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Weng Z, Mai Z, Yuan J, Liu Q, Deng F, Yang H, Ling Y, Xie X, Lin X, Lin T, Chen J, Wei X, Luo K, Fu J, Wen J. Evolution of genome and immunogenome in esophageal squamous cell carcinomas driven by neoadjuvant chemoradiotherapy. Int J Cancer 2024; 155:2021-2035. [PMID: 39081132 DOI: 10.1002/ijc.35118] [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: 03/25/2024] [Revised: 06/26/2024] [Accepted: 07/05/2024] [Indexed: 10/04/2024]
Abstract
Neoadjuvant chemoradiotherapy (NCRT) followed by surgery is a standard treatment for locally advanced esophageal squamous cell carcinomas (ESCCs). However, the evolution of genome and immunogenome in ESCCs driven by NCRT remains incompletely elucidated. We performed whole-exome sequencing of 51 ESCC tumors collected before and after NCRT, 36 of which were subjected to transcriptome sequencing. Clonal analysis identified clonal extinction in 13 ESCC patients wherein all pre-NCRT clones disappeared after NCRT, and clonal persistence in 9 patients wherein clones endured following NCRT. The clone-persistent patients showed higher pre-NCRT genomic intratumoral heterogeneity and worse prognosis than the clone-extinct ones. In contrast to the clone-extinct patients, the clone-persistent patients demonstrated a high proportion of subclonal neoantigens within pre-treatment specimens. Transcriptome analysis revealed increased immune infiltrations and up-regulated immune-related pathways after NCRT, especially in the clone-extinct patients. The number of T cell receptor-neoantigen interactions was higher in the clone-extinct patients than in the clone-persistent ones. The decrease in T cell repertoire evenness positively correlated to the decreased number of clonal neoantigens after NCRT, especially in the clone-extinct patients. In conclusion, we identified two prognosis-related clonal dynamic modes driven by NCRT in ESCCs. This study extended our knowledge of the ESCC genome and immunogenome evolutions driven by NCRT.
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Affiliation(s)
- Zelin Weng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zihang Mai
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jianye Yuan
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
| | - Qianwen Liu
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fangqi Deng
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hong Yang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yihong Ling
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiuying Xie
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaodan Lin
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ting Lin
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiyang Chen
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoli Wei
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kongjia Luo
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jianhua Fu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jing Wen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Esophageal Cancer Institute, Sun Yat-sen University Cancer Center, Guangzhou, China
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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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3
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Frydendahl A, Nors J, Rasmussen MH, Henriksen TV, Nesic M, Reinert T, Afterman D, Lauterman T, Kuzman M, Gonzalez S, Glavas D, Smadback J, Maloney D, Levativ J, Yahalom M, Ptashkin R, Tavassoly I, Donenhirsh Z, White E, Kandasamy R, Alon U, Nordentoft I, Lindskrog SV, Dyrskjøt L, Jaensch C, Løve US, Andersen PV, Thorlacius-Ussing O, Iversen LH, Gotschalck KA, Zviran A, Oklander B, Andersen CL. Detection of circulating tumor DNA by tumor-informed whole-genome sequencing enables prediction of recurrence in stage III colorectal cancer patients. Eur J Cancer 2024; 211:114314. [PMID: 39316995 DOI: 10.1016/j.ejca.2024.114314] [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: 03/22/2024] [Revised: 08/22/2024] [Accepted: 09/02/2024] [Indexed: 09/26/2024]
Abstract
INTRODUCTION Circulating tumor (ctDNA) can be used to detect residual disease after cancer treatment. Detecting low-level ctDNA is challenging, due to the limited number of recoverable ctDNA fragments at any target loci. In response, we applied tumor-informed whole-genome sequencing (WGS), leveraging thousands of mutations for ctDNA detection. METHODS Performance was evaluated in serial plasma samples (n = 1283) from 144 stage III colorectal cancer patients. Tumor/normal WGS was used to establish a patient-specific mutational fingerprint, which was searched for in 20x WGS plasma profiles. For reproducibility, paired aliquots of 172 plasma samples were analyzed in two independent laboratories. De novo variant calling was performed for serial plasma samples with a ctDNA level > 10 % (n = 17) to explore genomic evolution. RESULTS WGS-based ctDNA detection was prognostic of recurrence: post-operation (Hazard ratio [HR] 6.75, 95 %CI 3.18-14.3, p < 0.001), post-adjuvant chemotherapy (HR 28.9, 95 %CI 10.1-82.8; p < 0.001), and during surveillance (HR 22.8, 95 %CI 13.7-37.9, p < 0.0001). The 3-year cumulative incidence of ctDNA detection in recurrence patients was 95 %. ctDNA was detected a median of 8.7 months before radiological recurrence. The independently analyzed plasma aliquots showed excellent agreement (Cohens Kappa=0.9, r = 0.99). Genomic characterization of serial plasma revealed significant evolution in mutations and copy number alterations, and the timing of mutational processes, such as 5-fluorouracil-induced mutations. CONCLUSION Our study supports the use of WGS for sensitive ctDNA detection and demonstrates that post-treatment ctDNA detection is highly prognostic of recurrence. Furthermore, plasma WGS can identify genomic differences distinguishing the primary tumor and relapsing metastasis, and monitor treatment-induced genomic changes.
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Affiliation(s)
- Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Jesper Nors
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Tenna V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Marijana Nesic
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | - Eric White
- C2i Genomics Inc., New York, NY 10014, USA
| | | | - Ury Alon
- C2i Genomics, Ltd., Haifa, Israel
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Sia V Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | | | - Uffe S Løve
- Department of Surgery, Viborg Regional Hospital, Denmark
| | - Per V Andersen
- Department of Surgery, Odense University Hospital, Denmark
| | | | - Lene H Iversen
- Department of Clinical Medicine, Aarhus University, Denmark; Department of Surgery, Aarhus University Hospital, Denmark
| | - Kåre A Gotschalck
- Department of Clinical Medicine, Aarhus University, Denmark; Department of Surgery, Randers Regional Hospital, Denmark
| | | | | | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark.
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Torreggiani S, Castellan FS, Aksentijevich I, Beck DB. Somatic mutations in autoinflammatory and autoimmune disease. Nat Rev Rheumatol 2024:10.1038/s41584-024-01168-8. [PMID: 39394526 DOI: 10.1038/s41584-024-01168-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2024] [Indexed: 10/13/2024]
Abstract
Somatic mutations (also known as acquired mutations) are emerging as common, age-related processes that occur in all cells throughout the body. Somatic mutations are canonically linked to malignant processes but over the past decade have been increasingly causally connected to benign diseases including rheumatic conditions. Here we outline the contribution of somatic mutations to complex and monogenic immunological diseases with a detailed review of unique aspects associated with such causes. Somatic mutations can cause early- or late-onset rheumatic monogenic diseases but also contribute to the pathogenesis of complex inflammatory and immune-mediated diseases, affect disease progression and define new clinical subtypes. Although even variants with a low variant allele fraction can be pathogenic, clonal dynamics could lead to changes over time in the proportion of mutant cells, with possible phenotypic consequences for the individual. Thus, somatic mutagenesis and clonal expansion have relevant implications in genetic testing and counselling. On the basis of both increased recognition of somatic diseases in clinical practice and improved technical and bioinformatic processes, we hypothesize that there will be an ever-expanding list of somatic mutations in various genes leading to inflammatory conditions, particularly in late-onset disease.
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Affiliation(s)
- Sofia Torreggiani
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Epidemiology and Human Genetics, Graduate Program in Life Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Flore S Castellan
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David B Beck
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA.
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5
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Maury EA, Jones A, Seplyarskiy V, Nguyen TTL, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Park PJ, Akbarian S, Brennand K, Reilly S, Lee EA, Sunyaev SR, Walsh CA, Chess A. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science 2024; 386:217-224. [PMID: 39388546 DOI: 10.1126/science.adq1456] [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: 05/01/2024] [Accepted: 08/16/2024] [Indexed: 10/12/2024]
Abstract
Germline mutations modulate the risk of developing schizophrenia (SCZ). Much less is known about the role of mosaic somatic mutations in the context of SCZ. Deep (239×) whole-genome sequencing (WGS) of brain neurons from 61 SCZ cases and 25 controls postmortem identified mutations occurring during prenatal neurogenesis. SCZ cases showed increased somatic variants in open chromatin, with increased mosaic CpG transversions (CpG>GpG) and T>G mutations at transcription factor binding sites (TFBSs) overlapping open chromatin, a result not seen in controls. Some of these variants alter gene expression, including SCZ risk genes and genes involved in neurodevelopment. Although these mutational processes can reflect a difference in factors indirectly involved in disease, increased somatic mutations at developmental TFBSs could also potentially contribute to SCZ.
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Affiliation(s)
- Eduardo A Maury
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA 02115, USA
- Bioinformatics and Integrative Genomics Program and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Attila Jones
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vladimir Seplyarskiy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thanh Thanh L Nguyen
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT 06520, USA
| | - Chaggai Rosenbluh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taejong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Sattar Khoshkhoo
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yasmine Chahine
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sijing Zhao
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sanan Venkatesh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elise Root
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Georgios Voloudakis
- Center for Disease Neurogenomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panagiotis Roussos
- Center for Disease Neurogenomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Schahram Akbarian
- Department of Psychiatry and Neuroscience, Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
| | - Kristen Brennand
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT 06520, USA
| | - Steven Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Eunjung A Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Andrew Chess
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
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6
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Zhang M, Zhang X, Xu Y, Xiang Y, Zhang B, Xie Z, Wu Q, Lou C. High-resolution and programmable RNA-IN and RNA-OUT genetic circuit in living mammalian cells. Nat Commun 2024; 15:8768. [PMID: 39384754 PMCID: PMC11464720 DOI: 10.1038/s41467-024-52962-7] [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: 05/18/2024] [Accepted: 09/26/2024] [Indexed: 10/11/2024] Open
Abstract
RNAs and their encoded proteins intricately regulate diverse cell types and states within the human body. Dysregulated RNA expressions or mutations can lead to various diseased cell states, including tumorigenesis. Detecting and manipulating these endogenous RNAs offers significant promise for restoring healthy cell states and targeting tumors both in research and clinical contexts. This study presents an RNA-IN and RNA-OUT genetic circuit capable dynamically sensing and manipulating any RNA target in a programmable manner. The RNA-IN module employes a programmable CRISPR-associated protease (CASP) complex for RNA detection, while the RNA-OUT module utilizes an engineered protease-responsive dCas9-VPR activator. Additionally, the CASP module can detect point mutations by harnessing an uncovered dual-nucleotide synergistic switching effect within the CASP complex, resulting in the amplification of point-mutation signals from initially undetectable levels (1.5-fold) to a remarkable 94-fold. We successfully showcase the circuit's ability to rewire endogenous RNA-IN signals to activate endogenous progesterone biosynthesis pathway, dynamically monitor adipogenic differentiation of mesenchymal stem cells (MSCs) and the epithelial-to-mesenchmal trans-differentiation, as well as selective killing of tumor cells. The programmable RNA-IN and RNA-OUT circuit exhibits tremendous potential for applications in gene therapy, biosensing and design of synthetic regulatory networks.
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Affiliation(s)
- Min Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xue Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yongyue Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yanhui Xiang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Bo Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chunbo Lou
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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7
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Tomkova M, McClellan MJ, Crevel G, Shahid AM, Mozumdar N, Tomek J, Shepherd E, Cotterill S, Schuster-Böckler B, Kriaucionis S. Human DNA polymerase ε is a source of C>T mutations at CpG dinucleotides. Nat Genet 2024:10.1038/s41588-024-01945-x. [PMID: 39390083 DOI: 10.1038/s41588-024-01945-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/11/2024] [Indexed: 10/12/2024]
Abstract
C-to-T transitions in CpG dinucleotides are the most prevalent mutations in human cancers and genetic diseases. These mutations have been attributed to deamination of 5-methylcytosine (5mC), an epigenetic modification found on CpGs. We recently linked CpG>TpG mutations to replication and hypothesized that errors introduced by polymerase ε (Pol ε) may represent an alternative source of mutations. Here we present a new method called polymerase error rate sequencing (PER-seq) to measure the error spectrum of DNA polymerases in isolation. We find that the most common human cancer-associated Pol ε mutant (P286R) produces an excess of CpG>TpG errors, phenocopying the mutation spectrum of tumors carrying this mutation and deficiencies in mismatch repair. Notably, we also discover that wild-type Pol ε has a sevenfold higher error rate when replicating 5mCpG compared to C in other contexts. Together, our results from PER-seq and human cancers demonstrate that replication errors are a major contributor to CpG>TpG mutagenesis in replicating cells, fundamentally changing our understanding of this important disease-causing mutational mechanism.
