and chromosomal instability shape somatic genomes in systemic sclerosis. Nat Commun 2024; 15:8889. [PMID: 39406724 PMCID: PMC11480385 DOI: 10.1038/s41467-024-53332-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 10/09/2024] [Indexed: 10/19/2024] Open
Abstract
Systemic sclerosis is a connective tissue disorder characterized by excessive fibrosis that primarily affects women, and can present as a multisystem pathology. Roughly 4-22% of patients with systemic sclerosis develop cancer, which drastically worsens prognosis. However, the mechanisms underlying systemic sclerosis initiation, propagation, and cancer development are poorly understood. We hypothesize that the inflammation and immune response associated with systemic sclerosis can trigger DNA damage, leading to elevated somatic mutagenesis, a hallmark of pre-cancerous tissues. To test our hypothesis, we culture clonal lineages of fibroblasts from the lung tissues of controls and systemic sclerosis patients and compare their mutation burdens and spectra. We find an overall increase in all major mutation types in systemic sclerosis samples compared to control lung samples, from small-scale events such as single base substitutions and insertions/deletions, to chromosome-level changes, including copy-number changes and structural variants. In the genomes of patients with systemic sclerosis, we find evidence of somatic hypermutation or kategis (typically only seen in cancer genomes), we identify mutation signatures closely resembling the error-prone translesion polymerase Polη activity, and observe an activation-induced deaminase-like mutation signature, which overlaps with genomic regions displaying kataegis.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Thomas Blouin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - James McCollum
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Latarsha Porcher
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - François Virard
- University Claude Bernard Lyon 1, INSERM U1052-CNRS UMR5286, Cancer Research Center, Centre Léon Bérard, Lyon, France
| | - Jiri Zavadil
- International Agency for Research on Cancer WHO, Epigenomics and Mechanisms Branch, Lyon, France
| | - Carol Feghali-Bostwick
- Department of Medicine, Division of Rheumatology, Medical University of South Carolina, Charleston, SC, USA
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA.
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3
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Axelsson J, LeBlanc D, Shojaeisaadi H, Meier MJ, Fitzgerald DM, Nachmanson D, Carlson J, Golubeva A, Higgins J, Smith T, Lo FY, Pilsner R, Williams A, Salk J, Marchetti F, Yauk C. Frequency and spectrum of mutations in human sperm measured using duplex sequencing correlate with trio-based de novo mutation analyses. Sci Rep 2024; 14:23134. [PMID: 39379474 PMCID: PMC11461794 DOI: 10.1038/s41598-024-73587-2] [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: 03/26/2024] [Accepted: 09/18/2024] [Indexed: 10/10/2024] Open
Abstract
De novo mutations (DNMs) are drivers of genetic disorders. However, the study of DNMs is hampered by technological limitations preventing accurate quantification of ultra-rare mutations. Duplex Sequencing (DS) theoretically has < 1 error/billion base-pairs (bp). To determine the DS utility to quantify and characterize DNMs, we analyzed DNA from blood and spermatozoa from six healthy, 18-year-old Swedish men using the TwinStrand DS mutagenesis panel (48 kb spanning 20 genic and intergenic loci). The mean single nucleotide variant mutation frequency (MF) was 1.2 × 10- 7 per bp in blood and 2.5 × 10- 8 per bp in sperm, with the most common base substitution being C > T. Blood MF and substitution spectrum were similar to those reported in blood cells with an orthogonal method. The sperm MF was in the same order of magnitude and had a strikingly similar spectrum to DNMs from publicly available whole genome sequencing data from human pedigrees (1.2 × 10- 8 per bp). DS revealed much larger numbers of insertions and deletions in sperm over blood, driven by an abundance of putative extra-chromosomal circular DNAs. The study indicates the strong potential of DS to characterize human DNMs to inform factors that contribute to disease susceptibility and heritable genetic risks.
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Affiliation(s)
- Jonatan Axelsson
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
- Reproductive Medicine Centre, Skåne University Hospital, Malmö, Sweden.
- Department of Translational Medicine, Lund University, Malmö, Sweden.
- Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Danielle LeBlanc
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | | | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | | | | | | | | | | | | | - Fang Yin Lo
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Richard Pilsner
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Jesse Salk
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Carole Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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Young CL, Beichman AC, Mas-Ponte D, Hemker SL, Zhu L, Kitzman JO, Shirts BH, Harris K. A maternal germline mutator phenotype in a family affected by heritable colorectal cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.12.08.23299304. [PMID: 38196581 PMCID: PMC10775336 DOI: 10.1101/2023.12.08.23299304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Variation in DNA repair genes can increase cancer risk by elevating the rate of oncogenic mutation. Defects in one such gene, MUTYH, are known to elevate the incidence of colorectal cancer in a recessive Mendelian manner. Recent evidence has also linked MUTYH to a mutator phenotype affecting normal somatic cells as well as the female germline. Here, we use whole genome sequencing to measure germline de novo mutation rates in a large extended family containing both mothers and fathers who are affected by pathogenic MUTYH variation. By developing novel methodology that uses siblings as "surrogate parents" to identify de novo mutations, we were able to include mutation data from several children whose parents were unavailable for sequencing. In the children of mothers affected by the pathogenic MUTYH genotype p.Y179C/V234M, we identify an elevation of the C>A mutation rate that is weaker than mutator effects previously reported to be caused by other pathogenic MUTYH genotypes, suggesting that mutation rates in normal tissues may be useful for classifying cancer-associated variation along a continuum of severity. Surprisingly, we detect no significant elevation of the C>A mutation rate in children born to a father with the same MUTYH genotype, and we similarly find that the mutator effect of the mouse homolog Mutyh appears to be localized to embryonic development, not the spermatocytes. Our results suggest that maternal MUTYH variants can cause germline mutations by attenuating the repair of oxidative DNA damage in the early embryo.
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Affiliation(s)
- Candice L. Young
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195
- Department of Molecular and Cellular Biology, University of Washington, 1705 NE Pacific St, Seattle, WA 98195
| | - Annabel C. Beichman
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195
| | - David Mas-Ponte
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195
| | - Shelby L. Hemker
- Department of Human Genetics, University of Michigan, 1241 Catherine St, Ann Arbor, MI 48109
| | - Luke Zhu
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA 98195
| | - Jacob O. Kitzman
- Department of Human Genetics, University of Michigan, 1241 Catherine St, Ann Arbor, MI 48109
| | - Brian H. Shirts
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St, Seattle, WA 98195
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, P.O. Box 19024, Seattle, WA 98109
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5
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Lin PH, Chan JY, Guan P, Hong JH, Lim AH, Ng CCY, Yeong JPS, Lee JY, Liu W, Lim JCT, Pang ST, Teh BT. Aristolochic acid-related renal cell carcinoma exhibits a distinct tumor-immune microenvironment favoring response to immune checkpoint blockade. J Pathol 2024. [PMID: 39360336 DOI: 10.1002/path.6349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 10/04/2024]
Abstract
Immune checkpoint blockade (ICB) is currently the standard of care for metastatic renal cell carcinoma (RCC), but treatment responses remain unpredictable. Aristolochic acid (AA), a prevalent supplement additive in Taiwan, has been associated with RCC and induces signature mutations, although its effect on the tumor-immune microenvironment (TIME) is unclear. We aimed to investigate the immune profile of AA-positive RCCs and explore its potential role as a susceptible candidate for ICB. Tissue samples from 22 patients with clear cell RCC (ccRCC) were collected for whole-exome sequencing to determine the genetic features and AA mutational signature (the discovery cohort). The corresponding RNA was sent for NanoString PanCancer IO 360 gene expression analysis to explore the immunological features. The formalin-fixed, parafilm-embedded slides of ccRCCs were sent for multiplex immunohistochemistry/immunofluorescence stain using Vectra system to evaluate the TIME. Tissues from two patients with metastatic RCC demonstrating complete response to ICB were sent for studies to validate the findings (the index patients). The results showed that AA mutational signatures with high tumor mutational burden (TMB) were present in 31.81% of the tumors in the discovery cohort. Three distinct clusters were observed through NanoString analysis. Clusters 1 and 3 were composed mainly of AA-positive RCCs. Cluster 3 RCCs exhibited higher tumor inflammation signature scores and higher immune cell type scores. Vectra analysis revealed a higher percentage of CD15+ and BATF3+ cells in cluster 1, whereas the percentage of CD8+ cells was potentially higher in cluster 3. Strong AA mutational signatures were found in the tumors of two index patients, and both were grouped to cluster 3. In conclusion, AA may induce higher TMB and alter the immune microenvironment in RCCs, which makes the tumors more susceptible to ICB. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Po-Hung Lin
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | | | - Peiyong Guan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jing Han Hong
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Abner Herbert Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Joe Poh Sheng Yeong
- Integrative Biology for Theranostics Lab, Cancer Signaling & Therapies Programme, Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
- Pathology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Wei Liu
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore, Singapore
| | - Jeffrey Chun Tatt Lim
- Integrative Biology for Theranostics Lab, Cancer Signaling & Therapies Programme, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - See-Tong Pang
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Bin Tean Teh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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6
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Peirone S, Tirtei E, Campello A, Parlato C, Guarrera S, Mareschi K, Marini E, Asaftei SD, Bertero L, Papotti M, Priante F, Perrone S, Cereda M, Fagioli F. Impaired neutrophil-mediated cell death drives Ewing's Sarcoma in the background of Down syndrome. Front Oncol 2024; 14:1429833. [PMID: 39421445 PMCID: PMC11484044 DOI: 10.3389/fonc.2024.1429833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 09/11/2024] [Indexed: 10/19/2024] Open
Abstract
Introduction Ewing Sarcoma (EWS) has been reported in seven children with Down syndrome (DS). To date, a detailed assessment of this solid tumour in DS patients is yet to be made. Methods Here, we characterise a chemo-resistant mediastinal EWS in a 2-year-old DS child, the youngest ever reported case, by exploiting sequencing approaches. Results The tumour showed a neuroectodermal development driven by the EWSR1-FLI1 fusion. The inherited myeloperoxidase deficiency of the patient caused failure of neutrophil-mediated cell death and promoted genomic instability. Discussion In this context, the tumour underwent genome-wide near haploidisation resulting in a massive overexpression of pro-inflammatory cytokines. Recruitment of defective neutrophils fostered rapid evolution of this EWS.
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Affiliation(s)
- Serena Peirone
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
- Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
| | - Elisa Tirtei
- Paediatric Oncology Department, Regina Margherita Children’s Hospital, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Anna Campello
- Paediatric Oncology Department, Regina Margherita Children’s Hospital, Turin, Italy
| | - Caterina Parlato
- Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Katia Mareschi
- Paediatric Oncology Department, Regina Margherita Children’s Hospital, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Elena Marini
- Paediatric Oncology Department, Regina Margherita Children’s Hospital, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | | | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Mauro Papotti
- Pathology Unit, Department of Oncology, University of Turin, Turin, Italy
| | - Francesca Priante
- Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Sarah Perrone
- Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Matteo Cereda
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
- Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
| | - Franca Fagioli
- Paediatric Oncology Department, Regina Margherita Children’s Hospital, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
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7
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Basurto-Lozada P, Vázquez-Cruz ME, Molina-Aguilar C, Jiang A, Deacon DC, Cerrato-Izaguirre D, Simonin-Wilmer I, Arriaga-González FG, Contreras-Ramírez KL, Dawson ET, Wong-Ramirez JRC, Ramos-Galguera JI, Álvarez-Cano A, García-Ortega DY, García-Salinas OI, Hidalgo-Miranda A, Cisneros-Villanueva M, Martínez-Said H, Arends MJ, Ferreira I, Tullett M, Olvera-León R, van der Weyden L, Del Castillo Velasco Herrera M, Roldán-Marín R, Vidaurri de la Cruz H, Tavares-de-la-Paz LA, Hinojosa-Ugarte D, Belote RL, Bishop DT, Díaz-Gay M, Alexandrov LB, Sánchez-Pérez Y, In GK, White RM, Possik PA, Judson-Torres RL, Adams DJ, Robles-Espinoza CD. Ancestry and somatic profile predict acral melanoma origin and prognosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.21.24313911. [PMID: 39399030 PMCID: PMC11469390 DOI: 10.1101/2024.09.21.24313911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Acral melanoma, which is not ultraviolet (UV)-associated, is the most common type of melanoma in several low- and middle-income countries including Mexico. Latin American samples are significantly underrepresented in global cancer genomics studies, which directly affects patients in these regions as it is known that cancer risk and incidence may be influenced by ancestry and environmental exposures. To address this, here we characterise the genome and transcriptome of 128 acral melanoma tumours from 96 Mexican patients, a population notable because of its genetic admixture. Compared with other studies of melanoma, we found fewer frequent mutations in classical driver genes such as BRAF , NRAS or NF1 . While most patients had predominantly Amerindian genetic ancestry, those with higher European ancestry had increased frequency of BRAF mutations and a lower number of structural variants. These BRAF -mutated tumours have a transcriptional profile similar to cutaneous non-volar melanocytes, suggesting that acral melanomas in these patients may arise from a distinct cell of origin compared to other tumours arising in these locations. KIT mutations were found in a subset of these tumours, and transcriptional profiling defined three expression clusters; these characteristics were associated with overall survival. We highlight novel low-frequency drivers, such as SPHKAP , which correlate with a distinct genomic profile and clinical characteristics. Our study enhances knowledge of this understudied disease and underscores the importance of including samples from diverse ancestries in cancer genomics studies.
