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Molefi T, Mabonga L, Hull R, Sebitloane M, Dlamini Z. From Genes to Clinical Practice: Exploring the Genomic Underpinnings of Endometrial Cancer. Cancers (Basel) 2025; 17:320. [PMID: 39858102 PMCID: PMC11763595 DOI: 10.3390/cancers17020320] [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: 11/04/2024] [Revised: 01/08/2025] [Accepted: 01/11/2025] [Indexed: 01/27/2025] Open
Abstract
Endometrial cancer (EC), a prevalent gynecological malignancy, presents significant challenges due to its genetic complexity and heterogeneity. The genomic landscape of EC is underpinned by genetic alterations, such as mutations in PTEN, PIK3CA, and ARID1A, and chromosomal abnormalities. The identification of molecular subtypes-POLE ultramutated, microsatellite instability (MSI), copy number low, and copy number high-illustrates the diverse genetic profiles within EC and underscores the need for subtype-specific therapeutic strategies. The integration of multi-omics technologies such as single-cell genomics and spatial transcriptomics has revolutionized our understanding and approach to studying EC and offers a holistic perspective that enhances the ability to identify novel biomarkers and therapeutic targets. The translation of these multi-omics findings into personalized medicine and precision oncology is increasingly feasible in clinical practice. Targeted therapies such as PI3K/AKT/mTOR inhibitors have demonstrated the potential for improved treatment efficacy tailored to specific genetic alterations. Despite these advancements, challenges persist in terms of variability in patient responses, the integration of genomic data into clinical workflows, and ethical considerations. This review explores the genomic underpinnings of EC, from genes to clinical practice. It highlights the ongoing need for multidisciplinary research and collaboration to address the complexities of EC and improve diagnosis, treatment, and patient outcomes.
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Affiliation(s)
- Thulo Molefi
- Discipline of Obstetrics and Gynaecology, School of Clinical Medicine, University of KwaZulu-Natal, Durban 4002, South Africa;
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Research Institute (PACRI), University of Pretoria, Hartfield, Pretoria 0028, South Africa; (L.M.); (R.H.)
- Department of Medical Oncology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Lloyd Mabonga
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Research Institute (PACRI), University of Pretoria, Hartfield, Pretoria 0028, South Africa; (L.M.); (R.H.)
| | - Rodney Hull
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Research Institute (PACRI), University of Pretoria, Hartfield, Pretoria 0028, South Africa; (L.M.); (R.H.)
| | - Motshedisi Sebitloane
- Discipline of Obstetrics and Gynaecology, School of Clinical Medicine, University of KwaZulu-Natal, Durban 4002, South Africa;
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Research Institute (PACRI), University of Pretoria, Hartfield, Pretoria 0028, South Africa; (L.M.); (R.H.)
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Chung T, Oh S, Won J, Park J, Yoo JE, Hwang HK, Choi GH, Kang CM, Han DH, Kim S, Park YN. Genomic and transcriptomic signatures of sequential carcinogenesis from papillary neoplasm to biliary tract cancer. J Hepatol 2025:S0168-8278(25)00013-3. [PMID: 39832657 DOI: 10.1016/j.jhep.2025.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 12/23/2024] [Accepted: 01/01/2025] [Indexed: 01/22/2025]
Abstract
BACKGROUND & AIMS Papillary neoplasms of the biliary tree, including intraductal papillary neoplasms (IPN) and intracholecystic papillary neoplasms (ICPN), are recognized as precancerous lesions. However, the genetic characteristics underlying sequential carcinogenesis remain unclear. METHODS Whole-exome sequencing was performed on 166 neoplasms (33 intrahepatic IPNs, 44 extrahepatic IPNs, and 89 ICPNs), and 41 associated carcinomas. Nine available cases were also subjected to spatial transcriptomic analysis. RESULTS Mutations in the MAPK (48%), genomic integrity maintenance (42%), and Wnt/β-catenin (33%) pathways were prevalent in intrahepatic IPNs, extrahepatic IPNs, and ICPNs, respectively. KRAS mutations were enriched in intrahepatic IPN (42%, P<0.001), whereas SMAD4 mutations were enriched in extrahepatic IPN (21%, P=0.005). ICPNs frequently exhibit CTNNB1 mutations, particularly in low-grade lesions. Mutational signature analysis revealed that SBS1 and SBS5 signatures were homogeneously enriched in intrahepatic IPN, in contrast to the heterogeneous distribution of SBS1, SBS2, SBS5, SBS13, SBS7b, and SBS23 in extrahepatic IPN and ICPN. Copy number aberrations gradually increased