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Affiliation(s)
- Marketa Tomkova
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.
| | | | - Gilles Crevel
- Molecular and Cellular Sciences, St George's University London, London, UK
| | | | - Nandini Mozumdar
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Jakub Tomek
- Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Emelie Shepherd
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Sue Cotterill
- Molecular and Cellular Sciences, St George's University London, London, UK
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8
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Nguyen DD, Hooper WF, Liu W, Chu TR, Geiger H, Shelton JM, Shah M, Goldstein ZR, Winterkorn L, Helland A, Sigouros M, Manohar J, Moyer J, Al Assaad M, Semaan A, Cohen S, Madorsky Rowdo F, Wilkes D, Osman M, Singh RR, Sboner A, Valentine HL, Abbosh P, Tagawa ST, Nanus DM, Nauseef JT, Sternberg CN, Molina AM, Scherr D, Inghirami G, Mosquera JM, Elemento O, Robine N, Faltas BM. The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution. Nature 2024:10.1038/s41586-024-07955-3. [PMID: 39385020 DOI: 10.1038/s41586-024-07955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/14/2024] [Indexed: 10/11/2024]
Abstract
Advanced urothelial cancer is a frequently lethal disease characterized by marked genetic heterogeneity1. In this study, we investigated the evolution of genomic signatures caused by endogenous and external mutagenic processes and their interplay with complex structural variants (SVs). We superimposed mutational signatures and phylogenetic analyses of matched serial tumours from patients with urothelial cancer to define the evolutionary dynamics of these processes. We show that APOBEC3-induced mutations are clonal and early, whereas chemotherapy induces mutational bursts of hundreds of late subclonal mutations. Using a genome graph computational tool2, we observed frequent high copy-number circular amplicons characteristic of extrachromosomal DNA (ecDNA)-forming SVs. We characterized the distinct temporal patterns of APOBEC3-induced and chemotherapy-induced mutations within ecDNA-forming SVs, gaining new insights into the timing of these mutagenic processes relative to ecDNA biogenesis. We discovered that most CCND1 amplifications in urothelial cancer arise within circular ecDNA-forming SVs. ecDNA-forming SVs persisted and increased in complexity, incorporating additional DNA segments and contributing to the evolution of treatment resistance. Oxford Nanopore Technologies long-read whole-genome sequencing followed by de novo assembly mapped out CCND1 ecDNA structure. Experimental modelling of CCND1 ecDNA confirmed its role as a driver of treatment resistance. Our findings define fundamental mechanisms that drive urothelial cancer evolution and have important therapeutic implications.
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Affiliation(s)
- Duy D Nguyen
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Weisi Liu
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | | | | | - Michael Sigouros
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jyothi Manohar
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jenna Moyer
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Majd Al Assaad
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alissa Semaan
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sandra Cohen
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Florencia Madorsky Rowdo
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - David Wilkes
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mohamed Osman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rahul R Singh
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Henkel L Valentine
- Nuclear Dynamics and Cancer program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Phillip Abbosh
- Nuclear Dynamics and Cancer program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Urology, Einstein Healthcare Network, Philadelphia, PA, USA
| | - Scott T Tagawa
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - David M Nanus
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Jones T Nauseef
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Cora N Sternberg
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ana M Molina
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Douglas Scherr
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Bishoy M Faltas
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
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9
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Williams JS, Lujan SA, Arana ME, Burkholder AB, Tumbale PP, Williams RS, Kunkel TA. High fidelity DNA ligation prevents single base insertions in the yeast genome. Nat Commun 2024; 15:8730. [PMID: 39379399 PMCID: PMC11461686 DOI: 10.1038/s41467-024-53063-1] [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: 04/24/2024] [Accepted: 09/30/2024] [Indexed: 10/10/2024] Open
Abstract
Finalization of eukaryotic nuclear DNA replication relies on DNA ligase 1 (LIG1) to seal DNA nicks generated during Okazaki Fragment Maturation (OFM). Using a mutational reporter in Saccharomyces cerevisiae, we previously showed that mutation of the high-fidelity magnesium binding site of LIG1Cdc9 strongly increases the rate of single-base insertions. Here we show that this rate is increased across the nuclear genome, that it is synergistically increased by concomitant loss of DNA mismatch repair (MMR), and that the additions occur in highly specific sequence contexts. These discoveries are all consistent with incorporation of an extra base into the nascent lagging DNA strand that can be corrected by MMR following mutagenic ligation by the Cdc9-EEAA variant. There is a strong preference for insertion of either dGTP or dTTP into 3-5 base pair mononucleotide sequences with stringent flanking nucleotide requirements. The results reveal unique LIG1Cdc9-dependent mutational motifs where high fidelity DNA ligation of a subset of OFs is critical for preventing mutagenesis across the genome.
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Affiliation(s)
- Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Mercedes E Arana
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Adam B Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Percy P Tumbale
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.
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10
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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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11
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Young CL, Beichman AC, Mas Ponte D, Hemker SL, Zhu L, Kitzman J, 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] [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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12
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Jayakrishnan R, Kwiatkowski DJ, Rose MG, Nassar AH. Topography of mutational signatures in non-small cell lung cancer: emerging concepts, clinical applications, and limitations. Oncologist 2024; 29:833-841. [PMID: 38907669 PMCID: PMC11449018 DOI: 10.1093/oncolo/oyae091] [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: 12/08/2023] [Accepted: 04/16/2024] [Indexed: 06/24/2024] Open
Abstract
The genome of a cell is continuously battered by a plethora of exogenous and endogenous processes that can lead to damaged DNA. Repair mechanisms correct this damage most of the time, but failure to do so leaves mutations. Mutations do not occur in random manner, but rather typically follow a more or less specific pattern due to known or imputed mutational processes. Mutational signature analysis is the process by which the predominant mutational process can be inferred for a cancer and can be used in several contexts to study both the genesis of cancer and its response to therapy. Recent pan-cancer genomic efforts such as "The Cancer Genome Atlas" have identified numerous mutational signatures that can be categorized into single base substitutions, doublet base substitutions, or small insertions/deletions. Understanding these mutational signatures as they occur in non-small lung cancer could improve efforts at prevention, predict treatment response to personalized treatments, and guide the development of therapies targeting tumor evolution. For non-small cell lung cancer, several mutational signatures have been identified that correlate with exposures such as tobacco smoking and radon and can also reflect endogenous processes such as aging, APOBEC activity, and loss of mismatch repair. Herein, we provide an overview of the current knowledge of mutational signatures in non-small lung cancer.
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Affiliation(s)
- Ritujith Jayakrishnan
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - David J Kwiatkowski
- Department of Pulmonary Medicine, Brigham and Women's Hospital, Boston, MA, 02115, United States
| | - Michal G Rose
- Yale University School of Medicine and Cancer Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, United States
- Department of Medicine, Medical Oncology Division, Yale Cancer Center, New Haven, CT, United States
| | - Amin H Nassar
- Yale University School of Medicine and Cancer Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, United States
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13
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Lascaux P, Hoslett G, Tribble S, Trugenberger C, Antičević I, Otten C, Torrecilla I, Koukouravas S, Zhao Y, Yang H, Aljarbou F, Ruggiano A, Song W, Peron C, Deangeli G, Domingo E, Bancroft J, Carrique L, Johnson E, Vendrell I, Fischer R, Ng AWT, Ngeow J, D'Angiolella V, Raimundo N, Maughan T, Popović M, Milošević I, Ramadan K. TEX264 drives selective autophagy of DNA lesions to promote DNA repair and cell survival. Cell 2024; 187:5698-5718.e26. [PMID: 39265577 DOI: 10.1016/j.cell.2024.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 06/04/2024] [Accepted: 08/10/2024] [Indexed: 09/14/2024]
Abstract
DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that lysosomes process topoisomerase 1 cleavage complexes (TOP1cc) DNA lesions in vertebrates. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival at clinically relevant doses of topoisomerase 1 inhibitors. TOP1cc are exported from the nucleus to lysosomes through a transient alteration of the nuclear envelope and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating the delivery of TOP1cc to lysosomes in an MRE11-nuclease- and ATR-kinase-dependent manner. We found an evolutionarily conserved role for selective autophagy in DNA repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients.
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Affiliation(s)
- Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sara Tribble
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Camilla Trugenberger
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ivan Antičević
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Cecile Otten
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Stelios Koukouravas
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Yichen Zhao
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hongbin Yang
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Cristiano Peron
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Giulio Deangeli
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 2PY, UK
| | - Enric Domingo
- Department of Oncology, Medical Sciences Division, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - James Bancroft
- Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK
| | - Loïc Carrique
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK
| | - Errin Johnson
- Dunn School Bioimaging Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK
| | - Alvin Wei Tian Ng
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Vincenzo D'Angiolella
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Nuno Raimundo
- Penn State College of Medicine, Department of Cellular and Molecular Physiology, Hershey, PA 17033, USA; Multidisciplinary Institute for Aging, Center for Innovation in Biomedicine and Biotechnology, University of Coimbra, Coimbra 3000-370, Portugal
| | - Tim Maughan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - Marta Popović
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Ira Milošević
- Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK; Multidisciplinary Institute for Aging, Center for Innovation in Biomedicine and Biotechnology, University of Coimbra, Coimbra 3000-370, Portugal
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore.
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14
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Tran P, Mishra P, Williams LG, Moskalenko R, Sharma S, Nilsson AK, Watt DL, Andersson P, Bergh A, Pursell ZF, Chabes A. Altered dNTP pools accelerate tumor formation in mice. Nucleic Acids Res 2024:gkae843. [PMID: 39360631 DOI: 10.1093/nar/gkae843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/10/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
Alterations in deoxyribonucleoside triphosphate (dNTP) pools have been linked to increased mutation rates and genome instability in unicellular organisms and cell cultures. However, the role of dNTP pool changes in tumor development in mammals remains unclear. In this study, we present a mouse model with a point mutation at the allosteric specificity site of ribonucleotide reductase, RRM1-Y285A. This mutation reduced ribonucleotide reductase activity, impairing the synthesis of deoxyadenosine triphosphate (dATP) and deoxyguanosine triphosphate (dGTP). Heterozygous Rrm1+/Y285A mice exhibited distinct alterations in dNTP pools across various organs, shorter lifespans and earlier tumor onset compared with wild-type controls. Mutational spectrum analysis of tumors revealed two distinct signatures, one resembling a signature extracted from a human cancer harboring a mutation of the same amino acid residue in ribonucleotide reductase, RRM1Y285C. Our findings suggest that mutations in enzymes involved in dNTP metabolism can serve as drivers of cancer development.