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8
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Kopetz S, Murphy DA, Pu J, Ciardiello F, Desai J, Van Cutsem E, Wasan HS, Yoshino T, Saffari H, Zhang X, Hamilton P, Xie T, Yaeger R, Tabernero J. Molecular profiling of BRAF-V600E-mutant metastatic colorectal cancer in the phase 3 BEACON CRC trial. Nat Med 2024:10.1038/s41591-024-03235-9. [PMID: 39313594 DOI: 10.1038/s41591-024-03235-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 08/06/2024] [Indexed: 09/25/2024]
Abstract
The BEACON CRC study demonstrated that encorafenib (Enco)+cetuximab (Cetux)±binimetinib (Bini) significantly improved overall survival (OS) versus Cetux + chemotherapy in previously treated patients with BRAF-V600E-mutant mCRC, providing the basis for the approval of the Enco+Cetux regimen in the United States and the European Union. A greater understanding of biomarkers predictive of response to Enco+Cetux±Bini treatment is of clinical relevance. In this prespecified, exploratory biomarker analysis of the BEACON CRC study, we characterize genomic and transcriptomic correlates of clinical outcomes and acquired resistance mechanisms through integrated clinical and molecular analysis, including whole-exome and -transcriptome tissue sequencing and circulating tumor DNA genomic profiling. Tumors with higher immune signatures showed a trend towards increased OS benefit with Enco+Bini+Cetux. RAS, MAP2K1 and MET alterations were most commonly acquired with Enco+Cetux±Bini, and more frequent in patients with a high baseline cell-cycle gene signature; baseline TP53 mutation was associated with acquired MET amplification. Acquired mutations were subclonal and polyclonal, with evidence of increased tumor mutation rate with Enco+Cetux±Bini and mutational signatures (SBS17a/b). These findings support treatment with Enco+Cetux±Bini for patients with BRAF-V600E-mutant mCRC and provide insights into the biology of response and resistance to MAPK-pathway-targeted therapy. ClinicalTrials.gov registration: NCT02928224.
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Affiliation(s)
- Scott Kopetz
- University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | | | - Jie Pu
- Pfizer, New York, NY, USA
| | | | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Eric Van Cutsem
- University Hospitals Gasthuisberg Leuven and KU Leuven, Leuven, Belgium
| | | | | | | | | | | | | | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Josep Tabernero
- Vall d'Hebron Hospital Campus and Vall d'Hebron Institute of Oncology (VHIO), University of Vic-Central University of Catalonia, Barcelona, Spain
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9
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Xue Y, Liu L, Zhang Y, He Y, Wang J, Ma Z, Li TJ, Zhang J, Huang Y, Gao YQ. Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer. Mol Cancer 2024; 23:190. [PMID: 39243015 PMCID: PMC11378415 DOI: 10.1186/s12943-024-02100-0] [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: 06/28/2024] [Accepted: 08/23/2024] [Indexed: 09/09/2024] Open
Abstract
Epigenetic alterations, such as those in chromatin structure and DNA methylation, have been extensively studied in a number of tumor types. But oral cancer, particularly oral adenocarcinoma, has received far less attention. Here, we combined laser-capture microdissection and muti-omics mini-bulk sequencing to systematically characterize the epigenetic landscape of oral cancer, including chromatin architecture, DNA methylation, H3K27me3 modification, and gene expression. In carcinogenesis, tumor cells exhibit reorganized chromatin spatial structures, including compromised compartment structures and altered gene-gene interaction networks. Notably, some structural alterations are observed in phenotypically non-malignant paracancerous but not in normal cells. We developed transformer models to identify the cancer propensity of individual genome loci, thereby determining the carcinogenic status of each sample. Insights into cancer epigenetic landscapes provide evidence that chromatin reorganization is an important hallmark of oral cancer progression, which is also linked with genomic alterations and DNA methylation reprogramming. In particular, regions of frequent copy number alternations in cancer cells are associated with strong spatial insulation in both cancer and normal samples. Aberrant methylation reprogramming in oral squamous cell carcinomas is closely related to chromatin structure and H3K27me3 signals, which are further influenced by intrinsic sequence properties. Our findings indicate that structural changes are both significant and conserved in two distinct types of oral cancer, closely linked to transcriptomic alterations and cancer development. Notably, the structural changes remain markedly evident in oral adenocarcinoma despite the considerably lower incidence of genomic copy number alterations and lesser extent of methylation alterations compared to squamous cell carcinoma. We expect that the comprehensive analysis of epigenetic reprogramming of different types and subtypes of primary oral tumors can provide additional guidance to the design of novel detection and therapy for oral cancer.
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Affiliation(s)
- Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lu Liu
- Changping Laboratory, Beijing, 102206, China
| | - Ye Zhang
- Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
- Department of Oral Pathology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - Yueying He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jingyao Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zicheng Ma
- Changping Laboratory, Beijing, 102206, China
| | - Tie-Jun Li
- Department of Oral Pathology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - Jianyun Zhang
- Department of Oral Pathology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China.
| | - Yanyi Huang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, 528107, China.
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Changping Laboratory, Beijing, 102206, China.
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.
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10
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Zych MG, Contreras M, Vashisth M, Mammel AE, Ha G, Hatch EM. RCC1 depletion drives protein transport defects and rupture in micronuclei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611299. [PMID: 39282444 PMCID: PMC11398501 DOI: 10.1101/2024.09.04.611299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Micronuclei (MN) are a commonly used marker of chromosome instability that form when missegregated chromatin recruits its own nuclear envelope (NE) after mitosis. MN frequently rupture, which results in genome instability, upregulation of metastatic genes, and increased immune signaling. MN rupture is linked to NE defects, but the cause of these defects is poorly understood. Previous work from our lab found that chromosome identity correlates with rupture timing for small MN, i.e. MN containing a short chromosome, with more euchromatic chromosomes forming more stable MN with fewer nuclear lamina gaps. Here we demonstrate that histone methylation promotes rupture and nuclear lamina defects in small MN. This correlates with increased MN size, and we go on to find that all MN have a constitutive nuclear export defect that drives MN growth and nuclear lamina gap expansion, making the MN susceptible to rupture. We demonstrate that these export defects arise from decreased RCC1 levels in MN and that additional loss of RCC1 caused by low histone methylation in small euchromatic MN results in additional import defects that suppress nuclear lamina gaps and MN rupture. Through analysis of mutational signatures associated with early and late rupturing chromosomes in the Pan-Cancer Analysis of Whole Genomes (PCAWG) dataset, we identify an enrichment of APOBEC and DNA polymerase E hypermutation signatures in chromothripsis events on early and mid rupturing chromosomes, respectively, suggesting that MN rupture timing could determine the landscape of structural variation in chromothripsis. Our study defines a new model of MN rupture where increased MN growth, caused by defects in protein export, drives gaps in nuclear lamina organization that make the MN susceptible to membrane rupture with long-lasting effects on genome architecture.
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11
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Cornish AJ, Gruber AJ, Kinnersley B, Chubb D, Frangou A, Caravagna G, Noyvert B, Lakatos E, Wood HM, Thorn S, Culliford R, Arnedo-Pac C, Househam J, Cross W, Sud A, Law P, Leathlobhair MN, Hawari A, Woolley C, Sherwood K, Feeley N, Gül G, Fernandez-Tajes J, Zapata L, Alexandrov LB, Murugaesu N, Sosinsky A, Mitchell J, Lopez-Bigas N, Quirke P, Church DN, Tomlinson IPM, Sottoriva A, Graham TA, Wedge DC, Houlston RS. The genomic landscape of 2,023 colorectal cancers. Nature 2024; 633:127-136. [PMID: 39112709 PMCID: PMC11374690 DOI: 10.1038/s41586-024-07747-9] [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: 11/14/2022] [Accepted: 06/24/2024] [Indexed: 08/17/2024]
Abstract
Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2-9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia colipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11-13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.
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Affiliation(s)
- Alex J Cornish
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, Konstanz, Germany
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- University College London Cancer Institute, London, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Frangou
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Boris Noyvert
- Cancer Research UK Centre and Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Steve Thorn
- Department of Oncology, University of Oxford, Oxford, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jacob Househam
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - William Cross
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | | | - Aliah Hawari
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Connor Woolley
- Department of Oncology, University of Oxford, Oxford, UK
| | - Kitty Sherwood
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nathalie Feeley
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Güler Gül
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Luis Zapata
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Nirupa Murugaesu
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alona Sosinsky
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Jonathan Mitchell
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Philip Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Andrea Sottoriva
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
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12
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Haas R, Frame G, Khan S, Neilsen BK, Hong BH, Yeo CPX, Yamaguchi TN, Ong EHW, Zhao W, Carlin B, Yeo ELL, Tan KM, Bugh YZ, Zhu C, Hugh-White R, Livingstone J, Poon DJJ, Chu PL, Patel Y, Tao S, Ignatchenko V, Kurganovs NJ, Higgins GS, Downes MR, Loblaw A, Vesprini D, Kishan AU, Chua MLK, Kislinger T, Boutros PC, Liu SK. The Proteogenomics of Prostate Cancer Radioresistance. CANCER RESEARCH COMMUNICATIONS 2024; 4:2463-2479. [PMID: 39166898 PMCID: PMC11411600 DOI: 10.1158/2767-9764.crc-24-0292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/23/2024] [Accepted: 08/15/2024] [Indexed: 08/23/2024]
Abstract
Prostate cancer is frequently treated with radiotherapy. Unfortunately, aggressive radioresistant relapses can arise, and the molecular underpinnings of radioresistance are unknown. Modern clinical radiotherapy is evolving to deliver higher doses of radiation in fewer fractions (hypofractionation). We therefore analyzed genomic, transcriptomic, and proteomic data to characterize prostate cancer radioresistance in cells treated with both conventionally fractionated and hypofractionated radiotherapy. Independent of fractionation schedule, resistance to radiotherapy involved massive genomic instability and abrogation of DNA mismatch repair. Specific prostate cancer driver genes were modulated at the RNA and protein levels, with distinct protein subcellular responses to radiotherapy. Conventional fractionation led to a far more aggressive biomolecular response than hypofractionation. Testing preclinical candidates identified in cell lines, we revealed POLQ (DNA Polymerase Theta) as a radiosensitizer. POLQ-modulated radioresistance in model systems and was predictive of it in large patient cohorts. The molecular response to radiation is highly multimodal and sheds light on prostate cancer lethality. SIGNIFICANCE Radiation is standard of care in prostate cancer. Yet, we have little understanding of its failure. We demonstrate a new paradigm that radioresistance is fractionation specific and identified POLQ as a radioresistance modulator.
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Affiliation(s)
- Roni Haas
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Gavin Frame
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Beth K Neilsen
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, California
| | - Boon Hao Hong
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Celestia P X Yeo
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Enya H W Ong
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Wenyan Zhao
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Benjamin Carlin
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Eugenia L L Yeo
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Kah Min Tan
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Yuan Zhe Bugh
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Chenghao Zhu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Rupert Hugh-White
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Julie Livingstone
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Dennis J J Poon
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Pek Lim Chu
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Yash Patel
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Shu Tao
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | | | | | - Geoff S Higgins
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Michelle R Downes
- Division of Anatomic Pathology, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Andrew Loblaw
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Danny Vesprini
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Amar U Kishan
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, California
| | - Melvin L K Chua
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Department of Urology, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Stanley K Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
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13
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Hartwich TMP, Mansolf M, Demirkiran C, Greenman M, Bellone S, McNamara B, Nandi SP, Alexandrov LB, Yang-Hartwich Y, Coma S, Pachter J, Santin AD. Preclinical evaluation of avutometinib and defactinib in high-grade endometrioid endometrial cancer. Cancer Med 2024; 13:e70210. [PMID: 39240189 PMCID: PMC11378359 DOI: 10.1002/cam4.70210] [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: 04/05/2024] [Revised: 08/02/2024] [Accepted: 08/26/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND High-grade endometrial cancers (EAC) are aggressive tumors with a high risk of progression after treatment. As EAC may harbor mutations in the RAS/MAPK pathways, we evaluated the preclinical in vitro and in vivo efficacy of avutometinib, a RAF/MEK clamp, in combination with the focal adhesion kinase (FAK) inhibitors defactinib or VS-4718, against multiple primary EAC cell lines and xenografts. METHODS Whole-exome sequencing (WES) was used to evaluate the genetic landscape of five primary EAC cell lines. The in vitro activity of avutometinib and defactinib as single agents and in combination was evaluated using cell viability, cell cycle, and cytotoxicity assays. Mechanistic studies were performed using Western blot assays while in vivo experiments were completed in UTE10 engrafted mice treated with either vehicle, avutometinib, VS-4718, or their combination through oral gavage. RESULTS WES results demonstrated multiple EAC cell lines to harbor genetic derangements in the RAS/MAPK pathway including KRAS/PTEN/PIK3CA/BRAF/ARID1A, potentially sensitizing to FAK and RAF/MEK inhibition. Five out of five of the EAC cell lines demonstrated in vitro sensitivity to FAK and/or RAF/MEK inhibition. By Western blot assays, exposure of EAC cell lines to defactinib, avutometinib, and their combination demonstrated decreased phosphorylated FAK (p-FAK) as well as decreased p-MEK and p-ERK. In vivo the combination of avutometinib/VS-4718 demonstrated superior tumor growth inhibition compared to single-agent treatment and controls starting at Day 9 (p < 0.02 and p < 0.04) in UTE10 xenografts. CONCLUSIONS Avutometinib, defactinib, and to a larger extent their combinations, demonstrated promising in vitro and in vivo activity against EAC cell lines and xenografts. These preclinical data support the potential clinical evaluation of this combination in high-grade EAC patients.