from low- to high-grade intraepithelial neoplasia and eventually to carcinoma. Phylogenetic analysis revealed that 89% of carcinomas were derived from IPN/ICPN through sequential carcinogenesis, with the majority sharing driver mutations between IPN/ICPN and carcinoma. Furthermore, multifocal, independent carcinogenesis events were observed in IPNs/ICPNs, resulting in mutationally distinct carcinoma lesions. Carcinogenesis of IPN/ICPN occurs in multiple subclones through mutational accumulation and transcriptomic alterations that affect vascular development, cell morphogenesis, extracellular matrix organization, and growth factor response. CONCLUSIONS With the largest IPN/ICPN cohort reported to date, our study provides a genome- and spatial transcriptome-level portrait of sequential carcinogenesis and differences in the anatomical location of biliary papillary neoplasms. IMPACT AND IMPLICATIONS Biliary tract cancer is a fatal malignancy. However, its genome-level sequential carcinogenesis from intraepithelial neoplasia to carcinoma has not yet been evaluated in a sufficiently large cohort. Papillary lesions of the bile duct and gallbladder are collectively termed intraductal papillary neoplasms (IPN) of the bile duct and intracholecystic papillary neoplasms (ICPN), respectively. They are primarily diagnosed based on histopathological studies. This study provides a comprehensive mutational and spatial transcriptomic landscape of papillary neoplasms of the bile duct and gallbladder. The results of this study offer insights into the mechanism of sequential carcinogenesis in papillary biliary tract tumors, pathology-genomics correlation, and potential therapeutic targets.
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Affiliation(s)
- Taek Chung
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seungho Oh
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jeongsoo Won
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jiho Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jeong Eun Yoo
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ho Kyoung Hwang
- Department of Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gi Hong Choi
- Department of Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chang Moo Kang
- Department of Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dai Hoon Han
- Department of Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea; POSTECH Biotechnology Center, Pohang University of Science and Technology, Pohang, Republic of Korea.
| | - Young Nyun Park
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
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53
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Yang M, Zheng G, Chen F, Tang H, Liu Y, Gao X, Huang Y, Lv Z, Li B, Yang M, Bu Q, Zhu L, Yu P, Huo Z, Wei X, Chen X, Huang Y, He Z, Xia X, Bai J. Molecular characterization of EBV-associated primary pulmonary lymphoepithelial carcinoma by multiomics analysis. BMC Cancer 2025; 25:85. [PMID: 39815193 PMCID: PMC11734413 DOI: 10.1186/s12885-024-13410-3] [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: 07/09/2024] [Accepted: 12/30/2024] [Indexed: 01/18/2025] Open
Abstract
BACKGROUND Primary pulmonary lymphoepithelial carcinoma (pLEC) is a subtype of non-small cell lung cancer (NSCLC) characterized by Epstein-Barr virus (EBV) infection. However, the molecular pathogenesis of pLEC remains poorly understood. METHODS In this study, we explored pLEC using whole-exome sequencing (WES) and RNA-whole-transcriptome sequencing (RNA-seq) technologies. Datasets of normal lung tissue, other types of NSCLC, and EBV-positive nasopharyngeal carcinoma (EBV+-NPC) were obtained from public databases. Furthermore, we described the gene signatures, viral integration, cell quantification, cell death and immune infiltration of pLEC. RESULTS Compared with other types of NSCLC and EBV+-NPC, pLEC patients exhibited a lower somatic mutation burden and extensive copy number deletions, including 1p36.23, 3p21.1, 7q11.23, and 11q23.3. Integration of EBV associated dysregulation of gene expression, with CNV-altered regions coinciding with EBV integration sites. Specifically, ZBTB16 and ERRFI1 were downregulated by CNV loss, and the FOXD family genes were overexpressed with CNV gain. Decreased expression of the FOXD family might be associated with a favorable prognosis in pLEC patients, and these patients exhibited enhanced cytotoxicity. CONCLUSION Compared with other types of NSCLC and NPC, pLEC has distinct molecular characteristics. EBV integration, the aberrant expression of genes, as well as the loss of CNVs, may play a crucial role in the pathogenesis of pLEC. However, further research is needed to assess the potential role of the FOXD gene family as a biomarker.