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Affiliation(s)
- Phong Tran
- Department of Medical Biochemistry and Biophysics, Umeå University, Linnaeus väg 6, Umeå, SE 90736, Sweden
| | - Pradeep Mishra
- Department of Medical Biochemistry and Biophysics, Umeå University, Linnaeus väg 6, Umeå, SE 90736, Sweden
| | - Leonard G Williams
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Roman Moskalenko
- Department of Pathology, Sumy State University, Kharkivska st. 116, Sumy 40007, Ukraine
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Linnaeus väg 6, Umeå, SE 90736, Sweden
| | - Anna Karin Nilsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Linnaeus väg 6, Umeå, SE 90736, Sweden
| | - Danielle L Watt
- Department of Medical Biochemistry and Biophysics, Umeå University, Linnaeus väg 6, Umeå, SE 90736, Sweden
- School of Medicine and School of Dental Medicine, UConn Health, 300 UConn Health Blvd, Farmington, CT 06030, USA
| | - Pernilla Andersson
- Pathology Unit, Department of Medical Biosciences, Umeå University, Daniel Naezéns väg 6M, Umeå, SE 90737, Sweden
| | - Anders Bergh
- Pathology Unit, Department of Medical Biosciences, Umeå University, Daniel Naezéns väg 6M, Umeå, SE 90737, Sweden
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Linnaeus väg 6, Umeå, SE 90736, Sweden
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15
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Backman S, Botling J, Nord H, Ghosal S, Stålberg P, Juhlin CC, Almlöf J, Sundin A, Zhang L, Moens L, Eriksson B, Welin S, Hellman P, Skogseid B, Pacak K, Mollazadegan K, Åkerström T, Crona J. The evolutionary history of metastatic pancreatic neuroendocrine tumours reveals a therapy driven route to high-grade transformation. J Pathol 2024. [PMID: 39360347 DOI: 10.1002/path.6348] [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: 02/13/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 10/04/2024]
Abstract
Tumour evolution with acquisition of more aggressive disease characteristics is a hallmark of disseminated cancer. Metastatic pancreatic neuroendocrine tumours (PanNETs) in particular may progress from a low/intermediate to a high-grade disease. The aim of this work was to understand the molecular mechanisms underlying metastatic progression as well as PanNET transformation from a low/intermediate to a high-grade disease. We performed multi-omics analysis (genome/exome sequencing, total RNA-sequencing and methylation array) of 32 longitudinal samples from six patients with metastatic low/intermediate grade PanNET. The clonal composition of tumour lesions and underlying phylogeny of each patient were determined with bioinformatics analyses. Findings were validated in post-alkylating chemotherapy samples from 24 patients with PanNET using targeted next generation sequencing. We validate the current PanNET evolutionary model with MEN1 inactivation that occurs very early in tumourigenesis. This was followed by pronounced genetic diversity on both spatial and temporal levels, with parallel and convergent tumour evolution involving the ATRX/DAXX and mechanistic target of the rapamycin (mTOR) pathways. Following alkylating chemotherapy treatment, some PanNETs developed mismatch repair deficiency and acquired a hypermutational phenotype. This was validated among 16 patients with PanNET who had high-grade progression after alkylating chemotherapy, of whom eight had a tumour mutational burden >50 (50%). In comparison, among the eight patients who did not show high-grade progression, 0 had a tumour mutational burden >50 (0%; odds ratio 'infinite', 95% confidence interval 1.8 to 'infinite', p = 0.02). Our findings contribute to broaden the understanding of metastatic/high-grade PanNETs and suggests that therapy driven disease evolution is an important hallmark of this disease. © 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. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Samuel Backman
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Helena Nord
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Suman Ghosal
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Peter Stålberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - C Christofer Juhlin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Almlöf
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Sundin
- Section of Radiology, Molecular Imaging, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Liang Zhang
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Lotte Moens
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Barbro Eriksson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Staffan Welin
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Per Hellman
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Britt Skogseid
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | | | - Tobias Åkerström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Joakim Crona
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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16
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Puttick C, Jones TP, Leung MM, Galvez-Cancino F, Liu J, Varas-Godoy M, Rowan A, Pich O, Martinez-Ruiz C, Bentham R, Dijkstra KK, Black JRM, Rosenthal R, Kanu N, Litchfield K, Salgado R, Moore DA, Van Loo P, Jamal-Hanjani M, Quezada SA, Swanton C, McGranahan N. MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution. Nat Genet 2024:10.1038/s41588-024-01883-8. [PMID: 39358601 DOI: 10.1038/s41588-024-01883-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/25/2024] [Indexed: 10/04/2024]
Abstract
Disruption of the class I human leukocyte antigen (HLA) molecules has important implications for immune evasion and tumor evolution. We developed major histocompatibility complex loss of heterozygosity (LOH), allele-specific mutation and measurement of expression and repression (MHC Hammer). We identified extensive variability in HLA allelic expression and pervasive HLA alternative splicing in normal lung and breast tissue. In lung TRACERx and lung and breast TCGA cohorts, 61% of lung adenocarcinoma (LUAD), 76% of lung squamous cell carcinoma (LUSC) and 35% of estrogen receptor-positive (ER+) cancers harbored class I HLA transcriptional repression, while HLA tumor-enriched alternative splicing occurred in 31%, 11% and 15% of LUAD, LUSC and ER+ cancers. Consistent with the importance of HLA dysfunction in tumor evolution, in LUADs, HLA LOH was associated with metastasis and LUAD primary tumor regions seeding a metastasis had a lower effective neoantigen burden than non-seeding regions. These data highlight the extent and importance of HLA transcriptomic disruption, including repression and alternative splicing in cancer evolution.
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Affiliation(s)
- Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas P Jones
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Michelle M Leung
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Felipe Galvez-Cancino
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Immunology Unit, Immune Regulation and Tumour Immunotherapy Laboratory, Research Department of Haematology, University College London Cancer Institute, London, UK
- Immune Regulation and Immune Interactions Group, Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiali Liu
- Cancer Immunology Unit, Immune Regulation and Tumour Immunotherapy Laboratory, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Manuel Varas-Godoy
- Cancer Cell Biology Laboratory, Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- 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
| | - Carlos Martinez-Ruiz
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Robert Bentham
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Krijn K Dijkstra
- 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
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - James R M Black
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
| | - David A Moore
- 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
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Immunology Unit, Immune Regulation and Tumour Immunotherapy Laboratory, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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17
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Kim SC, Seo HY, Lee JO, Maeng JE, Shin YK, Lee SH, Jang JY, Ku JL. Establishment, characterization, and biobanking of 36 pancreatic cancer organoids: prediction of metastasis in resectable pancreatic cancer. Cell Oncol (Dordr) 2024; 47:1627-1647. [PMID: 38619751 PMCID: PMC11467084 DOI: 10.1007/s13402-024-00939-5] [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] [Accepted: 03/13/2024] [Indexed: 04/16/2024] Open
Abstract
PURPOSE Early dissemination of primary pancreatic ductal adenocarcinoma (PDAC) is the main cause of dismal prognosis as it highly limits possible treatment options. A number of PDAC patients experience distant metastasis even after treatment due to the metastatic clones. We aimed to demonstrate the molecular architecture of borderline resectable PDAC manifests cancer dissemination of PDAC. METHODS Here, 36 organoids isolated from primary tumor masses of PDAC patients with diverse metastatic statues are presented. Whole-exome sequencing and RNA sequencing were performed and drug responses to clinically relevant 18 compounds were assessed. RESULTS Our results revealed that borderline resectable PDAC organoids exhibited distinct patterns according to their metastatic potency highlighted by multiple genetic and transcriptional factors and strong variances in drug responses. CONCLUSIONS These data suggest that the presence of metastatic PDAC can be identified by integrating molecular compositions and drug responses of borderline resectable PDAC.
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Affiliation(s)
- Soon-Chan Kim
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ha-Young Seo
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Ja-Oh Lee
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Ju Eun Maeng
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Young-Kyoung Shin
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Sang Hyub Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
| | - Jin-Young Jang
- Department of Surgery, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul, 03080, South Korea.
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
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18
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Kazandjian D, Diamond B, Papadimitriou M, Hill E, Sklavenitis-Pistofidis R, Ziccheddu B, Blaney P, Chojnacka M, Durante M, Maclachlan K, Young R, Usmani S, Davies F, Getz G, Ghobrial I, Korde N, Morgan G, Maura F, Landgren O. Genomic Profiling to Contextualize the Results of Intervention for Smoldering Multiple Myeloma. Clin Cancer Res 2024; 30:4482-4490. [PMID: 38652812 PMCID: PMC11444893 DOI: 10.1158/1078-0432.ccr-24-0210] [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: 01/19/2024] [Revised: 03/15/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
PURPOSE Early intervention for high-risk smoldering multiple myeloma (HR-SMM) achieves deep and prolonged responses. It is unclear if beneficial outcomes are due to the treatment of less complex, susceptible disease or inaccuracy in clinical definition of cases entered. EXPERIMENTAL DESIGN In this study, we interrogated whole-genome and whole-exome sequencing for 54 patients across two HR-SMM interventional studies (NCT01572480 and NCT02279394). RESULTS We reveal that the genomic landscape of treated HR-SMM is generally simple as compared with newly diagnosed multiple myeloma counterparts with less inactivation of tumor suppressor genes, RAS pathway mutations, MYC disruption, and APOBEC contribution. The absence of these events parallels that of indolent precursor conditions, possibly explaining overall excellent outcomes. However, some patients harboring genomic complexity fail to sustain response and experience resistant, progressive disease. Overall, clinical risk scores do not effectively discriminate between genomically indolent and aggressive disease. CONCLUSIONS Genomic profiling can contextualize the advantage of early intervention in SMM and guide personalization of therapy. See related commentary by Weinhold and Rasche, p. 4263.
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Affiliation(s)
- Dickran Kazandjian
- Myeloma Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Benjamin Diamond
- Myeloma Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Marios Papadimitriou
- Myeloma Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Elizabeth Hill
- Myeloma Program, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Bachisio Ziccheddu
- Myeloma Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Patrick Blaney
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY
| | - Monika Chojnacka
- Myeloma Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Michael Durante
- Myeloma Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Kylee Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Young
- Myeloma Program, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Saad Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Faith Davies
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Irene Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Neha Korde
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gareth Morgan
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY
| | - Francesco Maura
- Myeloma Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Ola Landgren
- Myeloma Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
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19
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Budczies J, Kazdal D, Menzel M, Beck S, Kluck K, Altbürger C, Schwab C, Allgäuer M, Ahadova A, Kloor M, Schirmacher P, Peters S, Krämer A, Christopoulos P, Stenzinger A. Tumour mutational burden: clinical utility, challenges and emerging improvements. Nat Rev Clin Oncol 2024; 21:725-742. [PMID: 39192001 DOI: 10.1038/s41571-024-00932-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/29/2024]
Abstract
Tumour mutational burden (TMB), defined as the total number of somatic non-synonymous mutations present within the cancer genome, varies across and within cancer types. A first wave of retrospective and prospective research identified TMB as a predictive biomarker of response to immune-checkpoint inhibitors and culminated in the disease-agnostic approval of pembrolizumab for patients with TMB-high tumours based on data from the Keynote-158 trial. Although the applicability of outcomes from this trial to all cancer types and the optimal thresholds for TMB are yet to be ascertained, research into TMB is advancing along three principal avenues: enhancement of TMB assessments through rigorous quality control measures within the laboratory process, including the mitigation of confounding factors such as limited panel scope and low tumour purity; refinement of the traditional TMB framework through the incorporation of innovative concepts such as clonal, persistent or HLA-corrected TMB, tumour neoantigen load and mutational signatures; and integration of TMB with established and emerging biomarkers such as PD-L1 expression, microsatellite instability, immune gene expression profiles and the tumour immune contexture. Given its pivotal functions in both the pathogenesis of cancer and the ability of the immune system to recognize tumours, a profound comprehension of the foundational principles and the continued evolution of TMB are of paramount relevance for the field of oncology.
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Affiliation(s)
- Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Translational Lung Research Center (TLRC) Heidelberg, Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
- Center for Personalized Medicine (ZPM), Heidelberg, Germany.
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center (TLRC) Heidelberg, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Michael Menzel
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Susanne Beck
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Klaus Kluck
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Christian Altbürger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Constantin Schwab
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Aysel Ahadova
- Department of Applied Tumour Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumour Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumour Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumour Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Solange Peters
- Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne University, Lausanne, Switzerland
| | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Petros Christopoulos
- Translational Lung Research Center (TLRC) Heidelberg, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumour Diseases at Heidelberg University Hospital, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Translational Lung Research Center (TLRC) Heidelberg, Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
- Center for Personalized Medicine (ZPM), Heidelberg, Germany.
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20
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Cannataro VL, Glasmacher KA, Hampson CE. Mutations, substitutions, and selection: Linking mutagenic processes to cancer using evolutionary theory. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167268. [PMID: 38823460 DOI: 10.1016/j.bbadis.2024.167268] [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: 02/14/2024] [Revised: 04/25/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Cancers are the product of evolutionary events, where molecular variation occurs and accumulates in tissues and tumors. Sequencing of this molecular variation informs not only which variants are driving tumorigenesis, but also the mechanisms behind what is fueling mutagenesis. Both of these details are crucial for preventing premature deaths due to cancer, whether it is by targeting the variants driving the cancer phenotype or by measures to prevent exogenous mutations from contributing to somatic evolution. Here, we review tools to determine both molecular signatures and cancer drivers, and avenues by which these metrics may be linked.