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Affiliation(s)
- Tobias Max Philipp Hartwich
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, New Haven, Connecticut, USA
| | - Miranda Mansolf
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, New Haven, Connecticut, USA
| | - Cem Demirkiran
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, New Haven, Connecticut, USA
| | - Michelle Greenman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, New Haven, Connecticut, USA
| | - Stefania Bellone
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, New Haven, Connecticut, USA
| | - Blair McNamara
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, New Haven, Connecticut, USA
| | - Shuvro P Nandi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Yang Yang-Hartwich
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, New Haven, Connecticut, USA
| | - Silvia Coma
- Verastem Oncology, Needham, Massachusetts, USA
| | | | - Alessandro D Santin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, New Haven, Connecticut, USA
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14
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Nunes L, Li F, Wu M, Luo T, Hammarström K, Torell E, Ljuslinder I, Mezheyeuski A, Edqvist PH, Löfgren-Burström A, Zingmark C, Edin S, Larsson C, Mathot L, Osterman E, Osterlund E, Ljungström V, Neves I, Yacoub N, Guðnadóttir U, Birgisson H, Enblad M, Ponten F, Palmqvist R, Xu X, Uhlén M, Wu K, Glimelius B, Lin C, Sjöblom T. Prognostic genome and transcriptome signatures in colorectal cancers. Nature 2024; 633:137-146. [PMID: 39112715 PMCID: PMC11374687 DOI: 10.1038/s41586-024-07769-3] [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: 04/24/2023] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Colorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGFβ pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.
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Affiliation(s)
- Luís Nunes
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Fuqiang Li
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Meizhen Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Tian Luo
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Klara Hammarström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emma Torell
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ingrid Ljuslinder
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Carl Zingmark
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Chatarina Larsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Osterman
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emerik Osterlund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Inês Neves
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nicole Yacoub
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Unnur Guðnadóttir
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helgi Birgisson
- Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Malin Enblad
- Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Xun Xu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
| | - Mathias Uhlén
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kui Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Cong Lin
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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15
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Guan P, Chen J, Mo C, Fukawa T, Zhang C, Cai X, Li M, Hong JH, Chan JY, Ng CCY, Lee JY, Wong SF, Liu W, Zeng X, Wang P, Xiao R, Rajasegaran V, Myint SS, Lim AMS, Yeong JPS, Tan PH, Ong CK, Xu T, Du Y, Bai F, Yao X, Teh BT, Tan J. Comprehensive molecular characterization of collecting duct carcinoma for therapeutic vulnerability. EMBO Mol Med 2024; 16:2132-2145. [PMID: 39122888 PMCID: PMC11393068 DOI: 10.1038/s44321-024-00102-5] [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: 02/19/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 08/12/2024] Open
Abstract
Collecting duct carcinoma (CDC) is an aggressive rare subtype of kidney cancer with unmet clinical needs. Little is known about its underlying molecular alterations and etiology, primarily due to its rarity, and lack of preclinical models. This study aims to comprehensively characterize molecular alterations in CDC and identify its therapeutic vulnerabilities. Through whole-exome and transcriptome sequencing, we identified KRAS hotspot mutations (G12A/D/V) in 3/13 (23%) of the patients, in addition to known TP53, NF2 mutations. 3/13 (23%) patients carried a mutational signature (SBS22) caused by aristolochic acid (AA) exposures, known to be more prevalent in Asia, highlighting a geologically specific disease etiology. We further discovered that cell cycle-related pathways were the most predominantly dysregulated pathways. Our drug screening with our newly established CDC preclinical models identified a CDK9 inhibitor LDC000067 that specifically inhibited CDC tumor growth and prolonged survival. Our study not only improved our understanding of oncogenic molecular alterations of Asian CDC, but also identified cell-cycle machinery as a therapeutic vulnerability, laying the foundation for clinical trials to treat patients with such aggressive cancer.
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Affiliation(s)
- Peiyong Guan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Jianfeng Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Chengqiang Mo
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Tomoya Fukawa
- Department of Urology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Chao Zhang
- Department of Genitourinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, P. R. China
| | - Xiuyu Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Mei Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jing Han Hong
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Jing Yi Lee
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Suet Far Wong
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Wei Liu
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Xian Zeng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Peili Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Rong Xiao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Vikneswari Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Abner Ming Sun Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Republic of Singapore
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Republic of Singapore
- Division of Pathology, Singapore General Hospital, Singapore, Republic of Singapore
- Luma Medical Centre, Singapore, Republic of Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Tao Xu
- Department of Urology, Peking University People's Hospital, Beijing, 100044, China
| | - Yiqing Du
- Department of Urology, Peking University People's Hospital, Beijing, 100044, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xin Yao
- Department of Genitourinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, P. R. China.
| | - Bin Tean Teh
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore.
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Republic of Singapore.
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, Republic of Singapore.
| | - Jing Tan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore.
- Hainan Academy of Medical Science, Hainan Medical University, Haikou, PR China.
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16
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Mukohara F, Iwata K, Ishino T, Inozume T, Nagasaki J, Ueda Y, Suzawa K, Ueno T, Ikeda H, Kawase K, Saeki Y, Kawashima S, Yamashita K, Kawahara Y, Nakamura Y, Honobe-Tabuchi A, Watanabe H, Dansako H, Kawamura T, Suzuki Y, Honda H, Mano H, Toyooka S, Kawazu M, Togashi Y. Somatic mutations in tumor-infiltrating lymphocytes impact on antitumor immunity. Proc Natl Acad Sci U S A 2024; 121:e2320189121. [PMID: 39167601 PMCID: PMC11363295 DOI: 10.1073/pnas.2320189121] [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: 12/01/2023] [Accepted: 07/05/2024] [Indexed: 08/23/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) exert clinical efficacy against various types of cancers by reinvigorating exhausted CD8+ T cells that can expand and directly attack cancer cells (cancer-specific T cells) among tumor-infiltrating lymphocytes (TILs). Although some reports have identified somatic mutations in TILs, their effect on antitumor immunity remains unclear. In this study, we successfully established 18 cancer-specific T cell clones, which have an exhaustion phenotype, from the TILs of four patients with melanoma. We conducted whole-genome sequencing for these T cell clones and identified various somatic mutations in them with high clonality. Among the somatic mutations, an SH2D2A loss-of-function frameshift mutation and TNFAIP3 deletion could activate T cell effector functions in vitro. Furthermore, we generated CD8+ T cell-specific Tnfaip3 knockout mice and showed that Tnfaip3 function loss in CD8+ T cell increased antitumor immunity, leading to remarkable response to PD-1 blockade in vivo. In addition, we analyzed bulk CD3+ T cells from TILs in additional 12 patients and identified an SH2D2A mutation in one patient through amplicon sequencing. These findings suggest that somatic mutations in TILs can affect antitumor immunity and suggest unique biomarkers and therapeutic targets.
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Affiliation(s)
- Fumiaki Mukohara
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama University, Okayama700-8558, Japan
| | - Kazuma Iwata
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama University, Okayama700-8558, Japan
| | - Takamasa Ishino
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Takashi Inozume
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba260-8670, Japan
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba260-8717, Japan
- Department of Dermatology, University of Yamanashi, Yamanashi409-3898, Japan
| | - Joji Nagasaki
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
| | - Youki Ueda
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
| | - Ken Suzawa
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama University, Okayama700-8558, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo104-0045, Japan
| | - Hideki Ikeda
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba260-8717, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Katsushige Kawase
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba260-8717, Japan
- Department of Otorhinolaryngology/Head & Neck Surgery, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Yuka Saeki
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba260-8670, Japan
| | - Shusuke Kawashima
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba260-8670, Japan
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba260-8717, Japan
| | | | - Yu Kawahara
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba260-8670, Japan
- Department of Skin Oncology/Dermatology, Saitama Medical University International Medical Center, Saitama350-1298, Japan
| | - Yasuhiro Nakamura
- Department of Skin Oncology/Dermatology, Saitama Medical University International Medical Center, Saitama350-1298, Japan
| | | | - Hiroko Watanabe
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
| | - Hiromichi Dansako
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
| | - Tatsuyoshi Kawamura
- Department of Dermatology, University of Yamanashi, Yamanashi409-3898, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba277-8568, Japan
| | - Hiroaki Honda
- Department of Pathology, Tokyo Women's Medical University, Shinjuku-ku, Tokyo162-8666, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo104-0045, Japan
| | - Shinichi Toyooka
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama University, Okayama700-8558, Japan
| | - Masahito Kawazu
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba260-8717, Japan
- Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo104-0045, Japan
| | - Yosuke Togashi
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba260-8717, Japan
- Kindai University, Faculty of Medicine, Osaka-Sayama, Osaka589-0014, Japan
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17
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Martin S, Katainen R, Taira A, Välimäki N, Ristimäki A, Seppälä T, Renkonen-Sinisalo L, Lepistö A, Tahkola K, Mattila A, Koskensalo S, Mecklin JP, Rajamäki K, Palin K, Aaltonen LA. Lynch syndrome-associated and sporadic microsatellite unstable colorectal cancers: different patterns of clonal evolution yield highly similar tumours. Hum Mol Genet 2024:ddae124. [PMID: 39180486 DOI: 10.1093/hmg/ddae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/22/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
Microsatellite unstable colorectal cancer (MSI-CRC) can arise through germline mutations in mismatch repair (MMR) genes in individuals with Lynch syndrome (LS), or sporadically through promoter methylation of the MMR gene MLH1. Despite the different origins of hereditary and sporadic MSI tumours, their genomic features have not been extensively compared. A prominent feature of MMR-deficient genomes is the occurrence of many indels in short repeat sequences, an understudied mutation type due to the technical challenges of variant calling in these regions. In this study, we performed whole genome sequencing and RNA-sequencing on 29 sporadic and 14 hereditary MSI-CRCs. We compared the tumour groups by analysing genome-wide mutation densities, microsatellite repeat indels, recurrent protein-coding variants, signatures of single base, doublet base, and indel mutations, and changes in gene expression. We show that the mutational landscapes of hereditary and sporadic MSI-CRCs, including mutational signatures and mutation densities genome-wide and in microsatellites, are highly similar. Only a low number of differentially expressed genes were found, enriched to interferon-γ regulated immune response pathways. Analysis of the variance in allelic fractions of somatic variants in each tumour group revealed higher clonal heterogeneity in sporadic MSI-CRCs. Our results suggest that the differing molecular origins of MMR deficiency in hereditary and sporadic MSI-CRCs do not result in substantial differences in the mutational landscapes of these tumours. The divergent patterns of clonal evolution between the tumour groups may have clinical implications, as high clonal heterogeneity has been associated with decreased tumour immunosurveillance and reduced responsiveness to immunotherapy.
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Affiliation(s)
- Samantha Martin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Riku Katainen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Aurora Taira
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Niko Välimäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, 00290 Helsinki, Finland
| | - Toni Seppälä
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Haartmaninkatu 4, 00290 Helsinki, Finland
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital and TAYS Cancer Centre, Kuntokatu 2, 33520 Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University, Kalevantie 4, 33100 Tampere, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Anna Lepistö
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Kyösti Tahkola
- Faculty of Medicine and Health Technology, Tampere University, Kalevantie 4, 33100 Tampere, Finland
- Department of Surgery, Central Finland Health Care District, Keskussairaalantie 19, 40620 Jyväskylä, Finland
| | - Anne Mattila
- Department of Surgery, Central Finland Health Care District, Keskussairaalantie 19, 40620 Jyväskylä, Finland
| | - Selja Koskensalo
- The HUCH Gastrointestinal Clinic, Helsinki University Central Hospital, Stenbäckinkatu 9A, 00029 Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Research, The Wellbeing Services of Central Finland, Hoitajatie 1, 40620 Jyväskylä, Finland
- Department of Sport and Health Sciences, University of Jyväskylä, Seminaarinkatu 15, 40014 Jyväskylä, Finland
| | - Kristiina Rajamäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Kimmo Palin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Lauri A Aaltonen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
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18
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Haas R, Patel Y, Liu LY, Huang RR, Weiner A, Yamaguchi TN, Agrawal R, Boutros PC, Reiter RE. Divergent Evolution in Bilateral Prostate Cancer: a Case Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.22.24312320. [PMID: 39228741 PMCID: PMC11370525 DOI: 10.1101/2024.08.22.24312320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Multifocal prostate cancer is a prevalent phenomenon, with most cases remaining uncharacterized from a genomic perspective. A patient presented with bilateral prostate cancer. On systematic biopsy, two indistinguishable clinicopathologic lesions were detected. Whole-genome sequencing displayed somatically unrelated tumours with distinct driver CNA regions, suggesting independent origins of the two tumors. We demonstrated that similar clinicopathologic multifocal tumours, which might be interpreted as clonal disease, can in fact represent independent cancers. Genetic prognostics can prevent mischaracterization of multifocal disease to enable optimal patient management.