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Affiliation(s)
- Meiling Yang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Guixian Zheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Fukun Chen
- Geneplus-Beijing Institute, Beijing, China
| | - Haijuan Tang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Yaoyao Liu
- Geneplus-Beijing Institute, Beijing, China
| | - Xuan Gao
- Geneplus-Beijing Institute, Beijing, China
| | - Yu Huang
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Zili Lv
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Benhua Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Maolin Yang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Qing Bu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Lixia Zhu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Pengli Yu
- Geneplus-Beijing Institute, Beijing, China
| | - Zengyu Huo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Xinyan Wei
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Xiaoli Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Yanbing Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Zhiyi He
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | | | - Jing Bai
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China.
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China.
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54
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Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. NATURE AGING 2025:10.1038/s43587-024-00794-x. [PMID: 39806003 DOI: 10.1038/s43587-024-00794-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/12/2024] [Indexed: 01/16/2025]
Abstract
DNA methylation marks have recently been used to build models known as epigenetic clocks, which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In an analysis of multimodal data from 9,331 human individuals, we found that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping allows mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging more rapidly or slowly than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.
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Affiliation(s)
- Zane Koch
- Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA
| | - Adam Li
- Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Steven Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - Trey Ideker
- Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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Stratton MR, Humphreys L, Alexandrov LB, Balmain A, Brennan P, Campbell PJ, Phillips DH. Implementing Mutational Epidemiology on a Global Scale: Lessons from Mutographs. Cancer Discov 2025; 15:22-27. [PMID: 39801236 DOI: 10.1158/2159-8290.cd-24-1687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 11/25/2024] [Indexed: 02/11/2025]
Abstract
The Mutographs Cancer Grand Challenge team aimed to discover unknown causes of cancer through mutational epidemiology, an alliance of cancer epidemiology and somatic genomics. By generating whole-genome sequences from thousands of cancers and normal tissues from more than 30 countries on five continents, it discovered unsuspected mutagenic exposures affecting millions of people, raised the possibility that some carcinogens act by altering forces of selection in tissue microenvironments rather than by mutagenesis, and demonstrated changes to the direction of somatic evolution in normal cells of the human body in response to exogenous exposures and noncancer diseases. See related article by Bressan et al., p. 16 See related article by Bhattacharjee et al., p. 28 See related article by Goodwin et al., p. 34.
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Affiliation(s)
- Michael R Stratton
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, California
- Department of Bioengineering, UC San Diego, La Jolla, California
- Moores Cancer Center, UC San Diego, La Jolla, California
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - David H Phillips
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom
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Kubitschek J, Takhaveev V, Mingard C, Rochlitz M, Reinert P, Keller G, Kloter T, Fernández Cereijo R, Huber S, McKeague M, Sturla S. Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide. Nucleic Acids Res 2025; 53:gkae1320. [PMID: 39831306 PMCID: PMC11744188 DOI: 10.1093/nar/gkae1320] [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: 01/22/2024] [Revised: 12/20/2024] [Accepted: 01/16/2025] [Indexed: 01/22/2025] Open
Abstract
Temozolomide kills cancer cells by forming O6-methylguanine (O6-MeG), which leads to cell cycle arrest and apoptosis. However, O6-MeG repair by O6-methylguanine-DNA methyltransferase (MGMT) contributes to drug resistance. Characterizing genomic profiles of O6-MeG could elucidate how O6-MeG accumulation is influenced by repair, but there are no methods to map genomic locations of O6-MeG. Here, we developed an immunoprecipitation- and polymerase-stalling-based method, termed O6-MeG-seq, to locate O6-MeG across the whole genome at single-nucleotide resolution. We analyzed O6-MeG formation and repair across sequence contexts and functional genomic regions in relation to MGMT expression in a glioblastoma-derived cell line. O6-MeG signatures were highly similar to mutational signatures from patients previously treated with temozolomide. Furthermore, MGMT did not preferentially repair O6-MeG with respect to sequence context, chromatin state or gene expression level, however, may protect oncogenes from mutations. Finally, we found an MGMT-independent strand bias in O6-MeG accumulation in highly expressed genes. These data provide high resolution insight on how O6-MeG formation and repair are impacted by genome structure and nucleotide sequence. Further, O6-MeG-seq is expected to enable future studies of DNA modification signatures as diagnostic markers for addressing drug resistance and preventing secondary cancers.