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Affiliation(s)
| | - Kira A Glasmacher
- Emmanuel College, 400 Fenway, Boston, MA 02115, United States of America
| | - Caralynn E Hampson
- Emmanuel College, 400 Fenway, Boston, MA 02115, United States of America
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21
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Cun HT, Bernard L, Lande KT, Lawson BC, Nesbakken AJ, Davidson B, Lindemann K, Fellman B, Sørlie T, Soliman PT, Eriksson AGZ. Comprehensive molecular characterization of early stage grade 3 endometrioid endometrial adenocarcinoma. Gynecol Oncol 2024; 189:138-145. [PMID: 39126895 DOI: 10.1016/j.ygyno.2024.07.677] [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: 04/11/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024]
Abstract
OBJECTIVE The treatment for stage IB grade 3 endometrioid endometrial adenocarcinoma is challenging with variable practice. Molecular characterization may help identify adjuvant therapy strategies beyond stage. We aimed to better understand the molecular features of these tumors by characterizing them by ProMisE classification, mutational signature, and commonly mutated genes. METHODS Patients with stage IB grade 3 EEC at two institutions were included. Immunohistochemistry and whole exome sequencing were performed on archival FFPE tissue sections to determine ProMisE classification. Personal Cancer Genome Reporter was used for somatic variant annotation, and mutational signatures were generated based on COSMIC single base substitution mutational signatures. RESULTS 46 patients were included with variable adjuvant treatment. Nine patients recurred (19.6%), most with extra-abdominal disease (n = 5, or 55.6%). 10 had POLE mutations (21.7%), 18 were MMR deficient (39.1%), 6 had abnormal p53 (13.0%), and 12 were p53 wildtype (26.1%). There were no recurrences in the POLE subgroup. A dominant mutational signature was identified in 38 patients: 17 SBS5 signature (44.7%), 10 SBS15 or SBS44 signature (26.3%), 7 SBS10a or SBS10b signature (18.4%), 3 SBS14 signature (7.9%), and 1 SBS40 signature (2.6%). The six patients that recurred had a SBS5 signature. Frequently mutated genes included ARID1A (n = 30, 65%), PTEN (n = 28, 61%), MUC16 (n = 27, 59%), and PIK3CA (n = 25, 54%). CONCLUSIONS This comprehensive evaluation found a molecularly diverse cohort of tumors, despite the same histology, stage and grade. Mutational signature SBS5 correlated with a high risk of recurrence. Further refining of endometrial cancer classification may enable more precise patient stratification and personalized treatment approaches.
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Affiliation(s)
- Han T Cun
- Section of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Chicago, Chicago, USA.
| | - Laurence Bernard
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, McGill University Health Centre, Montreal, Canada
| | - Karin Teien Lande
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Barrett C Lawson
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Anne-Jorunn Nesbakken
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Ben Davidson
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kristina Lindemann
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Gynecologic Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Bryan Fellman
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pamela T Soliman
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Ane Gerda Zahl Eriksson
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Gynecologic Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway.
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22
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Tsaalbi-Shtylik A, Mingard C, Räz M, Oka R, Manders F, Van Boxtel R, De Wind N, Sturla SJ. DNA mismatch repair controls the mutagenicity of Polymerase ζ-dependent translesion synthesis at methylated guanines. DNA Repair (Amst) 2024; 142:103755. [PMID: 39216121 DOI: 10.1016/j.dnarep.2024.103755] [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: 05/05/2024] [Revised: 07/27/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
By replicating damaged nucleotides, error-prone DNA translesion synthesis (TLS) enables the completion of replication, albeit at the expense of fidelity. TLS of helix-distorting DNA lesions, that usually have reduced capacity of basepairing, comprises insertion opposite the lesion followed by extension, the latter in particular by polymerase ζ (Pol ζ). However, little is known about involvement of Pol ζ in TLS of non- or poorly-distorting, but miscoding, lesions such as O6-methyldeoxyguanosine (O6-medG). Using purified Pol ζ we describe that the enzyme can misincorporate thymidine opposite O6-medG and efficiently extend from terminal mismatches, suggesting its involvement in the mutagenicity of O6-medG. Surprisingly, O6-medG lesions induced by the methylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) appeared more, rather than less, mutagenic in Pol ζ-deficient mouse embryonic fibroblasts (MEFs) than in wild type MEFs. This suggested that in vivo Pol ζ participates in non-mutagenic TLS of O6-medG. However, we found that the Pol ζ-dependent misinsertions at O6-medG lesions are efficiently corrected by DNA mismatch repair (MMR), which masks the error-proneness of Pol ζ. We also found that the MNNG-induced mutational signature is determined by the adduct spectrum, and modulated by MMR. The signature mimicked single base substitution signature 11 in the catalogue of somatic mutations in cancer, associated with treatment with the methylating drug temozolomide. Our results unravel the individual roles of the major contributors to methylating drug-induced mutagenesis. Moreover, these results warrant caution as to the classification of TLS as mutagenic or error-free based on in vitro data or on the analysis of mutations induced in MMR-proficient cells.
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Affiliation(s)
| | - Cécile Mingard
- Department of Health Sciences and Technology, ETH Zürich, Zürich, 8092, Switzerland
| | - Michael Räz
- Department of Health Sciences and Technology, ETH Zürich, Zürich, 8092, Switzerland
| | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Utrecht, 3584CS, the Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Utrecht, 3584CS, the Netherlands
| | - Ruben Van Boxtel
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Utrecht, 3584CS, the Netherlands
| | - Niels De Wind
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333AL, the Netherlands.
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Zürich, 8092, Switzerland.
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23
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Ajay A, Begum T, Arya A, Kumar K, Ahmad S. Global and local genomic features together modulate the spontaneous single nucleotide mutation rate. Comput Biol Chem 2024; 112:108107. [PMID: 38875896 DOI: 10.1016/j.compbiolchem.2024.108107] [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: 08/10/2023] [Revised: 04/23/2024] [Accepted: 05/17/2024] [Indexed: 06/16/2024]
Abstract
Spontaneous mutations are evolutionary engines as they generate variants for the evolutionary downstream processes that give rise to speciation and adaptation. Single nucleotide mutations (SNM) are the most abundant type of mutations among them. Here, we perform a meta-analysis to quantify the influence of selected global genomic parameters (genome size, genomic GC content, genomic repeat fraction, number of coding genes, gene count, and strand bias in prokaryotes) and local genomic features (local GC content, repeat content, CpG content and the number of SNM at CpG islands) on spontaneous SNM rates across the tree of life (prokaryotes, unicellular eukaryotes, multicellular eukaryotes) using wild-type sequence data in two different taxon classification systems. We find that the spontaneous SNM rates in our data are correlated with many genomic features in prokaryotes and unicellular eukaryotes irrespective of their sample sizes. On the other hand, only the number of coding genes was correlated with the spontaneous SNM rates in multicellular eukaryotes primarily contributed by vertebrates data. Considering local features, we notice that local GC content and CpG content significantly were correlated with the spontaneous SNM rates in the unicellular eukaryotes, while local repeat fraction is an important feature in prokaryotes and certain specific uni- and multi-cellular eukaryotes. Such predictive features of the spontaneous SNM rates often support non-linear models as the best fit compared to the linear model. We also observe that the strand asymmetry in prokaryotes plays an important role in determining the spontaneous SNM rates but the SNM spectrum does not.
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Affiliation(s)
- Akash Ajay
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Tina Begum
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Ajay Arya
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Krishan Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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24
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Okada S, Serizawa M, Sato F, Goto S, Nagashima T, Ohshima K, Sugino T, Urakami K, Kenmotsu H, Akiyama Y, Yamaguchi K, Mukaigawa T. Biphenotypic sinonasal sarcoma diagnosed by detection of PAX3-MAML3 fusion gene using integrated whole-genome and transcriptome sequencing. Int Cancer Conf J 2024; 13:412-421. [PMID: 39398935 PMCID: PMC11464723 DOI: 10.1007/s13691-024-00703-4] [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: 03/03/2024] [Accepted: 07/04/2024] [Indexed: 10/15/2024] Open
Abstract
Biphenotypic sinonasal sarcoma (BSNS) is a double-phenotype sarcoma that shows differentiation in both the nervous and muscular systems. To date, whole-genome and transcriptome sequencing (WGTS) has not been used to analyze BSNS. We report a patient with BSNS who was diagnosed based on PAX3 rearrangement using WGTS. A 71-year-old Japanese male without remarkable symptoms showed a nasal tumor when undergoing computed tomography. Although pathological examination revealed a non-characteristic spindle cell tumor, a definitive diagnosis could not be made based on this examination. Endoscopic sinus surgery was performed for subsequent diagnosis, treatment, and WGTS. WGTS revealed a t(2; 4)(q35; q31.1) reciprocal translocation, resulting in a PAX3-MAML3 fusion gene, leading to a definitive diagnosis of BSNS. We also detected upregulation of the expression of PAX3, MAML3, and 11 known genes involved in neural and myogenic differentiation relevant to the BSNS phenotype. Hence, using WGTS in combination with conventional pathological diagnosis can contribute to a definitive diagnosis of rare cancers, including BSNS, by detecting chromosomal rearrangements or diagnostic markers.
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Affiliation(s)
- Shinichi Okada
- Division of Head and Neck Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo Nagaizumi-Cho Sunto-Gun, Shizuoka, 411-8777 Japan
| | - Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Fuyuki Sato
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Seiya Goto
- Division of Head and Neck Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo Nagaizumi-Cho Sunto-Gun, Shizuoka, 411-8777 Japan
| | - Takeshi Nagashima
- SRL, Tokyo, Japan
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Keiichi Ohshima
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
- Division of Genomic Medicine Promotion, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | | | - Takashi Mukaigawa
- Division of Head and Neck Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo Nagaizumi-Cho Sunto-Gun, Shizuoka, 411-8777 Japan
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25
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Ren P, Zhang J, Vijg J. Somatic mutations in aging and disease. GeroScience 2024; 46:5171-5189. [PMID: 38488948 PMCID: PMC11336144 DOI: 10.1007/s11357-024-01113-3] [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: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jie Zhang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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26
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Liu L, Zhang J, Wood S, Newell F, Leonard C, Koufariotis LT, Nones K, Dalley AJ, Chittoory H, Bashirzadeh F, Son JH, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Simpson PT, Fielding D, Waddell N, Pearson JV. Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology. BMC Genomics 2024; 25:898. [PMID: 39350042 PMCID: PMC11441263 DOI: 10.1186/s12864-024-10792-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Lung cancer is a heterogeneous disease and the primary cause of cancer-related mortality worldwide. Somatic mutations, including large structural variants, are important biomarkers in lung cancer for selecting targeted therapy. Genomic studies in lung cancer have been conducted using short-read sequencing. Emerging long-read sequencing technologies are a promising alternative to study somatic structural variants, however there is no current consensus on how to process data and call somatic events. In this study, we preformed whole genome sequencing of lung cancer and matched non-tumour samples using long and short read sequencing to comprehensively benchmark three sequence aligners and seven structural variant callers comprised of generic callers (SVIM, Sniffles2, DELLY in generic mode and cuteSV) and somatic callers (Severus, SAVANA, nanomonsv and DELLY in somatic modes). RESULTS Different combinations of aligners and variant callers influenced somatic structural variant detection. The choice of caller had a significant influence on somatic structural variant detection in terms of variant type, size, sensitivity, and accuracy. The performance of each variant caller was assessed by comparing to somatic structural variants identified by short-read sequencing. When compared to somatic structural variants detected with short-read sequencing, more events were detected with long-read sequencing. The mean recall of somatic variant events identified by long-read sequencing was higher for the somatic callers (72%) than generic callers (53%). Among the somatic callers when using the minimap2 aligner, SAVANA and Severus achieved the highest recall at 79.5% and 79.25% respectively, followed by nanomonsv with a recall of 72.5%. CONCLUSION Long-read sequencing can identify somatic structural variants in clincal samples. The longer reads have the potential to improve our understanding of cancer development and inform personalized cancer treatment.
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Affiliation(s)
- Lingchen Liu
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Jia Zhang
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Andrew J Dalley
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Haarika Chittoory
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Jung Hwa Son
- Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Daniel Steinfort
- Department of Thoracic Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | | | - Michael Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Australia
| | - Carl Pahoff
- Department of Thoracic Medicine, Gold Coast University Hospital, Southport, Australia
| | - Phan T Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, Australia
| | - Scott Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - David Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - Christopher Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - Peter T Simpson
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - David Fielding
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Australia.