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Affiliation(s)
- Roni Haas
- Department of Human Genetics, University of California, Los Angeles, USA
- Department of Urology, University of California, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
- Institute for Precision Health, University of California, Los Angeles, USA
| | - Yash Patel
- Department of Human Genetics, University of California, Los Angeles, USA
- Department of Urology, University of California, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
- Institute for Precision Health, University of California, Los Angeles, USA
| | - Lydia Y Liu
- Department of Human Genetics, University of California, Los Angeles, USA
- Department of Urology, University of California, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
- Institute for Precision Health, University of California, Los Angeles, USA
| | - Rong Rong Huang
- Department of Pathology, University of California, Los Angeles, USA
| | - Adam Weiner
- Department of Urology, University of California, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
- Institute for Precision Health, University of California, Los Angeles, USA
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, USA
- Department of Urology, University of California, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
- Institute for Precision Health, University of California, Los Angeles, USA
| | - Raag Agrawal
- Department of Human Genetics, University of California, Los Angeles, USA
- Department of Urology, University of California, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, USA
- Department of Urology, University of California, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
- Institute for Precision Health, University of California, Los Angeles, USA
| | - Robert E Reiter
- Department of Urology, University of California, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
- Institute for Precision Health, University of California, Los Angeles, USA
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19
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Hilton LK, Collinge B, Ben-Neriah S, Alduaij W, Shaalan H, Weng AP, Cruz M, Slack GW, Farinha P, Miyata-Takata T, Boyle M, Meissner B, Cook JR, Ondrejka SL, Ott G, Rosenwald A, Campo E, Amador C, Greiner TC, Raess PW, Song JY, Inghirami G, Jaffe ES, Weisenburger DD, Chan WC, Beiske K, Fu K, Delabie J, Pittaluga S, Iqbal J, Wright G, Sehn LH, Savage KJ, Mungall AJ, Feldman AL, Staudt LM, Steidl C, Rimsza LM, Morin RD, Scott DW. Motive and opportunity: MYC rearrangements in high-grade B-cell lymphoma with MYC and BCL2 rearrangements (an LLMPP study). Blood 2024; 144:525-540. [PMID: 38701426 PMCID: PMC11307266 DOI: 10.1182/blood.2024024251] [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: 02/09/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
ABSTRACT Rearrangements that place the oncogenes MYC, BCL2, or BCL6 adjacent to superenhancers are common in mature B-cell lymphomas. Lymphomas with diffuse large B-cell lymphoma (DLBCL) or high-grade morphology with both MYC and BCL2 rearrangements are classified as high-grade B-cell lymphoma with MYC and BCL2 rearrangements ("double hit"; HGBCL-DH-BCL2) and are associated with aggressive disease and poor outcomes. Although it is established that MYC rearrangements involving immunoglobulin (IG) loci are associated with inferior outcomes relative to those involving other non-IG superenhancers, the frequency of and mechanisms driving IG vs non-IG MYC rearrangements have not been elucidated. Here, we used custom targeted capture and/or whole-genome sequencing to characterize oncogene rearrangements across 883 mature B-cell lymphomas including Burkitt lymphoma, follicular lymphoma, DLBCL, and HGBCL-DH-BCL2 tumors. We demonstrate that, although BCL2 rearrangement topology is consistent across entities, HGBCL-DH-BCL2 have distinct MYC rearrangement architecture relative to tumors with single MYC rearrangements or with both MYC and BCL6 rearrangements (HGBCL-DH-BCL6), including both a higher frequency of non-IG rearrangements and different architecture of MYC::IGH rearrangements. The distinct MYC rearrangement patterns in HGBCL-DH-BCL2 occur on the background of high levels of somatic hypermutation across MYC partner loci in HGBCL-DH-BCL2, creating more opportunity to form these rearrangements. Furthermore, because 1 IGH allele is already disrupted by the existing BCL2 rearrangement, the MYC rearrangement architecture in HGBCL-DH-BCL2 likely reflects selective pressure to preserve both BCL2 and B-cell receptor expression. These data provide new mechanistic explanations for the distinct patterns of MYC rearrangements observed across different lymphoma entities.
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Affiliation(s)
- Laura K. Hilton
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Brett Collinge
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | | | - Waleed Alduaij
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Haya Shaalan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Manuela Cruz
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Graham W. Slack
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | | | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | | | - James R. Cook
- Department of Clinical Pathology, Cleveland Clinic, Cleveland, OH
| | | | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | | | - Elias Campo
- Hematopathology Section, Hospital Clinic of Barcelona, Institut d’Investigaciones Biomediques August Pi I Sunyer, University of Barcelona, Barcelona, Spain
| | - Catalina Amador
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL
| | - Timothy C. Greiner
- Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, NE
| | - Philipp W. Raess
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, Portland, OR
| | - Joo Y. Song
- Department of Pathology, City of Hope, Duarte, CA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Elaine S. Jaffe
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Dennis D. Weisenburger
- Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, NE
| | - Wing C. Chan
- Department of Pathology, City of Hope, Duarte, CA
| | - Klaus Beiske
- Department of Pathology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kai Fu
- Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Jan Delabie
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Javeed Iqbal
- Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, NE
| | - George Wright
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laurie H. Sehn
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Kerry J. Savage
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Andrew L. Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Louis M. Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Lisa M. Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ
| | - Ryan D. Morin
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
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20
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Bertoli RM, Chung YJ, Difilippantonio MJ, Wokasch A, Marasco MR, Klimaszewski H, Gammell S, Zhu YJ, Walker RL, Cao D, Khanna A, Walter MJ, Doroshow JH, Meltzer PS, Aplan PD. The DNA Methyltransferase Inhibitor 5-Aza-4'-thio-2'-Deoxycytidine Induces C>G Transversions and Acute Lymphoid Leukemia Development. Cancer Res 2024; 84:2518-2532. [PMID: 38832931 PMCID: PMC11293964 DOI: 10.1158/0008-5472.can-23-2785] [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: 09/12/2023] [Revised: 03/04/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
DNA methyltransferase inhibitors (DNMTi), most commonly cytidine analogs, are compounds that decrease 5'-cytosine methylation. DNMTi are used clinically based on the hypothesis that cytosine demethylation will lead to re-expression of tumor suppressor genes. 5-Aza-4'-thio-2'-deoxycytidine (Aza-TdCyd or ATC) is a recently described thiol-substituted DNMTi that has been shown to have anti-tumor activity in solid tumor models. In this study, we investigated the therapeutic potential of ATC in a murine transplantation model of myelodysplastic syndrome. ATC treatment led to the transformation of transplanted wild-type bone marrow nucleated cells into lymphoid leukemia, and healthy mice treated with ATC also developed lymphoid leukemia. Whole-exome sequencing revealed 1,000 acquired mutations, almost all of which were C>G transversions in a specific 5'-NCG-3' context. These mutations involved dozens of genes involved in human lymphoid leukemia, such as Notch1, Pten, Pax5, Trp53, and Nf1. Human cells treated in vitro with ATC showed 1,000 acquired C>G transversions in a similar context. Deletion of Dck, the rate-limiting enzyme for the cytidine salvage pathway, eliminated C>G transversions. Taken together, these findings demonstrate a highly penetrant mutagenic and leukemogenic phenotype associated with ATC. Significance: Treatment with a DNA methyltransferase inhibitor generates a distinct mutation signature and triggers leukemic transformation, which has important implications for the research and clinical applications of these inhibitors.
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Affiliation(s)
- Ryan M. Bertoli
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yang Jo Chung
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Michael J. Difilippantonio
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Anthony Wokasch
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Madison R.B. Marasco
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Haley Klimaszewski
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Susannah Gammell
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yuelin J. Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Robert L. Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Dengchao Cao
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ajay Khanna
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Matthew J. Walter
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Peter D. Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
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21
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Lee D, Hua M, Wang D, Song L, Zhang T, Hua X, Yu K, Yang XR, Chanock SJ, Shi J, Landi MT, Zhu B. Pan-cancer mutational signature analysis of 111,711 targeted sequenced tumors using SATS. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.05.18.23290188. [PMID: 37425683 PMCID: PMC10327246 DOI: 10.1101/2023.05.18.23290188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Tumor mutational signatures are informative for cancer diagnosis and treatment. However, targeted sequencing, commonly used in clinical settings, lacks specialized analytical tools and a dedicated catalogue of mutational signatures. Here, we introduce SATS, a scalable mutational signature analyzer for targeted sequencing data. SATS leverages tumor mutational burdens to identify and quantify signatures in individual tumors, overcoming the challenges of sparse mutations and variable gene panels. Validations across simulated data, pseudo-targeted sequencing data, and matched whole-genome and targeted sequencing samples show that SATS can accurately detect common mutational signatures and estimate their burdens. Applying SATS to 111,711 tumors from the AACR Project GENIE, we created a pan-cancer mutational signature catalogue specific to targeted sequencing. We further validated signatures in lung, breast and colorectal cancers using an additional 16,774 independent samples. This signature catalogue is a valuable resource for estimating signature burdens in individual targeted sequenced tumors, facilitating the integration of mutational signatures with clinical data.
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22
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Schuster DM, LeBlanc DPM, Zhou G, Meier MJ, Dodge AE, White PA, Long AS, Williams A, Hobbs C, Diesing A, Smith-Roe SL, Salk JJ, Marchetti F, Yauk CL. Dose-related Mutagenic and Clastogenic Effects of Benzo[b]fluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605228. [PMID: 39211269 PMCID: PMC11360995 DOI: 10.1101/2024.07.26.605228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are common environmental pollutants that originate from the incomplete combustion of organic materials. We investigated the clastogenicity and mutagenicity of benzo[ b ]fluoranthene (BbF), one of 16 priority PAHs, in MutaMouse males after a 28-day oral exposure. BbF causes robust dose-dependent increases in micronucleus frequency in peripheral blood, indicative of chromosome damage. Duplex Sequencing (DS), an error-corrected sequencing technology, reveals that BbF induces dose-dependent increases in mutation frequencies in bone marrow (BM) and liver. Mutagenicity is increased in intergenic relative to genic regions, suggesting a role for transcription-coupled repair of BbF-induced DNA damage. At higher doses, the maximum mutagenic response to BbF is higher in liver, which has a lower mitotic index but higher metabolic capacity than BM; however, mutagenic potency is comparable between the two tissues. BbF induces primarily C:G>A:T mutations, followed by C:G>T:A and C:G>G:C, indicating that BbF metabolites mainly target guanines and cytosines. The mutation spectrum of BbF correlates with cancer mutational signatures associated with tobacco exposure, supporting its contribution to the carcinogenicity of combustion-derived PAHs in humans. Overall, BbF's mutagenic effects are similar to benzo[ a ]pyrene, a well-studied mutagenic PAH. Our work showcases the utility of DS for effective mutagenicity assessment of environmental pollutants. Synopsis We used Duplex Sequencing to study the mutagenicity of benzo[ b ]fluoranthene across the mouse genome. Dose-dependent changes in mutation frequency and spectrum quantify its role in PAH-induced carcinogenicity.
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23
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Tandukar B, Deivendran D, Chen L, Cruz-Pacheco N, Sharma H, Xu A, Bandari AK, Chen DB, George C, Marty A, Cho RJ, Cheng J, Saylor D, Gerami P, Arron ST, Bastian BC, Shain AH. Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604673. [PMID: 39091884 PMCID: PMC11291049 DOI: 10.1101/2024.07.23.604673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic keratoses, and squamous cell carcinomas to understand the molecular transitions during skin carcinogenesis. Single-cell mutational analyses showed that most keratinocytes in normal skin had lower mutation burdens than melanocytes and fibroblasts, however keratinocytes with TP53 or NOTCH1 mutations had substantially higher mutation burdens, suggesting that these mutations prime keratinocytes for transformation by increasing their mutation rate. Mutational profiling and spatial transcriptomics on squamous cell carcinomas adjacent to actinic keratoses revealed TERT promoter and CDKN2A mutations emerging in actinic keratoses, whereas additional mutations inactivating ARID2 and activating the MAPK-pathway delineated the transition to squamous cell carcinomas. Spatial variation in gene expression patterns was common in both tumor and immune cells, with high expression of checkpoint molecules at the invasive front of tumors. In conclusion, this study documents key events during the evolution of cutaneous squamous cell carcinoma.