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Affiliation(s)
- Jasmina Kubitschek
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Vakil Takhaveev
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Cécile Mingard
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Martha I Rochlitz
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Patricia B Reinert
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Giulia Keller
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Tom Kloter
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Raúl Fernández Cereijo
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Sabrina M Huber
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Maureen McKeague
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
- Department of Chemistry, Faculty of Science, McGill University, 801 Sherbrooke St. West, Montreal, QCH3A 0B8, Canada
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, 3655 Prom. Sir William Osler, Montreal, QCH3G 1Y6, Canada
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
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57
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Kerle IA, Gross T, Kögler A, Arnold JS, Werner M, Eckardt JN, Möhrmann EE, Arlt M, Hutter B, Hüllein J, Richter D, Schneider MMK, Hlevnjak M, Möhrmann L, Hanf D, Heilig CE, Kreutzfeldt S, Teleanu MV, Schröck E, Hübschmann D, Horak P, Heining C, Fröhling S, Glimm H. Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology. NPJ Precis Oncol 2025; 9:9. [PMID: 39794422 PMCID: PMC11724059 DOI: 10.1038/s41698-024-00788-3] [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: 07/24/2024] [Accepted: 12/14/2024] [Indexed: 01/13/2025] Open
Abstract
Precision oncology offers new cancer treatment options, yet sequencing methods vary in type and scope. In this study, we compared whole-exome/whole-genome (WES/WGS) and transcriptome sequencing (TS) with broad panel sequencing by resequencing the same tumor DNA and RNA as well as normal tissue DNA for germline assessment, from 20 patients with rare or advanced tumors, who were originally sequenced by WES/WGS ± TS within the DKFZ/NCT/DKTK MASTER program from 2015 to 2020. Molecular analyses resulted in a median number of 2.5 (gene panel) to 3.5 (WES/WGS ± TS) treatment recommendations per patient. Our results showed that approximately half of the therapy recommendations (TRs) of both sequencing programs were identical, while approximately one-third of the TRs in WES/WGS ± TS relied on biomarkers not covered by the panel. Eight of 10 molecularly informed therapy implementations were supported by the panel, the remaining two were based on biomarkers absent from the panel, highlighting the potential additional clinical benefit of WGS and TS.
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Affiliation(s)
- Irina A Kerle
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany.
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.
- German Cancer Consortium (DKTK), partner site Dresden, Dresden, Germany.
| | - Thomas Gross
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Anja Kögler
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Jonas S Arnold
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany; ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Germany; National Center for Tumor Diseases Dresden (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Maximilian Werner
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, Dresden, Germany
| | - Jan-Niklas Eckardt
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- Else Kröner Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany
| | - Elena E Möhrmann
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, Dresden, Germany
| | - Marie Arlt
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany; ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Germany; National Center for Tumor Diseases Dresden (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Barbara Hutter
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Jennifer Hüllein
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Daniela Richter
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Translational Functional Cancer Genomics, Heidelberg, Germany
| | - Martin M K Schneider
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Mario Hlevnjak
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Lino Möhrmann
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, Dresden, Germany
| | - Dorothea Hanf
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, Dresden, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Simon Kreutzfeldt
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria-Veronica Teleanu
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Evelin Schröck
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany; ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Germany; National Center for Tumor Diseases Dresden (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Innovation and Service Unit for Bioinformatics and Precision Medicine (BPM), DKFZ, Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group (PRDM), Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Heining
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, Dresden, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, Dresden, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Translational Functional Cancer Genomics, Heidelberg, Germany
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Geisenberger C, Chimal E, Jurmeister P, Klauschen F. A cost-effective and scalable approach for DNA extraction from FFPE tissues. Biol Methods Protoc 2025; 10:bpaf003. [PMID: 39995602 PMCID: PMC11849955 DOI: 10.1093/biomethods/bpaf003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 12/17/2024] [Accepted: 01/08/2025] [Indexed: 02/26/2025] Open
Abstract
Genomic profiling of cancer plays an increasingly vital role for diagnosis and therapy planning. In addition, research of novel diagnostic applications such as DNA methylation profiling requires large training and validation cohorts. Currently, most diagnostic cases processed in pathology departments are stored as formalin-fixed and paraffin embedded tissue blocks (FFPE). Consequently, there is a growing demand for high-throughput extraction of nucleic acids from FFPE tissue samples. While proprietary kits are available, they are expensive and offer little flexibility. Here, we present ht-HiTE, a high-throughput implementation of a recently published and highly efficient DNA extraction protocol. This approach enables manual and automated processing of 96-well plates with a liquid handler, offers two options for purification and utilizes off-the-shelf reagents. Finally, we show that NGS and DNA methylation microarray data obtained from DNA processed with ht-HiTE are of equivalent quality as compared to a manual, kit-based approach.