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
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27
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John E, Lesluyes T, Baker TM, Tarabichi M, Gillenwater A, Wang JR, Van Loo P, Zhao X. Reconstructing oral cavity tumor evolution through brush biopsy. Sci Rep 2024; 14:22591. [PMID: 39343812 PMCID: PMC11439926 DOI: 10.1038/s41598-024-72946-3] [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: 02/11/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024] Open
Abstract
Oral potentially malignant disorders (OPMDs) with genomic alterations have a heightened risk of evolving into oral squamous cell carcinoma (OSCC). Currently, genomic data are typically obtained through invasive tissue biopsy. However, brush biopsy is a non-invasive method that has been utilized for identifying dysplastic cells in OPMD but its effectiveness in reflecting the genomic landscape of OPMDs remains uncertain. This pilot study investigates the potential of brush biopsy samples in accurately reconstructing the genomic profile and tumor evolution in a patient with both OPMD and OSCC. We analyzed single nucleotide variants (SNVs), copy number aberrations (CNAs), and subclonal architectures in paired tissue and brush biopsy samples. The results showed that brush biopsy effectively captured 90% of SNVs and had similar CNA profiles as those seen in its paired tissue biopsies in all lesions. It was specific, as normal buccal mucosa did not share these genomic alterations. Interestingly, brush biopsy revealed shared SNVs and CNAs between the distinct OPMD and OSCC lesions from the same patient, indicating a common ancestral origin. Subclonal reconstruction confirmed this shared ancestry, followed by divergent evolution of the lesions. These findings highlight the potential of brush biopsies in accurately representing the genomic profile of OPL and OSCC, proving insight into reconstructing tumor evolution.
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Affiliation(s)
- Evit John
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, FCT 10.6008, 77030, TX, Houston, USA
| | | | - Toby M Baker
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, FCT 10.6008, 77030, TX, Houston, USA
- The Francis Crick Institute, London, UK
| | - Maxime Tarabichi
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Ann Gillenwater
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, TX, Houston, USA
| | - Jennifer R Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, TX, Houston, USA
| | - Peter Van Loo
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, FCT 10.6008, 77030, TX, Houston, USA
- The Francis Crick Institute, London, UK
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, TX, Houston, USA
| | - Xiao Zhao
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, FCT 10.6008, 77030, TX, Houston, USA.
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, TX, Houston, USA.
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28
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Liu F, Hu N, Jiang K, Liu H, Wang M, Hu Y, Zhang T, Wu HH, Yang H, Weng H, Dong P, Giffen C, Zhu B, Lee MP, Abnet CC, Taylor PR, Liu Y, Liu Y, Goldstein AM. Mutational signatures in 175 Chinese gastric cancer patients. BMC Cancer 2024; 24:1208. [PMID: 39350044 PMCID: PMC11440915 DOI: 10.1186/s12885-024-12968-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 09/19/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Gastric cancer (GC), a molecularly heterogeneous disease, is the third leading cause of cancer death worldwide. The majority of GC cases worldwide occur in East Asia, predominantly China. Mutational Signature Framework offers an elegant approach to identify mutational processes present in tumors. METHODS To identify mutational signature patterns, we conducted whole exome sequencing (WES) analysis in Chinese patients with GC. Mutect2 and MutsigCV were used to identify significantly mutated genes in 175 Chinese GC cases using paired tumor-normal tissues. We investigated mutational signatures using Catalogue of Somatic Mutations in Cancer (COSMIC) Version 2 (V2) and Version 3 (V3). RESULTS We identified 104 mutated genes with P < 0.01. Seven genes (OR6B1, B2M, ELF3, RHOA, RPL22, TP53, ARIDIA) had q < 0.0001, including six previously associated with GC. Mutational signatures (COSMIC-V3) observed include 14 single base substitutions (SBS), one doublet base substitution (DBS) Signature A, and one InDel (ID2). The most frequent SBS signatures (SBS05, SBS01, SBS15, SBS20, SBS40) were also observed in 254 White GC cases from The Cancer Genome Atlas (TCGA) Project. However, SBS01 and SBS20 showed significant differences between Whites vs. All Asians (19.3% vs. 11.3% for SBS 1 (P = 0.012) and 11.4% vs. 5.9% for SBS20 (P = 0.025), respectively). Using COSMIC V2, signatures 6, 15, and 1 were the most frequent in Chinese GC cases. Further, most Chinese GC cases carried multiple signatures. CONCLUSIONS This effort represents the most detailed mutational signatures analysis of GC cases from China to date. Results hold promise for new insights in understanding risk and prognosis factors in GC.
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Affiliation(s)
- Fatao Liu
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, P. R. China
- Department of General Surgery, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200092, P. R. China
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Kewei Jiang
- Department of Gastrointestinal Surgery, Peking University People's Hospital, Beijing, 100044, P. R. China
| | - Huaitian Liu
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ying Hu
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ho-Hsiang Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Howard Yang
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Hao Weng
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, P. R. China
- Department of General Surgery, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200092, P. R. China
| | - Ping Dong
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, P. R. China
- Department of General Surgery, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200092, P. R. China
| | - Carol Giffen
- Information Management Services, Inc, Silver Spring, Bethesda, MD, 20904, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Maxwell P Lee
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Yun Liu
- Department of Oncology, Fudan University Pudong Medical Center, Shanghai, P. R. China.
| | - Yingbin Liu
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, P. R. China.
- Department of General Surgery, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200092, P. R. China.
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA.
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29
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Tian Y, Wang X, Wu C, Qiao J, Jin H, Li H. A protracted war against cancer drug resistance. Cancer Cell Int 2024; 24:326. [PMID: 39342202 PMCID: PMC11439304 DOI: 10.1186/s12935-024-03510-2] [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: 04/11/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
Currently, even the most effective anti-cancer therapies are often limited by the development of drug resistance and tumor relapse, which is a major challenge facing current cancer research. A deep understanding of the molecular and biochemical bases of drug efficacy that can help predict the clinical drug resistance, coupled with the evolution of systematic genomic and proteomic technologies, have facilitated studies identifying and elucidating the underlying mechanisms. In this review, we focus on several important issues on cancer drug resistance and provide a framework for understanding the common ways by which cancers develop resistance to therapeutic agents. With the increasing arsenal of novel anticancer agents and techniques, there are now unprecedented opportunities to understand and overcome drug resistance. The proteolysis targeting chimera (PROTAC) technology, immunotherapy, nanomedicine, and real-time monitoring of drug response all provide effective approaches for combating drug resistance. In addition to the advancement of therapeutic technologies, the revolution of treatment concept is also of great importance. We can take advantage of the interplay between drug sensitive and resistant subclones for combating cancer. However, there remains a long way to go in the protracted war against cancer drug resistance.
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Affiliation(s)
- Yuan Tian
- School of Lifesciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, P.R. China
| | - Xiaowei Wang
- Department of Thoracic Surgery/Clinical Research Center, The First Affiliated Hospital of Navy Medical University, 168 Changhai Road, Shanghai, 200433, P.R. China
| | - Cong Wu
- Department of Thoracic Surgery/Clinical Research Center, The First Affiliated Hospital of Navy Medical University, 168 Changhai Road, Shanghai, 200433, P.R. China
| | - Jiaming Qiao
- School of Lifesciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, P.R. China
| | - Hai Jin
- Department of Thoracic Surgery/Clinical Research Center, The First Affiliated Hospital of Navy Medical University, 168 Changhai Road, Shanghai, 200433, P.R. China.
| | - Huafei Li
- School of Lifesciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, P.R. China.
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30
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Guest RV, Goeppert B, Nault JC, Sia D. Morphomolecular pathology and Genomic Insights into the Cells of Origin of Cholangiocarcinoma and combined Hepatocellular-Cholangiocarcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00357-2. [PMID: 39341365 DOI: 10.1016/j.ajpath.2024.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 10/01/2024]
Abstract
Cholangiocarcinoma is a highly heterogenous group of malignancies that, despite recent progress in the understanding of its molecular pathogenesis and clinical management, continue to pose a major challenge to public health. The traditional view posits that cholangiocarcinomas derive from the neoplastic transformation of cholangiocytes lining the biliary tree. However, increasing genetic and experimental evidence has recently pointed to a more complex - and nuanced - scenario for the potential cell of origin of cholangiocarcinomas, with hepatocytes as well as hepatic stem/progenitor cells being considered as additional potential sources, depending on microenvironmental contexts including liver injury. The hypothesis of potentially diverse cells of origin for CCA, albeit controversial, is certainly not surprising given the plasticity of the cells populating the liver as well as the existence of liver cancer subtypes with mixed histological and molecular features. This review carefully looks at the current pathological, genomic and experimental evidence supporting the existence of multiple cells of origin of liver and biliary tract cancers, with particular focus on cholangiocarcinoma and combined hepatocellular-cholangiocarcinoma.
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Affiliation(s)
- Rachel V Guest
- Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, United Kingdom
| | - Benjamin Goeppert
- Institute of Pathology, RKH Klinikum Ludwigsburg, 71640 Ludwigsburg, Germany; Institute of Tissue Medicine and Pathology, University of Bern, Switzerland
| | - Jean-Charles Nault
- Centre de recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France; Liver unit, Avicenne Hospital, APHP, Bobigny, France, University Sorbonne Paris Nord, Bobigny, France
| | - Daniela Sia
- Division of Liver Diseases, Liver Cancer Program, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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31
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Zhang C, Lu YJ, Wang M, Chen B, Xiong F, Mitsopoulos C, Rossanese O, Li X, Clarke PA. Characterisation of APOBEC3B-Mediated RNA editing in breast cancer cells reveals regulatory roles of NEAT1 and MALAT1 lncRNAs. Oncogene 2024:10.1038/s41388-024-03171-5. [PMID: 39322638 DOI: 10.1038/s41388-024-03171-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 08/30/2024] [Accepted: 09/13/2024] [Indexed: 09/27/2024]
Abstract
RNA editing is a crucial post-transcriptional process that influences gene expression and increases the diversity of the proteome as a result of amino acid substitution. Recently, the APOBEC3 family has emerged as a significant player in this mechanism, with APOBEC3A (A3A) having prominent roles in base editing during immune and stress responses. APOBEC3B (A3B), another family member, has gained attention for its potential role in generating genomic DNA mutations in breast cancer. In this study, we coupled an inducible expression cell model with a novel methodology for identifying differential variants in RNA (DVRs) to map A3B-mediated RNA editing sites in a breast cancer cell model. Our findings indicate that A3B engages in selective RNA editing including targeting NEAT1 and MALAT1 long non-coding RNAs that are often highly expressed in tumour cells. Notably, the binding of these RNAs sequesters A3B and suppresses global A3B activity against RNA and DNA. Release of A3B from NEAT1/MALAT1 resulted in increased A3B activity at the expense of A3A activity suggesting a regulatory feedback loop between the two family members. This research substantially advances our understanding of A3B's role in RNA editing, its mechanistic underpinnings, and its potential relevance in the pathogenesis of breast cancer.
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Affiliation(s)
- Chi Zhang
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, UK
- Shanghai Institute of Biological Products, Shanghai, China
| | - Yu-Jing Lu
- Guangdong Medicine-Engineering Interdisciplinary Technology Research Centre, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Mei Wang
- Shanghai Institute of Biological Products, Shanghai, China
| | - Bingjie Chen
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, UK
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Feifei Xiong
- Shanghai Institute of Biological Products, Shanghai, China
| | - Costas Mitsopoulos
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, UK
| | - Olivia Rossanese
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, UK
| | - Xiuling Li
- Shanghai Institute of Biological Products, Shanghai, China.
| | - Paul A Clarke
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, UK.