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Affiliation(s)
- Bishal Tandukar
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Limin Chen
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Harsh Sharma
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Albert Xu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Aravind K. Bandari
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Daniel B. Chen
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Christopher George
- Department of Dermatology, Erasmus MC, Rotterdam, Netherlands
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Dermatology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Annika Marty
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Raymond J. Cho
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey Cheng
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Drew Saylor
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Boris C. Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - A. Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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24
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Xiang H, Luo R, Wang Y, Yang B, Xu S, Huang W, Tang S, Fang R, Chen L, Zhu N, Yu Z, Akesu S, Wei C, Xu C, Zhou Y, Gu J, Zhao J, Hou Y, Ding C. Proteogenomic insights into the biology and treatment of pan-melanoma. Cell Discov 2024; 10:78. [PMID: 39039072 PMCID: PMC11263678 DOI: 10.1038/s41421-024-00688-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/03/2024] [Indexed: 07/24/2024] Open
Abstract
Melanoma is one of the most prevalent skin cancers, with high metastatic rates and poor prognosis. Understanding its molecular pathogenesis is crucial for improving its diagnosis and treatment. Integrated analysis of multi-omics data from 207 treatment-naïve melanomas (primary-cutaneous-melanomas (CM, n = 28), primary-acral-melanomas (AM, n = 81), primary-mucosal-melanomas (MM, n = 28), metastatic-melanomas (n = 27), and nevi (n = 43)) provides insights into melanoma biology. Multivariate analysis reveals that PRKDC amplification is a prognostic molecule for melanomas. Further proteogenomic analysis combined with functional experiments reveals that the cis-effect of PRKDC amplification may lead to tumor proliferation through the activation of DNA repair and folate metabolism pathways. Proteome-based stratification of primary melanomas defines three prognosis-related subtypes, namely, the ECM subtype, angiogenesis subtype (with a high metastasis rate), and cell proliferation subtype, which provides an essential framework for the utilization of specific targeted therapies for particular melanoma subtypes. The immune classification identifies three immune subtypes. Further analysis combined with an independent anti-PD-1 treatment cohort reveals that upregulation of the MAPK7-NFKB signaling pathway may facilitate T-cell recruitment and increase the sensitivity of patients to immunotherapy. In contrast, PRKDC may reduce the sensitivity of melanoma patients to immunotherapy by promoting DNA repair in melanoma cells. These results emphasize the clinical value of multi-omics data and have the potential to improve the understanding of melanoma treatment.
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Affiliation(s)
- Hang Xiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sha Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wen Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shaoshuai Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Na Zhu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujie Akesu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuanyuan Wei
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jianying Gu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai, China.
| | - Jianyuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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25
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Culliford R, Lawrence SED, Mills C, Tippu Z, Chubb D, Cornish AJ, Browning L, Kinnersley B, Bentham R, Sud A, Pallikonda H, Frangou A, Gruber AJ, Litchfield K, Wedge D, Larkin J, Turajlic S, Houlston RS. Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma. Nat Commun 2024; 15:5935. [PMID: 39009593 PMCID: PMC11250826 DOI: 10.1038/s41467-024-49692-1] [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: 11/28/2023] [Accepted: 06/17/2024] [Indexed: 07/17/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a comprehensive description of its genomic landscape is lacking. We report the whole genome sequencing of 778 ccRCC patients enrolled in the 100,000 Genomes Project, providing for a detailed description of the somatic mutational landscape of ccRCC. We identify candidate driver genes, which as well as emphasising the major role of epigenetic regulation in ccRCC highlight additional biological pathways extending opportunities for therapeutic interventions. Genomic characterisation identified patients with divergent clinical outcome; higher number of structural copy number alterations associated with poorer prognosis, whereas VHL mutations were independently associated with a better prognosis. The observations that higher T-cell infiltration is associated with better overall survival and that genetically predicted immune evasion is not common supports the rationale for immunotherapy. These findings should inform personalised surveillance and treatment strategies for ccRCC patients.
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Affiliation(s)
- Richard Culliford
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Samuel E D Lawrence
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Zayd Tippu
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Oncology, University College London Cancer Institute, London, UK
| | - Robert Bentham
- Department of Oncology, University College London Cancer Institute, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Husayn Pallikonda
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Anna Frangou
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
- Algebraic Systems Biology, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Algebraic Systems Biology, Centre for Systems Biology Dresden, Dresden, Germany
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - David Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
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26
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Hinić S, van der Post RS, Vreede L, Schuurs-Hoeijmakers J, Koene S, Jansen EAM, Bervoets-Metge F, Mensenkamp AR, Hoogerbrugge N, Ligtenberg MJL, de Voer RM. The genomic landscape of breast and non-breast cancers from individuals with germline CHEK2 deficiency. JNCI Cancer Spectr 2024; 8:pkae044. [PMID: 38848470 PMCID: PMC11216722 DOI: 10.1093/jncics/pkae044] [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: 02/01/2024] [Revised: 03/20/2024] [Accepted: 04/11/2024] [Indexed: 06/09/2024] Open
Abstract
CHEK2 is considered to be involved in homologous recombination repair (HRR). Individuals who have germline pathogenic variants (gPVs) in CHEK2 are at increased risk to develop breast cancer and likely other primary cancers. PARP inhibitors (PARPi) have been shown to be effective in the treatment of cancers that present with HRR deficiency-for example, caused by inactivation of BRCA1/2. However, clinical trials have shown little to no efficacy of PARPi in patients with CHEK2 gPVs. Here, we show that both breast and non-breast cancers from individuals who have biallelic gPVs in CHEK2 (germline CHEK2 deficiency) do not present with molecular profiles that fit with HRR deficiency. This finding provides a likely explanation why PARPi therapy is not successful in the treatment of CHEK2-deficient cancers.
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Affiliation(s)
- Snežana Hinić
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Lilian Vreede
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Janneke Schuurs-Hoeijmakers
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Saskia Koene
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Franziska Bervoets-Metge
- Department of Pathology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
- Department of Pathology, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Research Institute for Medical Innovation, Nijmegen, The Netherlands
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27
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Hodder A, Leiter SM, Kennedy J, Addy D, Ahmed M, Ajithkumar T, Allinson K, Ancliff P, Bailey S, Barnard G, Burke GAA, Burns C, Cano-Flanagan J, Chalker J, Coleman N, Cheng D, Clinch Y, Dryden C, Ghorashian S, Griffin B, Horan G, Hubank M, May P, McDerra J, Nagrecha R, Nicholson J, O'Connor D, Pavasovic V, Quaegebeur A, Rao A, Roberts T, Samarasinghe S, Stasevich I, Tadross JA, Trayers C, Trotman J, Vora A, Watkins J, Chitty LS, Bowdin S, Armstrong R, Murray MJ, Hook CE, Tarpey P, Vedi A, Bartram J, Behjati S. Benefits for children with suspected cancer from routine whole-genome sequencing. Nat Med 2024; 30:1905-1912. [PMID: 38956197 PMCID: PMC11271414 DOI: 10.1038/s41591-024-03056-w] [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: 11/20/2023] [Accepted: 05/08/2024] [Indexed: 07/04/2024]
Abstract
Clinical whole-genome sequencing (WGS) has been shown to deliver potential benefits to children with cancer and to alter treatment in high-risk patient groups. It remains unknown whether offering WGS to every child with suspected cancer can change patient management. We collected WGS variant calls and clinical and diagnostic information from 281 children (282 tumors) across two English units (n = 152 from a hematology center, n = 130 from a solid tumor center) where WGS had become a routine test. Our key finding was that variants uniquely attributable to WGS changed the management in ~7% (20 out of 282) of cases while providing additional disease-relevant findings, beyond standard-of-care molecular tests, in 108 instances for 83 (29%) cases. Furthermore, WGS faithfully reproduced every standard-of-care molecular test (n = 738) and revealed several previously unknown genomic features of childhood tumors. We show that WGS can be delivered as part of routine clinical care to children with suspected cancer and can change clinical management by delivering unexpected genomic insights. Our experience portrays WGS as a clinically impactful assay for routine practice, providing opportunities for assay consolidation and for delivery of molecularly informed patient care.
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Affiliation(s)
- Angus Hodder
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sarah M Leiter
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Jonathan Kennedy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Dilys Addy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Munaza Ahmed
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Kieren Allinson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Phil Ancliff
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Shivani Bailey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gemma Barnard
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - G A Amos Burke
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Charlotte Burns
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Danny Cheng
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Caryl Dryden
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sara Ghorashian
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Blanche Griffin
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
| | - Gail Horan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michael Hubank
- North Thames Genomic Laboratory Hub, London, UK
- The Institute of Cancer Research, London, UK
| | - Phillippa May
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Joanna McDerra
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Rajvi Nagrecha
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David O'Connor
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Vesna Pavasovic
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Annelies Quaegebeur
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anupama Rao
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Thomas Roberts
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | | | - Iryna Stasevich
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - John A Tadross
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Claire Trayers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jamie Trotman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ajay Vora
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Watkins
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Lyn S Chitty
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah Bowdin
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ruth Armstrong
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Catherine E Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Patrick Tarpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- East Genomics Laboratory Hub, Cambridge, UK.
| | - Aditi Vedi
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | - Jack Bartram
- Great Ormond Street Hospital NHS Foundation Trust, London, UK.
- North Thames Genomic Laboratory Hub, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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Hayes V, Jiang J, Tapinos A, Huang R, Bornman R, Stricker P, Mutambirwa S, Wedge D, Jaratlerdsiri W. Kataegis associated mutational processes linked to adverse prostate cancer presentation in African men. RESEARCH SQUARE 2024:rs.3.rs-4597464. [PMID: 38978580 PMCID: PMC11230510 DOI: 10.21203/rs.3.rs-4597464/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Kataegis, the focal hypermutation of single base substitutions (SBS) in tumour genomes, has received little attention with respect to prostate cancer (PCa) associated molecular and clinical features. Most notably, data is lacking with regards to this tumour evolutionary phenomenon and PCa racial disparities, with African men disproportionately impacted. Here through comparison between African (n = 109) and non-African (n = 79) whole genome sequenced treatment naïve primary tumours, using a single analytical workflow we assessed for shared and unique features of kataegis. Linking kataegis to aggressive presentation, structural variant burden and copy number loss, we attributed APOBEC3 activity through higher rates of SBS2 to high-risk African tumours. While kataegis positive African patients presented with elevated prostate specific antigen levels, their tumours showed evolutionary unique trajectories marked by increased subclonal and structural variant-independent kataegis. The potential to exacerbate tumour heterogeneity emphases the significance of continued exploration of biological behaviours and environmental exposures for African patients.
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Affiliation(s)
| | - Jue Jiang
- Garvan Institute of Medical Research
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29
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Korenjak M, Temiz NA, Keita S, Chavanel B, Renard C, Sirand C, Cahais V, Mayel T, Vevang KR, Jacobs FC, Guo J, Smith WE, Oram MK, Tăbăran FA, Ahlat O, Cornax I, O'Sullivan MG, Das S, Nandi SP, Cheng Y, Alexandrov LB, Balbo S, Hecht SS, Senkin S, Virard F, Peterson LA, Zavadil J. Human cancer genomes harbor the mutational signature of tobacco-specific nitrosamines NNN and NNK. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.600253. [PMID: 38979250 PMCID: PMC11230374 DOI: 10.1101/2024.06.28.600253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Tobacco usage is linked to multiple cancer types and accounts for a quarter of all cancer-related deaths. Tobacco smoke contains various carcinogenic compounds, including polycyclic aromatic hydrocarbons (PAH), though the mutagenic potential of many tobacco-related chemicals remains largely unexplored. In particular, the highly carcinogenic tobacco-specific nitrosamines NNN and NNK form pre-mutagenic pyridyloxobutyl (POB) DNA adducts. In the study presented here, we identified genome-scale POB-induced mutational signatures in cell lines and rat tumors, while also investigating their role in human cancer. These signatures are characterized by T>N and C>T mutations forming from specific POB adducts damaging dT and dC residues. Analysis of 2,780 cancer genomes uncovered POB signatures in ∼180 tumors; from cancer types distinct from the ones linked to smoking-related signatures SBS4 and SBS92. This suggests that, unlike PAH compounds, the POB pathway may contribute uniquely to the mutational landscapes of certain hematological malignancies and cancers of the kidney, breast, prostate and pancreas.