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Affiliation(s)
- Christoph Geisenberger
- Institute of Pathology, Ludwig-Maximilians-Universität München, Thalkirchnerstr. 36, Munich, 80337, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and University Hospital Munich, Pettenkoferstr. 8a, Munich, 80336, Germany
| | - Edgar Chimal
- Institute of Pathology, Ludwig-Maximilians-Universität München, Thalkirchnerstr. 36, Munich, 80337, Germany
| | - Philipp Jurmeister
- Institute of Pathology, Ludwig-Maximilians-Universität München, Thalkirchnerstr. 36, Munich, 80337, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and University Hospital Munich, Pettenkoferstr. 8a, Munich, 80336, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Einsteinufer 17, Berlin, 10587, Germany
| | - Frederick Klauschen
- Institute of Pathology, Ludwig-Maximilians-Universität München, Thalkirchnerstr. 36, Munich, 80337, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and University Hospital Munich, Pettenkoferstr. 8a, Munich, 80336, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Einsteinufer 17, Berlin, 10587, Germany
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59
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Fujii E, Kato MK, Ono H, Yamaguchi M, Higuchi D, Koyama T, Komatsu M, Hamamoto R, Ishikawa M, Kato T, Kohno T, Shiraishi K, Yoshida H. TP53 Mutations and PD-L1 Amplification in Vulvar Adenocarcinoma of the Intestinal Type: Insights From Whole Exome Sequencing of 2 Cases. Int J Gynecol Pathol 2025:00004347-990000000-00218. [PMID: 39868745 DOI: 10.1097/pgp.0000000000001093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Vulvar adenocarcinoma of the intestinal type (VAIt) is a rare subtype of primary vulvar carcinoma, with ∼30 cases documented in the English literature. This study presents 2 new cases of HPV-independent VAIt with lymph node metastasis and discusses their clinical presentation, histopathologic features, and whole exome sequencing (WES) analysis. Both cases exhibited histologic features consistent with VAIt, including tubular, papillary, and mucinous carcinoma components. Immunohistochemical analysis showed p16 patchy staining, CDX2, CK20, and SATB2 positivity, while being negative for ER, PAX8, and CK7. WES revealed pathogenic TP53 mutations in both cases, accompanied by distinct additional mutations (GRIN2A and KDM6A in Case #1; CHD4 in Case #2). Common copy number alterations (CNAs) included TP53 loss of heterozygosity and CD274/PD-L1 amplification. However, other CNAs varied between the cases. Immunohistochemistry for p53 suggests the presence of both wild-type and mutant subclones, indicating that TP53 abnormalities may be acquired during tumor progression. Both tumors showed mutational signatures SBS1 and SBS5, associated with aging and DNA damage. Our findings deepen the understanding of the genetic events involved in the tumorigenesis of HPV-independent VAIt. Given the TP53 abnormalities and CD274/PD-L1 amplification, emerging p53-based therapies and immune checkpoint inhibitors may represent potential treatment targets. While these findings contribute to the understanding of VAIt tumorigenesis, further research is required to validate these observations in a larger cohort.