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32
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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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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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Kapadia CD, Williams N, Dawson KJ, Watson C, Yousefzadeh MJ, Le D, Nyamondo K, Cagan A, Waldvogel S, De La Fuente J, Leongamornlert D, Mitchell E, Florez MA, Aguilar R, Martell A, Guzman A, Harrison D, Niedernhofer LJ, King KY, Campbell PJ, Blundell J, Goodell MA, Nangalia J. Clonal dynamics and somatic evolution of haematopoiesis in mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613129. [PMID: 39345649 PMCID: PMC11429886 DOI: 10.1101/2024.09.17.613129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Haematopoietic stem cells maintain blood production throughout life. While extensively characterised using the laboratory mouse, little is known about how the population is sustained and evolves with age. We isolated stem cells and progenitors from young and old mice, identifying 221,890 somatic mutations genome-wide in 1845 single cell-derived colonies, and used phylogenetic analysis to infer the ontogeny and population dynamics of the stem cell pool. Mouse stem cells and progenitors accrue ~45 somatic mutations per year, a rate only about 2-fold greater than human progenitors despite the vastly different organismal sizes and lifespans. Phylogenetic patterns reveal that stem and multipotent progenitor cell pools are both established during embryogenesis, after which they independently self-renew in parallel over life. The stem cell pool grows steadily over the mouse lifespan to approximately 70,000 cells, self-renewing about every six weeks. Aged mice did not display the profound loss of stem cell clonal diversity characteristic of human haematopoietic ageing. However, targeted sequencing revealed small, expanded clones in the context of murine ageing, which were larger and more numerous following haematological perturbations and exhibited a selection landscape similar to humans. Our data illustrate both conserved features of population dynamics of blood and distinct patterns of age-associated somatic evolution in the short-lived mouse.
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Affiliation(s)
- Chiraag D. Kapadia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Kevin J. Dawson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Caroline Watson
- Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Matthew J. Yousefzadeh
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Columbia Center for Translational Immunology, Columbia Center for Human Longevity, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Duy Le
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Kudzai Nyamondo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Departments of Genetics, Pathology & Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Josephine De La Fuente
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Emily Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Marcus A. Florez
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Rogelio Aguilar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Alejandra Martell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Anna Guzman
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Katherine Y. King
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA
| | | | - Jamie Blundell
- Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Margaret A. Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
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Wiens M, Farahani H, Scott RW, Underhill TM, Bashashati A. Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries. Genome Res 2024; 34:1196-1210. [PMID: 39147582 PMCID: PMC11444184 DOI: 10.1101/gr.277066.122] [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: 08/05/2023] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
Single-cell sequencing methodologies such as scRNA-seq and scATAC-seq have become widespread and effective tools to interrogate tissue composition. Increasingly, variant callers are being applied to these methodologies to resolve the genetic heterogeneity of a sample, especially in the case of detecting the clonal architecture of a tumor. Typically, traditional bulk DNA variant callers are applied to the pooled reads of a single-cell library to detect candidate mutations. Recently, multiple studies have applied such callers on reads from individual cells, with some citing the ability to detect rare variants with higher sensitivity. Many studies apply these two approaches to the Chromium (10x Genomics) scRNA-seq and scATAC-seq methodologies. However, Chromium-based libraries may offer additional challenges to variant calling compared with existing single-cell methodologies, raising questions regarding the validity of variants obtained from such a workflow. To determine the merits and challenges of various variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries, we use sample libraries with matched bulk whole-genome sequencing to evaluate the performance of callers. We review caller performance, finding that bulk callers applied on pooled reads significantly outperform individual-cell approaches. We also evaluate variants unique to scRNA-seq and scATAC-seq methodologies, finding patterns of noise but also potential capture of RNA-editing events. Finally, we review the notion that variant calling at the single-cell level can detect rare somatic variants, providing empirical results that suggest resolving such variants is infeasible in single-cell Chromium libraries.
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Affiliation(s)
- Matthew Wiens
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 2B9, Canada
| | - Hossein Farahani
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 2B9, Canada
| | - R Wilder Scott
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 2B9, Canada
| | - T Michael Underhill
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 2B9, Canada
- Department of Cellular & Physiological Sciences, University of British Columbia, Vancouver, British Columbia V6T 2A1, Canada
| | - Ali Bashashati
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 2B9, Canada;
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada
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36
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Diossy M, Tisza V, Li H, Sahgal P, Zhou J, Sztupinszki Z, Young D, Nousome D, Kuo C, Jiang J, Chen Y, Ebner R, Sesterhenn IA, Moncur JT, Chesnut GT, Petrovics G, Klus GT, Valcz G, Nuzzo PV, Ribli D, Börcsök J, Prosz A, Krzystanek M, Ried T, Szuts D, Rizwan K, Kaochar S, Pathania S, D'Andrea AD, Csabai I, Srivastava S, Freedman ML, Dobi A, Spisak S, Szallasi Z. Frequent CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression. NPJ Precis Oncol 2024; 8:208. [PMID: 39294262 PMCID: PMC11411125 DOI: 10.1038/s41698-024-00705-8] [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: 02/27/2024] [Accepted: 09/11/2024] [Indexed: 09/20/2024] Open
Abstract
We analyzed genomic data from the prostate cancer of African- and European American men to identify differences contributing to racial disparity of outcome. We also performed FISH-based studies of Chromodomain helicase DNA-binding protein 1 (CHD1) loss on prostate cancer tissue microarrays. We created CHD1-deficient prostate cancer cell lines for genomic, drug sensitivity and functional homologous recombination (HR) activity analysis. Subclonal deletion of CHD1 was nearly three times as frequent in prostate tumors of African American than in European American men and it associates with rapid disease progression. CHD1 deletion was not associated with HR deficiency associated mutational signatures or HR deficiency as detected by RAD51 foci formation. This was consistent with the moderate increase of olaparib and talazoparib sensitivity with several CHD1 deficient cell lines showing talazoparib sensitivity in the clinically relevant concentration range. CHD1 loss may contribute to worse disease outcome in African American men.
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Affiliation(s)
- Miklos Diossy
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hua Li
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Pranshu Sahgal
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Denise Young
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Darryl Nousome
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Claire Kuo
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Jiji Jiang
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Yongmei Chen
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | | | | | | | - Gregory T Chesnut
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Gregory T Klus
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Gabor Valcz
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, 1051, Hungary
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dezso Ribli
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | | | - Aurel Prosz
- Danish Cancer Institute, Copenhagen, Denmark
| | | | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - David Szuts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Kinza Rizwan
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Salma Kaochar
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA, USA
- Department of Biology, University of Massachusetts, Boston, MA, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Shiv Srivastava
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Biochemistry and Molecular & Cell Biology, Georgetown University School of Medicine, Washington, DC, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA.
| | - Sandor Spisak
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- 2nd Department of Pathology and Department of Bioinformatics, Semmelweis University, Budapest, Hungary.
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Sugiyama T. Biochemical reconstitution of heat-induced mutational processes. PLoS One 2024; 19:e0310601. [PMID: 39288122 PMCID: PMC11407675 DOI: 10.1371/journal.pone.0310601] [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: 04/04/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Non-enzymatic spontaneous deamination of 5-methylcytosine, producing thymine, is the proposed etiology of cancer mutational signature 1, which is the most predominant signature in all cancers. Here, the proposed mutational process was reconstituted using synthetic DNA and purified proteins. First, single-stranded DNA containing 5-methylcytosine at CpG context was incubated at an elevated temperature to accelerate spontaneous DNA damage. Then, the DNA was treated with uracil DNA glycosylase to remove uracil residues that were formed by deamination of cytosine. The resulting DNA was then used as a template for DNA synthesis by yeast DNA polymerase δ. The DNA products were analyzed by next-generation DNA sequencing, and mutation frequencies were quantified. The observed mutations after this process were exclusively C>T mutations at CpG context, which was very similar to signature 1. When 5-methylcytosine modification and uracil DNA glycosylase were both omitted, C>T mutations were produced on C residues in all sequence contexts, but these mutations were diminished by uracil DNA glycosylase-treatment. These results indicate that the CpG>TpG mutations were produced by the deamination of 5-methylcytosine. Additional mutations, mainly C>G, were introduced by yeast DNA polymerase ζ on the heat-damaged DNA, indicating that G residues of the templates were also damaged. However, the damage on G residues was not converted to mutations with DNA polymerase δ or ε.
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Affiliation(s)
- Tomohiko Sugiyama
- Department of Biological Sciences, Ohio University, Athens, Ohio, United States of America
- Molecular and Cellular Biology Graduate Program, Ohio University, Athens, Ohio, United States of America
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Menon V, García-Ruiz A, Neveu S, Cartmel B, Ferrucci LM, Palmatier M, Ko C, Tsai KY, Nakamura M, Kim SR, Girardi M, Kornacker K, Brash DE. Pervasive Induction of Regulatory Mutation Microclones in Sun-exposed Skin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.12.612526. [PMID: 39345638 PMCID: PMC11429607 DOI: 10.1101/2024.09.12.612526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Carcinogen-induced mutations are thought near-random, with rare cancer-driver mutations underlying clonal expansion. Using high-fidelity Duplex Sequencing to reach a mutation frequency sensitivity of 4×10 -9 per nt, we report that sun exposure creates pervasive mutations at sites with ∼100-fold UV-sensitivity in RNA-processing gene promoters - cyclobutane pyrimidine dimer (CPD) hyperhotspots - and these mutations have a mini-driver clonal expansion phenotype. Numerically, human skin harbored 10-fold more genuine mutations than previously reported, with neonatal skin containing 90,000 per cell; UV signature mutations increased 8,000-fold in sun-exposed skin, averaging 3×10 -5 per nt. Clonal expansion by neutral drift or passenger formation was nil. Tumor suppressor gene hotspots reached variant allele frequency 0.1-10% via 30-3,000 fold clonal expansion, in occasional biopsies. CPD hyperhotspots reached those frequencies in every biopsy, with modest clonal expansion. In vitro, tumor hotspot mutations arose occasionally over weeks of chronic low-dose exposure, whereas CPD hyperhotspot mutations arose in days at 1000-fold higher frequencies, growing exponentially. UV targeted mini-drivers in every skin cell.
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39
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Lin DI, Quintanilha JCF, Danziger N, Lang L, Levitan D, Hayne C, Hiemenz MC, Smith DL, Albacker LA, Leibowitz J, Mata DA, Decker B, Lakis S, Patel NR, Graf RP, Elvin JA, Ross JS, Pattani V, Huang RSP, Wehn AK. Pan-tumor validation of a NGS fraction-based MSI analysis as a predictor of response to Pembrolizumab. NPJ Precis Oncol 2024; 8:204. [PMID: 39277692 PMCID: PMC11401835 DOI: 10.1038/s41698-024-00679-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/26/2024] [Indexed: 09/17/2024] Open
Abstract
Microsatellite instability high (MSI-H) and mismatch repair deficient (dMMR) tumor status have been demonstrated to predict patient response to immunotherapies. We developed and validated a next-generation sequencing (NGS)-based companion diagnostic (CDx) to detect MSI-H solid tumors via a comprehensive genomic profiling (CGP) assay, FoundationOne®CDx (F1CDx). To determine MSI status, F1CDx calculates the fraction of unstable microsatellite loci across >2000 loci using a fraction-based (FB) analysis. Across solid tumor types, F1CDx demonstrated a high analytical concordance with both PCR (n = 264) and IHC (n = 279) with an overall percent agreement (OPA) of 97.7% and 97.8%, respectively. As part of a retrospective bridging clinical study from KEYNOTE-158 Cohort K and KEYNOTE-164, patients with MSI-H tumors as determined by F1CDx demonstrated an objective response rate (ORR) of 43.0% to pembrolizumab. In real-world cancer patients from a deidentified clinicogenomic database, F1CDx was at least equivalent in assessing clinical outcome following immunotherapy compared with MMR IHC. Demonstrated analytical and clinical performance of F1CDx led to the pan-tumor FDA approval in 2022 of F1CDx to identify MSI-H solid tumor patients for treatment with pembrolizumab. F1CDx is an accurate, reliable, and FDA-approved method for the identification of MSI-H tumors for treatment with pembrolizumab.