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30
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Gerami P, Tandukar B, Deivendran D, Olivares S, Chen L, Tang J, Tan T, Sharma H, Bandari AK, Cruz-Pacheco N, Chang D, Marty A, Olshen A, Murad NF, Song J, Lee J, Yeh I, Hunter Shain A. Molecular effects of indoor tanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597225. [PMID: 38895302 PMCID: PMC11185634 DOI: 10.1101/2024.06.04.597225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background Tanning bed users have a significantly increased risk of melanoma, but it remains unclear how indoor tanning drives melanomagenesis. Tanning bed radiation is often thought of as a substitute for natural UV radiation despite differences in the maximum doses, UV content, body sites exposed, and patterns of melanoma that arise. Methods To better understand the epidemiologic trends and etiology of melanoma associated with tanning bed use, we described the patterns of melanoma in patients with quantifiable tanning bed usage and performed exome sequencing of 182 melanocytes from normal skin of a subset of these patients. Results Tanning bed users were more likely than non-users to have melanoma on body sites with low cumulative levels of sun damage and were more likely to have multiple melanomas. The melanocytes in normal appearing skin from tanning bed users had higher mutation burdens, a higher proportion of melanocytes with pathogenic mutations, and distinct mutational signatures. These differences were most prominent over body sites that experience comparatively less exposure to natural sunlight. Conclusions We conclude that tanning bed radiation induces melanoma by increasing the mutation burden of melanocytes and by mutagenizing a broader field of melanocytes than are typically exposed to natural sunlight. The unique signatures of mutations in skin cells of tanning users may be attributable to the distinct spectra of radiation emitted from solariums.
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Affiliation(s)
- Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bishal Tandukar
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Shantel Olivares
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Limin Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jessica Tang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Tuyet Tan
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Harsh Sharma
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Aravind K Bandari
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Darwin Chang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Annika Marty
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Adam Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Natalia Faraj Murad
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jing Song
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jungwha Lee
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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Sun L, Guo W, Guo L, Chen X, Zhou H, Yan S, Zhao G, Bao H, Wu X, Shao Y, Ying J, Lin L. Molecular landscape and multi-omic measurements of heterogeneity in fetal adenocarcinoma of the lung. NPJ Precis Oncol 2024; 8:99. [PMID: 38831114 PMCID: PMC11148097 DOI: 10.1038/s41698-024-00569-y] [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: 08/22/2023] [Accepted: 02/26/2024] [Indexed: 06/05/2024] Open
Abstract
Fetal adenocarcinoma of the lung (FLAC) is a rare form of lung adenocarcinoma and was divided into high-grade (H-FLAC) and low-grade (L-FLAC) subtypes. Despite the existence of some small case series studies, a comprehensive multi-omics study of FLAC has yet to be undertaken. In this study, we depicted the multi-omics landscapes of this rare lung cancer type by performing multi-regional sampling on 20 FLAC cases. A comparison of multi-omics profiles revealed significant differences between H-FLAC and L-FLAC in a multi-omic landscape. Two subtypes also showed distinct relationships between multi-layer intratumor heterogeneity (ITH). We discovered that a lower genetic ITH was significantly associated with worse recurrence-free survival and overall survival in FLAC patients, whereas higher methylation ITH in H-FLAC patients suggested a short survival. Our findings highlight the complex interplay between genetic and transcriptional heterogeneity in FLAC and suggest that different types of ITH may have distinct implications for patient prognosis.
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Affiliation(s)
- Li Sun
- 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, People's Republic of China
| | - Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
- Key Laboratory of Minimally Invasive Therapy Research for Lung Cancer, Chinese Academy of Medical Sciences, Beijing, China.
| | - Lei Guo
- 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, People's Republic of China
| | - Xiaoxi Chen
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Haitao Zhou
- Department of Thoracic Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Shi Yan
- Department of Thoracic Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Gang Zhao
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Yang Shao
- Geneseeq Research Institute, 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, People's Republic of China.
| | - Lin Lin
- 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, People's Republic of China.
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32
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Min Q, Zhang M, Lin D, Zhang W, Li X, Zhao L, Teng H, He T, Sun W, Fan J, Yu X, Chen J, Li J, Gao X, Dong B, Liu R, Liu X, Song Y, Cui Y, Lu SH, Li R, Guo M, Wang Y, Zhan Q. Genomic characterization and risk stratification of esophageal squamous dysplasia. MEDICAL REVIEW (2021) 2024; 4:244-256. [PMID: 38919397 PMCID: PMC11195426 DOI: 10.1515/mr-2024-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Objectives The majority of esophageal squamous dysplasia (ESD) patients progress slowly, while a subset of patients can undergo recurrence rapidly or progress to invasive cancer even after proper treatment. However, the molecular mechanisms underlying these clinical observations are still largely unknown. Methods By sequencing the genomic data of 160 clinical samples from 49 tumor-free ESD patients and 88 esophageal squamous cell carcinoma (ESCC) patients, we demonstrated lower somatic mutation and copy number alteration (CNA) burden in ESD compared with ESCC. Results Cross-species screening and functional assays identified ACSM5 as a novel driver gene for ESD progression. Furthermore, we revealed that miR-4292 promoted ESD progression and could serve as a non-invasive diagnostic marker for ESD. Conclusions These findings largely expanded our understanding of ESD genetics and tumorigenesis, which possessed promising significance for improving early diagnosis, reducing overtreatment, and identifying high-risk ESD patients.
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Affiliation(s)
- Qingjie Min
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | | | - Dongmei Lin
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xianfeng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Department of Gastroenterology, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lianmei Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Tao He
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
- Department of Pathology, Characteristic Medical Center of Chinese People’s Armed Police Force, Tianjin, China
| | - Wei Sun
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiawen Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiying Yu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jinting Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaohan Gao
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Dong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Central Laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Rui Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xuefeng Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongping Cui
- Shenzhen Peking University-The Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Shih-Hsin Lu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Peking University International Cancer Institute, Peking University, Beijing, China
- Soochow University Cancer Institute, Suzhou, China
- State Key Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
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Mills C, Sud A, Everall A, Chubb D, Lawrence SED, Kinnersley B, Cornish AJ, Bentham R, Houlston RS. Genetic landscape of interval and screen detected breast cancer. NPJ Precis Oncol 2024; 8:122. [PMID: 38806682 PMCID: PMC11133314 DOI: 10.1038/s41698-024-00618-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
Interval breast cancers (IBCs) are cancers diagnosed between screening episodes. Understanding the biological differences between IBCs and screen-detected breast-cancers (SDBCs) has the potential to improve mammographic screening and patient management. We analysed and compared the genomic landscape of 288 IBCs and 473 SDBCs by whole genome sequencing of paired tumour-normal patient samples collected as part of the UK 100,000 Genomes Project. Compared to SDBCs, IBCs were more likely to be lobular, higher grade, and triple negative. A more aggressive clinical phenotype was reflected in IBCs displaying features of genomic instability including a higher mutation rate and number of chromosomal structural abnormalities, defective homologous recombination and TP53 mutations. We did not however, find evidence to indicate that IBCs are associated with a significantly different immune response. While IBCs do not represent a unique molecular class of invasive breast cancer they exhibit a more aggressive phenotype, which is likely to be a consequence of the timing of tumour initiation. This information is relevant both with respect to treatment as well as informing the screening interval for mammography.
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Affiliation(s)
- Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre of Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Everall
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Samuel E D Lawrence
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- University College London Cancer Institute, University College London, London, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Robert Bentham
- University College London Cancer Institute, University College London, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK.
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34
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Gallon R, Brekelmans C, Martin M, Bours V, Schamschula E, Amberger A, Muleris M, Colas C, Dekervel J, De Hertogh G, Coupier J, Colleye O, Sepulchre E, Burn J, Brems H, Legius E, Wimmer K. Constitutional mismatch repair deficiency mimicking Lynch syndrome is associated with hypomorphic mismatch repair gene variants. NPJ Precis Oncol 2024; 8:119. [PMID: 38789506 PMCID: PMC11126593 DOI: 10.1038/s41698-024-00603-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Lynch syndrome (LS) and constitutional mismatch repair deficiency (CMMRD) are distinct cancer syndromes caused, respectively, by mono- and bi-allelic germline mismatch repair (MMR) variants. LS predisposes to mainly gastrointestinal and genitourinary cancers in adulthood. CMMRD predisposes to brain, haematological, and LS-spectrum cancers from childhood. Two suspected LS patients with first cancer diagnosis aged 27 or 38 years were found to be homozygous for an MMR (likely) pathogenic variant, MSH6 c.3226C>T (p.(Arg1076Cys)), or variant of uncertain significance (VUS), MLH1 c.306G>A (p.(Glu102=)). MLH1 c.306G>A was shown to cause leaky exon 3 skipping. The apparent genotype-phenotype conflict was resolved by detection of constitutional microsatellite instability in both patients, a hallmark feature of CMMRD. A hypomorphic effect of these and other variants found in additional late onset CMMRD cases, identified by literature review, likely explains a LS-like phenotype. CMMRD testing in carriers of compound heterozygous or homozygous MMR VUS may find similar cases and novel hypomorphic variants. Individualised management of mono- and bi-allelic carriers of hypomorphic MMR variants is needed until we better characterise the associated phenotypes.
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Affiliation(s)
- Richard Gallon
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | | | | | | | - Esther Schamschula
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Albert Amberger
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Martine Muleris
- Département de Génétique, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMRS_938, Sorbonne Université, Centre de Recherche Saint Antoine, Paris, France
| | - Chrystelle Colas
- Département de Génétique, Institut Curie, Paris, France
- INSERM U830, Université de Paris, Paris, France
| | - Jeroen Dekervel
- Department of Digestive Oncology, University Hospital Leuven, Leuven, Belgium
| | - Gert De Hertogh
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | | | | | | | - John Burn
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hilde Brems
- Centre for Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - Katharina Wimmer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.
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35
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Uryu H, Saeki K, Haeno H, Kapadia CD, Furudate K, Nangalia J, Chapman MS, Zhao L, Hsu JI, Zhao C, Chen S, Tanaka T, Li Z, Yang H, DiNardo C, Daver N, Pemmaraju N, Jain N, Ravandi F, Zhang J, Song X, Thompson E, Tang H, Little L, Gumbs C, Orlowski RZ, Qazilbash M, Bhalla K, Colla S, Kantarjian H, Shamanna RK, Ramos CB, Nakada D, Futreal PA, Shpall E, Goodell M, Garcia-Manero G, Takahashi K. Clonal evolution of hematopoietic stem cells after cancer chemotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595594. [PMID: 38826462 PMCID: PMC11142159 DOI: 10.1101/2024.05.23.595594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Normal hematopoietic stem and progenitor cells (HSPCs) inherently accumulate somatic mutations and lose clonal diversity with age, processes implicated in the development of myeloid malignancies 1 . The impact of exogenous stressors, such as cancer chemotherapies, on the genomic integrity and clonal dynamics of normal HSPCs is not well defined. We conducted whole-genome sequencing on 1,032 single-cell-derived HSPC colonies from 10 patients with multiple myeloma (MM), who had undergone various chemotherapy regimens. Our findings reveal that melphalan treatment distinctly increases mutational burden with a unique mutation signature, whereas other MM chemotherapies do not significantly affect the normal mutation rate of HSPCs. Among these therapy-induced mutations were several oncogenic drivers such as TET2 and PPM1D . Phylogenetic analysis showed a clonal architecture in post-treatment HSPCs characterized by extensive convergent evolution of mutations in genes such as TP53 and PPM1D . Consequently, the clonal diversity and structure of post-treatment HSPCs mirror those observed in normal elderly individuals, suggesting an accelerated clonal aging due to chemotherapy. Furthermore, analysis of matched therapy-related myeloid neoplasm (t-MN) samples, which occurred 1-8 years later, enabled us to trace the clonal origin of t-MNs to a single HSPC clone among a group of clones with competing malignant potential, indicating the critical role of secondary mutations in dictating clonal dominance and malignant transformation. Our findings suggest that cancer chemotherapy promotes an oligoclonal architecture with multiple HSPC clones possessing competing leukemic potentials, setting the stage for the selective emergence of a singular clone that evolves into t-MNs after acquiring secondary mutations. These results underscore the importance of further systematic research to elucidate the long-term hematological consequences of cancer chemotherapy.
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Battuello P, Corti G, Bartolini A, Lorenzato A, Sogari A, Russo M, Di Nicolantonio F, Bardelli A, Crisafulli G. Mutational signatures of colorectal cancers according to distinct computational workflows. Brief Bioinform 2024; 25:bbae249. [PMID: 38783705 PMCID: PMC11116831 DOI: 10.1093/bib/bbae249] [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: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.