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Affiliation(s)
| | | | | | | | | | - Cynthia Hayne
- Beth Israel Deaconess Medical Center, Boston, MA, USA
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40
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Pinheiro M, Wentzensen N, Dean M, Yeager M, Chen Z, Shastry A, Boland JF, Bass S, Burdett L, Lorey T, Mishra S, Castle PE, Schiffman M, Burk RD, Zhu B, Mirabello L. Somatic mutations in 3929 HPV positive cervical cells associated with infection outcome and HPV type. Nat Commun 2024; 15:7895. [PMID: 39266536 PMCID: PMC11393421 DOI: 10.1038/s41467-024-51713-y] [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: 12/05/2023] [Accepted: 08/13/2024] [Indexed: 09/14/2024] Open
Abstract
Invasive cervical cancers (ICC), caused by HPV infections, have a heterogeneous molecular landscape. We investigate the detection, timing, and HPV type specificity of somatic mutations in 3929 HPV-positive exfoliated cervical cell samples from individuals undergoing cervical screening in the U.S. using deep targeted sequencing in ICC cases, precancers, and HPV-positive controls. We discover a subset of hotspot mutations rare in controls (2.6%) but significantly more prevalent in precancers, particularly glandular precancer lesions (10.2%), and cancers (25.7%), supporting their involvement in ICC carcinogenesis. Hotspot mutations differ by HPV type, and HPV18/45-positive ICC are more likely to have multiple hotspot mutations compared to HPV16-positive ICC. The proportion of cells containing hotspot mutations is higher (i.e., higher variant allele fraction) in ICC and mutations are detectable up to 6 years prior to cancer diagnosis. Our findings demonstrate the feasibility of using exfoliated cervical cells for detection of somatic mutations as potential diagnostic biomarkers.
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Affiliation(s)
- Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Department of Biology, Hood College, Frederick, MD, USA
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Amulya Shastry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Thomas Lorey
- Regional Laboratory and Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Sambit Mishra
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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Rodrigues LM, Maistro S, Katayama MLH, Rocha VM, Lopez RVM, Lopes EFDT, Gonçalves FT, Fridman C, Serio PADMP, Barros LRC, Leite LAS, Segatelli V, Estevez-Diz MDP, Guindalini RSC, Ribeiro Junior U, Folgueira MAAK. Prevalence of germline variants in Brazilian pancreatic carcinoma patients. Sci Rep 2024; 14:21083. [PMID: 39256447 PMCID: PMC11387492 DOI: 10.1038/s41598-024-71884-4] [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: 05/06/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
We evaluated the prevalence of pathogenic/likely pathogenic germline variants (PGV) in Brazilian pancreatic adenocarcinoma (PC) patients, that represent a multiethnic population, in a cross-sectional study. We included 192 PC patients unselected for family history of cancer. We evaluated a panel of 113 cancer genes, through genomic DNA sequencing and 46 ancestry-informative markers, through multiplex PCR. The median age was 61 years; 63.5% of the patients presented disease clinical stages III or IV; 8.3% reported personal history of cancer; 4.7% and 16.1% reported first-degree relatives with PC or breast and/or prostate cancer, respectively. Although the main ancestry was European, there was considerable genetic composition admixture. Twelve patients (6.25%) were PGV carriers in PC predisposition genes (ATM, BRCA1, BRCA2, CDKN2A, MSH2, PALB2) and another 25 (13.0%) were PGV carriers in genes with a limited association or not previously associated with PC (ACD, BLM, BRIP1, CHEK2, ERCC4, FANCA, FANCE, FANCM, GALNT12, MITF, MRE11, MUTYH, POLE, RAD51B, RAD51C, RECQL4, SDHA, TERF2IP). The most frequently affected genes were CHEK2, ATM and FANC. In tumor samples from PGV carriers in ACD, BRIP1, MRE11, POLE, SDHA, TERF2IP, which were examined through exome sequencing, the main single base substitutions (SBS) mutational signature was SBS1+5+18, probably associated with age, tobacco smoking and reactive oxygen species. SBS3 associated with homologous repair deficiency was also represented, but on a lower scale. There was no difference in the frequency of PGV carriers between: (a) patients with or without first-degree relatives with cancer; and (b) patients with admixed ancestry versus those with predominantly European ancestry. Furthermore, there was no difference in overall survival between PGV carriers and non-carriers. Therefore, genetic testing should be offered to all Brazilian pancreatic cancer patients, regardless of their ancestry. Genes with limited or previously unrecognized associations with pancreatic cancer should be further investigated to clarify their role in cancer risk.
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Affiliation(s)
- Lívia Munhoz Rodrigues
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Simone Maistro
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Maria Lucia Hirata Katayama
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Vinícius Marques Rocha
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Rossana Veronica Mendoza Lopez
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Edia Filomena di Tullio Lopes
- Registro Hospitalar de Cancer, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, São Paulo, SP, Brazil
| | - Fernanda Toledo Gonçalves
- Departamento de Medicina Legal, Bioetica, Medicina do Trabalho e Medicina Física e Reabilitação, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Cintia Fridman
- Departamento de Medicina Legal, Bioetica, Medicina do Trabalho e Medicina Física e Reabilitação, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | | | - Luciana Rodrigues Carvalho Barros
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Luiz Antonio Senna Leite
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Vanderlei Segatelli
- Departamento de Patologia Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Maria Del Pilar Estevez-Diz
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | | | - Ulysses Ribeiro Junior
- Division of Digestive Surgery, Department of Gastroenterology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo FMUSP, Sao Paulo, SP, Brazil
| | - Maria Aparecida Azevedo Koike Folgueira
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil.
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Peroz M, Mananet H, Roussot N, Kaderbhai CG, Derangère V, Truntzer C, Ghiringhelli F. Clinical Interest in Exome-Based Analysis of Somatic Mutational Signatures for Non-Small Cell Lung Cancer. Cancers (Basel) 2024; 16:3115. [PMID: 39272973 PMCID: PMC11393922 DOI: 10.3390/cancers16173115] [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: 08/01/2024] [Revised: 08/29/2024] [Accepted: 09/06/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality. This study investigates the clinical interest of whole exome sequencing (WES) for analyzing somatic mutational signatures in patients with advanced or metastatic NSCLC treated with the current standard of care. METHODS Exome sequencing data and clinical characteristics from 132 patients with advanced or metastatic NSCLC were analyzed. Somatic mutational signatures including single base substitutions (SBSs), double base substitutions (DBSs), and copy number signatures were evaluated. Structural variations including tumor mutational burden (TMB), the number of neoantigens, TCR clonality, homologous recombination deficiency (HRD), copy number alterations (CNAs), and microsatellite instability (MSI) score were determined. The association between these genomic features, NSCLC subtypes, and patient outcomes (progression-free and overall survival) was evaluated. CONCLUSIONS Exome sequencing offers valuable insights into somatic mutational signatures in NSCLC. This study identified specific signatures associated with a poor response to immune checkpoint inhibitor (ICI) therapy and chemotherapy, potentially aiding treatment selection and identifying patients unlikely to benefit from these approaches.
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Affiliation(s)
- Morgane Peroz
- Platform of Transfer in Biological Oncology, Georges-Francois Leclerc Cancer Center-UNICANCER, 21000 Dijon, France
- Unité de Formation et de Recherche des Sciences de Santé, University of Burgundy-Franche-Comté, 21000 Dijon, France
- Unité Mixte de Recherche de l'Institut National de la Santé Et de la Recherche Médicale (INSERM) 1231, 21000 Dijon, France
| | - Hugo Mananet
- Platform of Transfer in Biological Oncology, Georges-Francois Leclerc Cancer Center-UNICANCER, 21000 Dijon, France
- Unité de Formation et de Recherche des Sciences de Santé, University of Burgundy-Franche-Comté, 21000 Dijon, France
- Unité Mixte de Recherche de l'Institut National de la Santé Et de la Recherche Médicale (INSERM) 1231, 21000 Dijon, France
| | - Nicolas Roussot
- Department of Medical Oncology, Georges François Leclerc Cancer Center-UNICANCER, 21000 Dijon, France
| | | | - Valentin Derangère
- Platform of Transfer in Biological Oncology, Georges-Francois Leclerc Cancer Center-UNICANCER, 21000 Dijon, France
- Unité de Formation et de Recherche des Sciences de Santé, University of Burgundy-Franche-Comté, 21000 Dijon, France
- Unité Mixte de Recherche de l'Institut National de la Santé Et de la Recherche Médicale (INSERM) 1231, 21000 Dijon, France
| | - Caroline Truntzer
- Platform of Transfer in Biological Oncology, Georges-Francois Leclerc Cancer Center-UNICANCER, 21000 Dijon, France
- Unité de Formation et de Recherche des Sciences de Santé, University of Burgundy-Franche-Comté, 21000 Dijon, France
- Unité Mixte de Recherche de l'Institut National de la Santé Et de la Recherche Médicale (INSERM) 1231, 21000 Dijon, France
| | - François Ghiringhelli
- Platform of Transfer in Biological Oncology, Georges-Francois Leclerc Cancer Center-UNICANCER, 21000 Dijon, France
- Unité de Formation et de Recherche des Sciences de Santé, University of Burgundy-Franche-Comté, 21000 Dijon, France
- Unité Mixte de Recherche de l'Institut National de la Santé Et de la Recherche Médicale (INSERM) 1231, 21000 Dijon, France
- Department of Medical Oncology, Georges François Leclerc Cancer Center-UNICANCER, 21000 Dijon, France
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43
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Vermulst M, Paskvan SL, Chung CS, Franke K, Clegg N, Minot S, Madeoy J, Long AS, Gout JF, Bielas JH. MADDD-seq, a novel massively parallel sequencing tool for simultaneous detection of DNA damage and mutations. Nucleic Acids Res 2024; 52:e76. [PMID: 39149908 PMCID: PMC11381349 DOI: 10.1093/nar/gkae632] [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: 10/28/2023] [Revised: 05/20/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024] Open
Abstract
Our genome is exposed to a wide variety of DNA-damaging agents. If left unrepaired, this damage can be converted into mutations that promote carcinogenesis or the development of genetically inherited diseases. As a result, researchers and clinicians require tools that can detect DNA damage and mutations with exceptional sensitivity. In this study, we describe a massively parallel sequencing tool termed Mutation And DNA Damage Detection-seq (MADDD-seq) that is capable of detecting O6-methyl guanine lesions and mutations simultaneously, with a single assay. To illustrate the dual capabilities of MADDD-seq, we treated WT and DNA repair deficient yeast cells with the DNA-damaging agent MNNG and tracked DNA lesions and mutations over a 24-h time period. This approach allowed us to identify thousands of DNA adducts and mutations in a single sequencing run and gain deep insight into the kinetics of DNA repair and mutagenesis.
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Affiliation(s)
- Marc Vermulst
- University of Southern California, Leonard Davis School of Gerontology, Los Angeles, CA, USA
| | - Samantha L Paskvan
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Claire S Chung
- University of Southern California, Leonard Davis School of Gerontology, Los Angeles, CA, USA
| | - Kathryn Franke
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nigel Clegg
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sam Minot
- Data Core, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jennifer Madeoy
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Annalyssa S Long
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
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44
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Jalan M, Sharma A, Pei X, Weinhold N, Buechelmaier ES, Zhu Y, Ahmed-Seghir S, Ratnakumar A, Di Bona M, McDermott N, Gomez-Aguilar J, Anderson KS, Ng CKY, Selenica P, Bakhoum SF, Reis-Filho JS, Riaz N, Powell SN. RAD52 resolves transcription-replication conflicts to mitigate R-loop induced genome instability. Nat Commun 2024; 15:7776. [PMID: 39237529 PMCID: PMC11377823 DOI: 10.1038/s41467-024-51784-x] [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: 12/15/2023] [Accepted: 08/15/2024] [Indexed: 09/07/2024] Open
Abstract
Collisions of the transcription and replication machineries on the same DNA strand can pose a significant threat to genomic stability. These collisions occur in part due to the formation of RNA-DNA hybrids termed R-loops, in which a newly transcribed RNA molecule hybridizes with the DNA template strand. This study investigated the role of RAD52, a known DNA repair factor, in preventing collisions by directing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Furthermore, RAD52's ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide evidence of an increased mutational burden from double-strand breaks at conserved R-loop sites in human tumor samples, which is increased in tumors with low RAD52 expression. In summary, this study underscores the importance of RAD52 in orchestrating the balance between replication and transcription processes to prevent collisions and maintain genome stability.
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Affiliation(s)
- Manisha Jalan
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA.
| | - Aman Sharma
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Xin Pei
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Nils Weinhold
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | | | - Yingjie Zhu
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
| | | | | | - Melody Di Bona
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
- Human Oncology and Pathogenesis, MSKCC, New York, NY, 10065, USA
| | - Niamh McDermott
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | | | - Kyrie S Anderson
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Bern, CH, 3008, Switzerland
- SIB, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
- Human Oncology and Pathogenesis, MSKCC, New York, NY, 10065, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
- AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA.