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Affiliation(s)
- Paolo Battuello
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giorgio Corti
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
| | - Alberto Sogari
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giovanni Crisafulli
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
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Díaz-Gay M, Zhang T, Hoang PH, Khandekar A, Zhao W, Steele CD, Otlu B, Nandi SP, Vangara R, Bergstrom EN, Kazachkova M, Pich O, Swanton C, Hsiung CA, Chang IS, Wong MP, Leung KC, Sang J, McElderry J, Yang L, Nowak MA, Shi J, Rothman N, Wedge DC, Homer R, Yang SR, Lan Q, Zhu B, Chanock SJ, Alexandrov LB, Landi MT. The mutagenic forces shaping the genomic landscape of lung cancer in never smokers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307318. [PMID: 38798417 PMCID: PMC11118654 DOI: 10.1101/2024.05.15.24307318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Lung cancer in never smokers (LCINS) accounts for up to 25% of all lung cancers and has been associated with exposure to secondhand tobacco smoke and air pollution in observational studies. Here, we evaluate the mutagenic exposures in LCINS by examining deep whole-genome sequencing data from a large international cohort of 871 treatment-naïve LCINS recruited from 28 geographical locations within the Sherlock-Lung study. KRAS mutations were 3.8-fold more common in adenocarcinomas of never smokers from North America and Europe, while a 1.6-fold higher prevalence of EGFR and TP53 mutations was observed in adenocarcinomas from East Asia. Signature SBS40a, with unknown cause, was found in most samples and accounted for the largest proportion of single base substitutions in adenocarcinomas, being enriched in EGFR-mutated cases. Conversely, the aristolochic acid signature SBS22a was almost exclusively observed in patients from Taipei. Even though LCINS exposed to secondhand smoke had an 8.3% higher mutational burden and 5.4% shorter telomeres, passive smoking was not associated with driver mutations in cancer driver genes or the activities of individual mutational signatures. In contrast, patients from regions with high levels of air pollution were more likely to have TP53 mutations while exhibiting shorter telomeres and an increase in most types of somatic mutations, including a 3.9-fold elevation of signature SBS4 (q-value=3.1 × 10-5), previously linked mainly to tobacco smoking, and a 76% increase of clock-like signature SBS5 (q-value=5.0 × 10-5). A positive dose-response effect was observed with air pollution levels, which correlated with both a decrease in telomere length and an elevation in somatic mutations, notably attributed to signatures SBS4 and SBS5. Our results elucidate the diversity of mutational processes shaping the genomic landscape of lung cancer in never smokers.
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Affiliation(s)
- Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher D. Steele
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Shuvro P. Nandi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Mariya Kazachkova
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Maria Pik Wong
- Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Kin Chung Leung
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, Department of Human Genetics, Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - Martin A Nowak
- Department of Mathematics, Harvard University, Cambridge, MA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
- Manchester NIHR Biomedical Research Centre, Manchester, UK
| | - Robert Homer
- Yale Surgery Pathology Department, Yale University, New Haven, CT, USA
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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Sipilä LJ, Katainen R, Aavikko M, Ravantti J, Donner I, Lehtonen R, Leivo I, Wolff H, Holmila R, Husgafvel-Pursiainen K, Aaltonen LA. Genome-wide somatic mutation analysis of sinonasal adenocarcinoma with and without wood dust exposure. Genes Environ 2024; 46:12. [PMID: 38711096 PMCID: PMC11071320 DOI: 10.1186/s41021-024-00306-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Sinonasal adenocarcinoma is a rare cancer, encompassing two different entities, the intestinal-type sinonasal adenocarcinoma (ITAC) and the non-intestinal-type sinonasal adenocarcinoma (non-ITAC). Occurrence of ITAC is strongly associated with exposure to hardwood dusts. In countries with predominant exposure to softwood dust the occurrence of sinonasal adenocarcinomas is lower and the relative amount of non-ITACs to ITACs is higher. The molecular mechanisms behind the tumorigenic effects of wood dust remain largely unknown. METHODS We carried out whole-genome sequencing of formalin-fixed paraffin-embedded (FFPE) samples of sinonasal adenocarcinomas from ten wood dust-exposed and six non-exposed individuals, with partial tobacco exposure data. Sequences were analyzed for the presence of mutational signatures matching COSMIC database signatures. Driver mutations and CN variant regions were characterized. RESULTS Mutation burden was higher in samples of wood dust-exposed patients (p = 0.016). Reactive oxygen species (ROS) damage-related mutational signatures were almost exclusively identified in ITAC subtype samples (p = 0.00055). Tobacco smoke mutational signatures were observed in samples of patients with tobacco exposure or missing information, but not in samples from non-exposed patients. A tetraploidy copy number (CN) signature was enriched in ITAC subtype (p = 0.042). CN variation included recurrent gains in COSMIC Cancer Gene Census genes TERT, SDHA, RAC1, ETV1, PCM1, and MYC. Pathogenic variants were observed most frequently in TP53, NF1, CHD2, BRAF, APC, and LRP1B. Driver mutations and copy number gains did not segregate by subtype. CONCLUSIONS Our analysis identified distinct mutational characteristics in ITAC and non-ITAC. Mutational signature analysis may eventually become useful for documentation of occupation-related cancer, while the exact mechanisms behind wood dust-driven carcinogenesis remain elusive. The presence of homologous recombination deficiency signatures implies a novel opportunity for treatment, but further studies are needed.
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Affiliation(s)
- Lauri J Sipilä
- Department of Medical and Clinical Genetics, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Finnish Cancer Registry, Unioninkatu 22, Helsinki, 00130, Finland
| | - Riku Katainen
- Department of Medical and Clinical Genetics, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mervi Aavikko
- Department of Medical and Clinical Genetics, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Janne Ravantti
- Department of Medical and Clinical Genetics, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Iikki Donner
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, 00014, Finland
| | - Rainer Lehtonen
- Department of Medical and Clinical Genetics, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland
| | - Ilmo Leivo
- Institute of Biomedicine, Pathology, University of Turku, Kiinamyllynkatu 10, Turku, D 5035, 20520, Finland
- Turku University Central Hospital, Turku, 20521, Finland
| | - Henrik Wolff
- Finnish Institute of Occupational Health, PB 40, Helsinki, 00251, Finland
- Department of Pathology, University of Helsinki, PB 20, Helsinki, 00014, Finland
| | - Reetta Holmila
- Finnish Institute of Occupational Health, PB 40, Helsinki, 00251, Finland
| | | | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland.
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8), PO Box 63, Helsinki, FI-00014, Finland.
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, 00290, Finland.
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Pancotti C, Rollo C, Codicè F, Birolo G, Fariselli P, Sanavia T. MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification. Bioinformatics 2024; 40:btae320. [PMID: 38754097 PMCID: PMC11139523 DOI: 10.1093/bioinformatics/btae320] [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: 11/28/2023] [Revised: 04/08/2024] [Accepted: 05/15/2024] [Indexed: 05/18/2024] Open
Abstract
MOTIVATION Mutational signatures are a critical component in deciphering the genetic alterations that underlie cancer development and have become a valuable resource to understand the genomic changes during tumorigenesis. Therefore, it is essential to employ precise and accurate methods for their extraction to ensure that the underlying patterns are reliably identified and can be effectively utilized in new strategies for diagnosis, prognosis, and treatment of cancer patients. RESULTS We present MUSE-XAE, a novel method for mutational signature extraction from cancer genomes using an explainable autoencoder. Our approach employs a hybrid architecture consisting of a nonlinear encoder that can capture nonlinear interactions among features, and a linear decoder which ensures the interpretability of the active signatures. We evaluated and compared MUSE-XAE with other available tools on both synthetic and real cancer datasets and demonstrated that it achieves superior performance in terms of precision and sensitivity in recovering mutational signature profiles. MUSE-XAE extracts highly discriminative mutational signature profiles by enhancing the classification of primary tumour types and subtypes in real world settings. This approach could facilitate further research in this area, with neural networks playing a critical role in advancing our understanding of cancer genomics. AVAILABILITY AND IMPLEMENTATION MUSE-XAE software is freely available at https://github.com/compbiomed-unito/MUSE-XAE.
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Affiliation(s)
- Corrado Pancotti
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Cesare Rollo
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Francesco Codicè
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Giovanni Birolo
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Piero Fariselli
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Tiziana Sanavia
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
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40
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Braxton AM, Kiemen AL, Grahn MP, Forjaz A, Parksong J, Mahesh Babu J, Lai J, Zheng L, Niknafs N, Jiang L, Cheng H, Song Q, Reichel R, Graham S, Damanakis AI, Fischer CG, Mou S, Metz C, Granger J, Liu XD, Bachmann N, Zhu Y, Liu Y, Almagro-Pérez C, Jiang AC, Yoo J, Kim B, Du S, Foster E, Hsu JY, Rivera PA, Chu LC, Liu F, Fishman EK, Yuille A, Roberts NJ, Thompson ED, Scharpf RB, Cornish TC, Jiao Y, Karchin R, Hruban RH, Wu PH, Wirtz D, Wood LD. 3D genomic mapping reveals multifocality of human pancreatic precancers. Nature 2024; 629:679-687. [PMID: 38693266 DOI: 10.1038/s41586-024-07359-3] [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: 01/11/2023] [Accepted: 03/26/2024] [Indexed: 05/03/2024]
Abstract
Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study1. Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution. To elucidate genetic relationships between and within PanINs, we developed a workflow in which 3D modelling guides multi-region microdissection and targeted and whole-exome sequencing. From these samples, we calculated a mean burden of 13 PanINs per cm3 and extrapolated that the normal intact adult pancreas harbours hundreds of PanINs, almost all with oncogenic KRAS hotspot mutations. We found that most PanINs originate as independent clones with distinct somatic mutation profiles. Some spatially continuous PanINs were found to contain multiple KRAS mutations; computational and in situ analyses demonstrated that different KRAS mutations localize to distinct cell subpopulations within these neoplasms, indicating their polyclonal origins. The extensive multifocality and genetic heterogeneity of PanINs raises important questions about mechanisms that drive precancer initiation and confer differential progression risk in the human pancreas. This detailed 3D genomic mapping of molecular alterations in human PanINs provides an empirical foundation for early detection and rational interception of pancreatic cancer.
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Affiliation(s)
- Alicia M Braxton
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Ashley L Kiemen
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mia P Grahn
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - André Forjaz
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeeun Parksong
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jaanvi Mahesh Babu
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiaying Lai
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lily Zheng
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Noushin Niknafs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liping Jiang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haixia Cheng
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qianqian Song
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rebecca Reichel
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Graham
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexander I Damanakis
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Catherine G Fischer
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie Mou
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cameron Metz
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julie Granger
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiao-Ding Liu
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Niklas Bachmann
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yutong Zhu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - YunZhou Liu
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Cristina Almagro-Pérez
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Ann Chenyu Jiang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeonghyun Yoo
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Bridgette Kim
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Scott Du
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Eli Foster
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jocelyn Y Hsu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Paula Andreu Rivera
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Linda C Chu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengze Liu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elliot K Fishman
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan Yuille
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Nicholas J Roberts
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth D Thompson
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Toby C Cornish
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Institute of Cancer Research, Henan Academy of Innovations in Medical Science, Zhengzhou, China.
| | - Rachel Karchin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pei-Hsun Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Denis Wirtz
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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41
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Senkin S, Moody S, Díaz-Gay M, Abedi-Ardekani B, Cattiaux T, Ferreiro-Iglesias A, Wang J, Fitzgerald S, Kazachkova M, Vangara R, Le AP, Bergstrom EN, Khandekar A, Otlu B, Cheema S, Latimer C, Thomas E, Atkins JR, Smith-Byrne K, Cortez Cardoso Penha R, Carreira C, Chopard P, Gaborieau V, Keski-Rahkonen P, Jones D, Teague JW, Ferlicot S, Asgari M, Sangkhathat S, Attawettayanon W, Świątkowska B, Jarmalaite S, Sabaliauskaite R, Shibata T, Fukagawa A, Mates D, Jinga V, Rascu S, Mijuskovic M, Savic S, Milosavljevic S, Bartlett JMS, Albert M, Phouthavongsy L, Ashton-Prolla P, Botton MR, Silva Neto B, Bezerra SM, Curado MP, Zequi SDC, Reis RM, Faria EF, de Menezes NS, Ferrari RS, Banks RE, Vasudev NS, Zaridze D, Mukeriya A, Shangina O, Matveev V, Foretova L, Navratilova M, Holcatova I, Hornakova A, Janout V, Purdue MP, Rothman N, Chanock SJ, Ueland PM, Johansson M, McKay J, Scelo G, Chanudet E, Humphreys L, de Carvalho AC, Perdomo S, Alexandrov LB, Stratton MR, Brennan P. Geographic variation of mutagenic exposures in kidney cancer genomes. Nature 2024; 629:910-918. [PMID: 38693263 PMCID: PMC11111402 DOI: 10.1038/s41586-024-07368-2] [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: 05/04/2023] [Accepted: 03/28/2024] [Indexed: 05/03/2024]
Abstract
International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not yet been identified by conventional epidemiology make a substantial contribution to cancer burden1. In clear cell renal cell carcinoma, obesity, hypertension and tobacco smoking are risk factors, but they do not explain the geographical variation in its incidence2. Underlying causes can be inferred by sequencing the genomes of cancers from populations with different incidence rates and detecting differences in patterns of somatic mutations. Here we sequenced 962 clear cell renal cell carcinomas from 11 countries with varying incidence. The somatic mutation profiles differed between countries. In Romania, Serbia and Thailand, mutational signatures characteristic of aristolochic acid compounds were present in most cases, but these were rare elsewhere. In Japan, a mutational signature of unknown cause was found in more than 70% of cases but in less than 2% elsewhere. A further mutational signature of unknown cause was ubiquitous but exhibited higher mutation loads in countries with higher incidence rates of kidney cancer. Known signatures of tobacco smoking correlated with tobacco consumption, but no signature was associated with obesity or hypertension, suggesting that non-mutagenic mechanisms of action underlie these risk factors. The results of this study indicate the existence of multiple, geographically variable, mutagenic exposures that potentially affect tens of millions of people and illustrate the opportunities for new insights into cancer causation through large-scale global cancer genomics.