- Molecular Biology Program, MSKCC, New York, NY, 10065, USA.
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45
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Davidson B, Teien Lande K, Nebdal D, Nesbakken AJ, Holth A, Lindemann K, Zahl Eriksson AG, Sørlie T. Endometrial carcinomas with ambiguous histology often harbor TP53 mutations. Virchows Arch 2024:10.1007/s00428-024-03912-7. [PMID: 39235515 DOI: 10.1007/s00428-024-03912-7] [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: 07/06/2024] [Revised: 08/01/2024] [Accepted: 08/25/2024] [Indexed: 09/06/2024]
Abstract
The objective of the present study was to characterize the molecular features of endometrial carcinomas with ambiguous histology. Eighteen carcinomas that could not be conclusively typed based on morphology and immunohistochemistry underwent analysis of mismatch repair (MMR) status, microsatellite status, and whole-exome sequencing. None of the tumors had pathogenic POLE mutation. Twelve tumors (67%) were microsatellite stable, and 6 (33%) had microsatellite instability. Fourteen tumors (78%) harbored TP53 mutations, and 2 (11%) had mutations in MMR genes. Eleven carcinomas (61%) were classified as copy number high and 7 (39%) as MSI-hypermutated, the latter including 3 tumors with TP53 mutation who concomitantly had MSI or mutation in a MMR gene. Other mutations that were found in > 1 tumor affected MUC16 (7 tumors), PIK3CA (6 tumors), PPP2R1A (6 tumors), ARID1A (5 tumors), PTEN (5 tumors), FAT1 (4 tumors), FAT4 (3 tumors), BRCA2 (2 tumors), ERBB2 (2 tumors), FBXW7 (2 tumors), MET (2 tumors), MTOR (2 tumors), JAK1 (2 tumors), and CSMD3 (2 tumors). At the last follow-up (median = 68.6 months), 8 patients had no evidence of disease, 1 patient was alive with disease, 8 patients were dead of disease, and 1 patient died of other cause. In conclusion, based on this series, the molecular landscape of endometrial carcinomas with ambiguous histology is dominated by TP53 mutations and the absence of POLE mutations, with heterogeneous molecular profile with respect to other genes. A high proportion of these tumors is clinically aggressive.
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Affiliation(s)
- Ben Davidson
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway.
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, N-0316, Oslo, Norway.
| | - Karin Teien Lande
- Department of Cancer Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
| | - Daniel Nebdal
- Department of Cancer Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
| | - Anne Jorunn Nesbakken
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
| | - Arild Holth
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
| | - Kristina Lindemann
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, N-0316, Oslo, Norway
- Section for Gynecologic Oncology, Division of Surgical Oncology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ane Gerda Zahl Eriksson
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, N-0316, Oslo, Norway
- Section for Gynecologic Oncology, Division of Surgical Oncology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Therese Sørlie
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, N-0316, Oslo, Norway.
- Department of Cancer Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway.
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46
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Basyuni S, Heskin L, Degasperi A, Black D, Koh GCC, Chmelova L, Rinaldi G, Bell S, Grybowicz L, Elgar G, Memari Y, Robbe P, Kingsbury Z, Caldas C, Abraham J, Schuh A, Jones L, Tischkowitz M, Brown MA, Davies HR, Nik-Zainal S. Large-scale analysis of whole genome sequencing data from formalin-fixed paraffin-embedded cancer specimens demonstrates preservation of clinical utility. Nat Commun 2024; 15:7731. [PMID: 39231944 PMCID: PMC11374794 DOI: 10.1038/s41467-024-51577-2] [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: 04/03/2024] [Accepted: 08/07/2024] [Indexed: 09/06/2024] Open
Abstract
Whole genome sequencing (WGS) provides comprehensive, individualised cancer genomic information. However, routine tumour biopsies are formalin-fixed and paraffin-embedded (FFPE), damaging DNA, historically limiting their use in WGS. Here we analyse FFPE cancer WGS datasets from England's 100,000 Genomes Project, comparing 578 FFPE samples with 11,014 fresh frozen (FF) samples across multiple tumour types. We use an approach that characterises rather than discards artefacts. We identify three artefactual signatures, including one known (SBS57) and two previously uncharacterised (SBS FFPE, ID FFPE), and develop an "FFPEImpact" score that quantifies sample artefacts. Despite inferior sequencing quality, FFPE-derived data identifies clinically-actionable variants, mutational signatures and permits algorithmic stratification. Matched FF/FFPE validation cohorts shows good concordance while acknowledging SBS, ID and copy-number artefacts. While FF-derived WGS data remains the gold standard, FFPE-samples can be used for WGS if required, using analytical advancements developed here, potentially democratising whole cancer genomics to many.
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Affiliation(s)
- Shadi Basyuni
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Laura Heskin
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Andrea Degasperi
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Daniella Black
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Gene C C Koh
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Lucia Chmelova
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Giuseppe Rinaldi
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Steven Bell
- Precision Breast Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Louise Grybowicz
- Cambridge Cancer Trials Centre, Department of Oncology, Cambridge University Hospitals, Cambridge, UK
| | - Greg Elgar
- Genomics England, One Canada Square, London, UK
| | - Yasin Memari
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Pauline Robbe
- Department of Oncology, University of Oxford, Oxford, UK
- RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Jean Abraham
- Precision Breast Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, UK
| | - Louise Jones
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | | | - Helen R Davies
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK.
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK.
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47
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van der Ham CG, Suurenbroek LC, Kleisman MM, Antić Ž, Lelieveld SH, Yeong M, Westera L, Sonneveld E, Hoogerbrugge PM, van der Velden VHJ, van Leeuwen FN, Kuiper RP. Mutational mechanisms in multiply relapsed pediatric acute lymphoblastic leukemia. Leukemia 2024:10.1038/s41375-024-02403-7. [PMID: 39232206 DOI: 10.1038/s41375-024-02403-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Pediatric acute lymphoblastic leukemia (ALL) is marked by low mutational load at initial diagnosis, which increases at relapse. To determine which processes are active in (relapsed) ALL and how they behave during disease progression before and after therapy, we performed whole genome sequencing on 97 tumor samples of 29 multiply relapsed ALL patients. Mutational load increased upon relapse in 28 patients and upon every subsequent relapse in 22 patients. In addition to two clock-like mutational processes, we identified UV-like damage, APOBEC activity, reactive oxygen species, thiopurine-associated damage and an unknown therapy component as drivers of mutagenesis. Mutational processes often affected patients over longer time periods, but could also occur in isolated events, suggesting the requirement of additional triggers. Thiopurine exposure was the most prominent source of new mutations in relapse, affecting over half of the studied patients in first and/or later relapse and causing potential relapse-driving mutations in multiple patients. Our data demonstrate that multiple mutational processes frequently act in parallel as prominent secondary drivers with dynamic activity during ALL development and progression.
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Affiliation(s)
| | | | | | - Željko Antić
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Marley Yeong
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Liset Westera
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | - Peter M Hoogerbrugge
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | | | | | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Department of Genetics, Utrecht University Medical Center, Utrecht University, Utrecht, The Netherlands.
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48
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Toma MM, Skorski T. Star wars against leukemia: attacking the clones. Leukemia 2024:10.1038/s41375-024-02369-6. [PMID: 39223295 DOI: 10.1038/s41375-024-02369-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
Leukemia, although most likely starts as a monoclonal genetic/epigenetic anomaly, is a polyclonal disease at manifestation. This polyclonal nature results from ongoing evolutionary changes in the genome/epigenome of leukemia cells to promote their survival and proliferation advantages. We discuss here how genetic and/or epigenetic aberrations alter intracellular microenvironment in individual leukemia clones and how extracellular microenvironment selects the best fitted clones. This dynamic polyclonal composition of leukemia makes designing an effective therapy a challenging task especially because individual leukemia clones often display substantial differences in response to treatment. Here, we discuss novel therapeutic approach employing single cell multiomics to identify and eradicate all individual clones in a patient.
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Affiliation(s)
- Monika M Toma
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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49
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Hwang J, Lee Y, Yoo SK, Kim JI. Image-based deep learning model using DNA methylation data predicts the origin of cancer of unknown primary. Neoplasia 2024; 55:101021. [PMID: 38943996 PMCID: PMC11261876 DOI: 10.1016/j.neo.2024.101021] [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: 04/30/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Cancer of unknown primary (CUP) is a rare type of metastatic cancer in which the origin of the tumor is unknown. Since the treatment strategy for patients with metastatic tumors depends on knowing the primary site, accurate identification of the origin site is important. Here, we developed an image-based deep-learning model that utilizes a vision transformer algorithm for predicting the origin of CUP. Using DNA methylation dataset of 8,233 primary tumors from The Cancer Genome Atlas (TCGA), we categorized 29 cancer types into 18 organ classes and extracted 2,312 differentially methylated CpG sites (DMCs) from non-squamous cancer group and 420 DMCs from squamous cell cancer group. Using these DMCs, we created organ-specific DNA methylation images and used them for model training and testing. Model performance was evaluated using 394 metastatic cancer samples from TCGA (TCGA-meta) and 995 samples (693 primary and 302 metastatic cancers) obtained from 20 independent external studies. We identified that the DNA methylation image reveals a distinct pattern based on the origin of cancer. Our model achieved an overall accuracy of 96.95 % in the TCGA-meta dataset. In the external validation datasets, our classifier achieved overall accuracies of 96.39 % and 94.37 % in primary and metastatic tumors, respectively. Especially, the overall accuracies for both primary and metastatic samples of non-squamous cell cancer were exceptionally high, with 96.79 % and 96.85 %, respectively.
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Affiliation(s)
- Jinha Hwang
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul, the Republic of Korea
| | - Yeajina Lee
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, the Republic of Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, the Republic of Korea
| | - Seong-Keun Yoo
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, the Republic of Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, the Republic of Korea.
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50
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Li X, Liu T, Bacchiocchi A, Li M, Cheng W, Wittkop T, Mendez FL, Wang Y, Tang P, Yao Q, Bosenberg MW, Sznol M, Yan Q, Faham M, Weng L, Halaban R, Jin H, Hu Z. Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction. EMBO Mol Med 2024; 16:2188-2209. [PMID: 39164471 PMCID: PMC11393307 DOI: 10.1038/s44321-024-00115-0] [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: 01/22/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 08/22/2024] Open
Abstract
While whole genome sequencing (WGS) of cell-free DNA (cfDNA) holds enormous promise for detection of molecular residual disease (MRD), its performance is limited by WGS error rate. Here we introduce AccuScan, an efficient cfDNA WGS technology that enables genome-wide error correction at single read-level, achieving an error rate of 4.2 × 10-7, which is about two orders of magnitude lower than a read-centric de-noising method. The application of AccuScan to MRD demonstrated analytical sensitivity down to 10-6 circulating variant allele frequency at 99% sample-level specificity. AccuScan showed 90% landmark sensitivity (within 6 weeks after surgery) and 100% specificity for predicting relapse in colorectal cancer. It also showed 67% sensitivity and 100% specificity in esophageal cancer using samples collected within one week after surgery. When AccuScan was applied to monitor immunotherapy in melanoma patients, the circulating tumor DNA (ctDNA) levels and dynamic profiles were consistent with clinical outcomes. Overall, AccuScan provides a highly accurate WGS solution for MRD detection, empowering ctDNA detection at parts per million range without requiring high sample input or personalized reagents.
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Affiliation(s)
- Xinxing Li
- Department of Gastrointestinal Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, P. R. China
| | - Tao Liu
- Department of Thoracic Surgery, Peking University First Hospital, Beijing, 100034, China
| | | | - Mengxing Li
- Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Wen Cheng
- Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Tobias Wittkop
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Fernando L Mendez
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Yingyu Wang
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Paul Tang
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Qianqian Yao
- Department of Medical Science, Shanghai YunSheng Medical Laboratory Co., Ltd, Shanghai, 200437, China
| | - Marcus W Bosenberg
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Mario Sznol
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Qin Yan
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Malek Faham
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Li Weng
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA.
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
| | - Hai Jin
- Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China.
| | - Zhiqian Hu
- Department of Gastrointestinal Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, P. R. China.
- Department of General Surgery, Changzheng Hospital Naval Medical University, Shanghai, 200003, P. R. China.
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