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Affiliation(s)
- Sergey Senkin
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Thomas Cattiaux
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Aida Ferreiro-Iglesias
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Stephen Fitzgerald
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Mariya Kazachkova
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Anh Phuong Le
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Saamin Cheema
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Emily Thomas
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Joshua Ronald Atkins
- Cancer Epidemiology Unit, The Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, The Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Christine Carreira
- Evidence Synthesis and Classification Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Priscilia Chopard
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Valérie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Pekka Keski-Rahkonen
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Jon W Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Sophie Ferlicot
- Service d'Anatomie Pathologique, Assistance Publique-Hôpitaux de Paris, Univeristé Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Mojgan Asgari
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Surasak Sangkhathat
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Worapat Attawettayanon
- Division of Urology, Department of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Beata Świątkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Łódź, Poland
| | - Sonata Jarmalaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania
- Department of Botany and Genetics, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Rasa Sabaliauskaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
| | - Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Dana Mates
- Occupational Health and Toxicology Department, National Center for Environmental Risk Monitoring, National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- Urology Department, Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Stefan Rascu
- Urology Department, Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Mirjana Mijuskovic
- Clinic of Nephrology, Faculty of Medicine, Military Medical Academy, Belgrade, Serbia
| | - Slavisa Savic
- Department of Urology, University Hospital Dr D. Misovic Clinical Center, Belgrade, Serbia
| | - Sasa Milosavljevic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - John M S Bartlett
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Monique Albert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Larry Phouthavongsy
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Patricia Ashton-Prolla
- Experimental Research Center, Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mariana R Botton
- Transplant Immunology and Personalized Medicine Unit, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Brasil Silva Neto
- Service of Urology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Post-Graduate Program in Medicine: Surgical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maria Paula Curado
- Department of Epidemiology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Stênio de Cássio Zequi
- Department of Urology, A. C. Camargo Cancer Center, São Paulo, Brazil
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, A.C. Camargo Cancer Center, São Paulo, Brazil
- Latin American Renal Cancer Group (LARCG), São Paulo, Brazil
- Department of Surgery, Division of Urology, Sao Paulo Federal University (UNIFESP), São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Minho University, Braga, Portugal
| | - Eliney Ferreira Faria
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil
- Department of Urology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Rosamonde E Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Naveen S Vasudev
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David Zaridze
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Anush Mukeriya
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Oxana Shangina
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Vsevolod Matveev
- Department of Urology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Oncology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Anna Hornakova
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ghislaine Scelo
- Observational and Pragmatic Research Institute Pte Ltd, Singapore, Singapore
| | - Estelle Chanudet
- Department of Pathology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Ana Carolina de Carvalho
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France.
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42
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Ganz J, Luquette LJ, Bizzotto S, Miller MB, Zhou Z, Bohrson CL, Jin H, Tran AV, Viswanadham VV, McDonough G, Brown K, Chahine Y, Chhouk B, Galor A, Park PJ, Walsh CA. Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes. Cell 2024; 187:1955-1970.e23. [PMID: 38503282 PMCID: PMC11062076 DOI: 10.1016/j.cell.2024.02.025] [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: 01/09/2023] [Revised: 12/06/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
Characterizing somatic mutations in the brain is important for disentangling the complex mechanisms of aging, yet little is known about mutational patterns in different brain cell types. Here, we performed whole-genome sequencing (WGS) of 86 single oligodendrocytes, 20 mixed glia, and 56 single neurons from neurotypical individuals spanning 0.4-104 years of age and identified >92,000 somatic single-nucleotide variants (sSNVs) and small insertions/deletions (indels). Although both cell types accumulate somatic mutations linearly with age, oligodendrocytes accumulated sSNVs 81% faster than neurons and indels 28% slower than neurons. Correlation of mutations with single-nucleus RNA profiles and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed across the genome similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These stark differences suggest an assortment of active mutagenic processes in oligodendrocytes and neurons.
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Affiliation(s)
- Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Sorbonne Université, Institut du Cerveau (Paris Brain Institute) ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Michael B Miller
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zinan Zhou
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Craig L Bohrson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Antuan V Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Gannon McDonough
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Brown
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yasmine Chahine
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Brian Chhouk
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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43
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Zhang T, Sang J, Hoang PH, Zhao W, Rosenbaum J, Johnson KE, Klimczak LJ, McElderry J, Klein A, Wirth C, Bergstrom EN, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence SM, Cole N, Zhu B, Przytycka TM, Shi J, Caporaso NE, Homer R, Pesatori AC, Consonni D, Imielinski M, Chanock SJ, Wedge DC, Gordenin DA, Alexandrov LB, Harris RS, Landi MT. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587805. [PMID: 38617360 PMCID: PMC11014539 DOI: 10.1101/2024.04.02.587805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher Wirth
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Frank Colon-Matos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M. Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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44
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Tesi B, Robinson KL, Abel F, Díaz de Ståhl T, Orrsjö S, Poluha A, Hellberg M, Wessman S, Samuelsson S, Frisk T, Vogt H, Henning K, Sabel M, Ek T, Pal N, Nyman P, Giraud G, Wille J, Pronk CJ, Norén-Nyström U, Borssén M, Fili M, Stålhammar G, Herold N, Tettamanti G, Maya-Gonzalez C, Arvidsson L, Rosén A, Ekholm K, Kuchinskaya E, Hallbeck AL, Nordling M, Palmebäck P, Kogner P, Smoler GK, Lähteenmäki P, Fransson S, Martinsson T, Shamik A, Mertens F, Rosenquist R, Wirta V, Tham E, Grillner P, Sandgren J, Ljungman G, Gisselsson D, Taylan F, Nordgren A. Diagnostic yield and clinical impact of germline sequencing in children with CNS and extracranial solid tumors-a nationwide, prospective Swedish study. THE LANCET REGIONAL HEALTH. EUROPE 2024; 39:100881. [PMID: 38803632 PMCID: PMC11129334 DOI: 10.1016/j.lanepe.2024.100881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/04/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024]
Abstract
Background Childhood cancer predisposition (ChiCaP) syndromes are increasingly recognized as contributing factors to childhood cancer development. Yet, due to variable availability of germline testing, many children with ChiCaP might go undetected today. We report results from the nationwide and prospective ChiCaP study that investigated diagnostic yield and clinical impact of integrating germline whole-genome sequencing (gWGS) with tumor sequencing and systematic phenotyping in children with solid tumors. Methods gWGS was performed in 309 children at diagnosis of CNS (n = 123, 40%) or extracranial (n = 186, 60%) solid tumors and analyzed for disease-causing variants in 189 known cancer predisposing genes. Tumor sequencing data were available for 74% (227/309) of patients. In addition, a standardized clinical assessment for underlying predisposition was performed in 95% (293/309) of patients. Findings The prevalence of ChiCaP diagnoses was 11% (35/309), of which 69% (24/35) were unknown at inclusion (diagnostic yield 8%, 24/298). A second-hit and/or relevant mutational signature was observed in 19/21 (90%) tumors with informative data. ChiCaP diagnoses were more prevalent among patients with retinoblastomas (50%, 6/12) and high-grade astrocytomas (37%, 6/16), and in those with non-cancer related features (23%, 20/88), and ≥2 positive ChiCaP criteria (28%, 22/79). ChiCaP diagnoses were autosomal dominant in 80% (28/35) of patients, yet confirmed de novo in 64% (18/28). The 35 ChiCaP findings resulted in tailored surveillance (86%, 30/35) and treatment recommendations (31%, 11/35). Interpretation Overall, our results demonstrate that systematic phenotyping, combined with genomics-based diagnostics of ChiCaP in children with solid tumors is feasible in large-scale clinical practice and critically guides personalized care in a sizable proportion of patients. Funding The study was supported by the Swedish Childhood Cancer Fund and the Ministry of Health and Social Affairs.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Frida Abel
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresita Díaz de Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Orrsjö
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Poluha
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maria Hellberg
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Sandra Wessman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sofie Samuelsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Tony Frisk
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Hartmut Vogt
- Crown Princess Victoria Children’s Hospital, and Division of Children’s and Women’s Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Karin Henning
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
- Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Torben Ek
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
- Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Niklas Pal
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Per Nyman
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Centre for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Geraldine Giraud
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Pediatric Oncology, Uppsala University Children’s Hospital, Uppsala, Sweden
- Department of Women’s and Children’s Health, Uppsala University, Sweden
| | - Joakim Wille
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
| | - Cornelis Jan Pronk
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
- Division of Molecular Hematology/Wallenberg Center for Molecular Medicine, Lund University, Sweden
| | | | - Magnus Borssén
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Maria Fili
- Division of Eye and Vision, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- St. Erik Eye Hospital, Stockholm, Sweden
| | - Gustav Stålhammar
- Division of Eye and Vision, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- St. Erik Eye Hospital, Stockholm, Sweden
| | - Nikolas Herold
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Giorgio Tettamanti
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Linda Arvidsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Anna Rosén
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Katja Ekholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | | | - Anna-Lotta Hallbeck
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Margareta Nordling
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Pia Palmebäck
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Per Kogner
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla Kanter Smoler
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Päivi Lähteenmäki
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Fransson
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alia Shamik
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Pernilla Grillner
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Gustaf Ljungman
- Pediatric Oncology, Uppsala University Children’s Hospital, Uppsala, Sweden
- Department of Women’s and Children’s Health, Uppsala University, Sweden
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
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Jaksik R, Szumała K, Dinh KN, Śmieja J. Multiomics-Based Feature Extraction and Selection for the Prediction of Lung Cancer Survival. Int J Mol Sci 2024; 25:3661. [PMID: 38612473 PMCID: PMC11011391 DOI: 10.3390/ijms25073661] [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: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Lung cancer is a global health challenge, hindered by delayed diagnosis and the disease's complex molecular landscape. Accurate patient survival prediction is critical, motivating the exploration of various -omics datasets using machine learning methods. Leveraging multi-omics data, this study seeks to enhance the accuracy of survival prediction by proposing new feature extraction techniques combined with unbiased feature selection. Two lung adenocarcinoma multi-omics datasets, originating from the TCGA and CPTAC-3 projects, were employed for this purpose, emphasizing gene expression, methylation, and mutations as the most relevant data sources that provide features for the survival prediction models. Additionally, gene set aggregation was shown to be the most effective feature extraction method for mutation and copy number variation data. Using the TCGA dataset, we identified 32 molecular features that allowed the construction of a 2-year survival prediction model with an AUC of 0.839. The selected features were additionally tested on an independent CPTAC-3 dataset, achieving an AUC of 0.815 in nested cross-validation, which confirmed the robustness of the identified features.
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Affiliation(s)
- Roman Jaksik
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Kamila Szumała
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Khanh Ngoc Dinh
- Irving Institute for Cancer Dynamics and Department of Statistics, Columbia University, New York, NY 10027, USA;
| | - Jarosław Śmieja
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
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46
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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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47
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Jin H, Gulhan DC, Geiger B, Ben-Isvy D, Geng D, Ljungström V, Park PJ. Accurate and sensitive mutational signature analysis with MuSiCal. Nat Genet 2024; 56:541-552. [PMID: 38361034 PMCID: PMC10937379 DOI: 10.1038/s41588-024-01659-0] [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: 04/16/2022] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
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Affiliation(s)
- Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benedikt Geiger
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Daniel Ben-Isvy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - David Geng
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Kaufmann TL, Schwarz RF. Improved identification of cancer mutational processes. Nat Genet 2024; 56:365-366. [PMID: 38454020 DOI: 10.1038/s41588-024-01679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Affiliation(s)
- Tom L Kaufmann
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Berlin, Germany.
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
| | - Roland F Schwarz
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
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Ishida Y, Murata T, Kakiuchi N, Ogawa S, Kabashima K. Emergence of multiple revertant keratinocyte clones in a patient with KID syndrome. J Eur Acad Dermatol Venereol 2024; 38:e285-e287. [PMID: 37907277 DOI: 10.1111/jdv.19595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Affiliation(s)
- Y Ishida
- Department of Dermatology, Kyoto University, Kyoto, Japan
| | - T Murata
- Department of Dermatology, Hyogo Medical University, Hyogo, Japan
| | - N Kakiuchi
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - S Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - K Kabashima
- Department of Dermatology, Kyoto University, Kyoto, Japan
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50
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Sasani TA, Quinlan AR, Harris K. Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice. eLife 2024; 12:RP89096. [PMID: 38381482 PMCID: PMC10942616 DOI: 10.7554/elife.89096] [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] [Indexed: 02/22/2024] Open
Abstract
Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.
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Affiliation(s)
- Thomas A Sasani
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | - Aaron R Quinlan
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
- Department of Biomedical Informatics, University of UtahSalt Lake CityUnited States
| | - Kelley Harris
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Herbold Computational Biology Program, Fred Hutch Cancer CenterSeattleUnited States
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