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Affiliation(s)
- Erisa Fujii
- Division of Genome Biology
- Departments of Gynecology
| | | | - Hanako Ono
- Department of Clinical Genomics, National Cancer Center Research Institute
| | - Maiko Yamaguchi
- Division of Genome Biology
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine
| | - Daiki Higuchi
- Division of Genome Biology
- Department of Obstetrics and Gynecology, Showa University School of Medicine
| | | | - Masaaki Komatsu
- Division of Medical AI Research and Development
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | | | | | | | - Kouya Shiraishi
- Division of Genome Biology
- Department of Clinical Genomics, National Cancer Center Research Institute
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60
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Zhang F, Wu X, Jiao T, Dua H, Guo Q, Cui C, Chi Z, Sheng X, Jiang D, Zhang Y, Wu J, Kong Y, Si L. Genomic characterization reveals distinct mutational landscape of acral melanoma in East Asian. J Genet Genomics 2025:S1673-8527(24)00371-0. [PMID: 39798666 DOI: 10.1016/j.jgg.2024.12.018] [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: 12/17/2024] [Revised: 12/24/2024] [Accepted: 12/24/2024] [Indexed: 01/15/2025]
Abstract
Acral melanoma, the most common melanoma subtype in East Asia, is associated with a poor prognosis. This study aims to comprehensively analyze the genomic characteristics of acral melanoma in East Asians. We conduct whole-genome sequencing of 55 acral melanoma tumors and perform data mining with relevant clinical data. Our findings reveal a unique mutational profile in East Asian acral melanoma, characterized by fewer point mutations and structural variations, a higher prevalence of NRAS mutations, and a lower frequency of BRAF mutations compared to patients of European descent. Notably, we identify previously underestimated ultraviolet radiation signatures and their significant association with BRAF and NRAS mutations. Structural rearrangement signatures indicate distinct mutational processes in BRAF-driven versus NRAS-driven tumors. We also find that homologous recombination deficiency with MAPK pathway mutations correlated with poor prognosis. The structural variations and amplifications in EP300, TERT, RAC1, and LZTR1 point to potential novel therapeutic targets tailored to East Asian populations. The high prevalence of whole-genome duplication events in BRAF/NRAS-mutated tumors suggests a synergistic carcinogenic effect that warrants further investigation. In summary, our study provides important insights into the genetic underpinnings of acral melanoma in East Asians, creating opportunities for targeted therapies.
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Affiliation(s)
- Fenghao Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China
| | - Xiaowen Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China
| | - Tao Jiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China
| | - Haizhen Dua
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China
| | - Qian Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China
| | - Chuanliang Cui
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China
| | - Zhihong Chi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China
| | - Xinan Sheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China
| | - Dezhi Jiang
- Beijing Kanghui Biotechnology Co. LTD, Beijing 100101, China
| | - Yuhong Zhang
- Clinical Research Division of Berry Oncology Corporation, Beijing 102206, China
| | - Jiayan Wu
- Beijing Kanghui Biotechnology Co. LTD, Beijing 100101, China; Clinical Research Division of Berry Oncology Corporation, Beijing 102206, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, Fujian 350020, China.
| | - Yan Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China.
| | - Lu Si
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing 100142, China.
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61
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Unger M, Loeffler CML, Žigutytė L, Sainath S, Lenz T, Vibert J, Mock A, Fröhling S, Graham TA, Carrero ZI, Kather JN. Deep Learning for Biomarker Discovery in Cancer Genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.06.631471. [PMID: 39829845 PMCID: PMC11741323 DOI: 10.1101/2025.01.06.631471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Background Genomic data is essential for clinical decision-making in precision oncology. Bioinformatic algorithms are widely used to analyze next-generation sequencing (NGS) data, but they face two major challenges. First, these pipelines are highly complex, involving multiple steps and the integration of various tools. Second, they generate features that are human-interpretable but often result in information loss by focusing only on predefined genetic properties. This limitation restricts the full potential of NGS data in biomarker extraction and slows the discovery of new biomarkers in precision oncology. Methods We propose an end-to-end deep learning (DL) approach for analyzing NGS data. Specifically, we developed a multiple instance learning DL framework that integrates somatic mutation sequences to predict two compound biomarkers: microsatellite instability (MSI) and homologous recombination deficiency (HRD). To achieve this, we utilized data from 3,184 cancer patients obtained from two public databases: The Cancer Genome Atlas (TCGA) and the Clinical Proteome Tumor Analysis Consortium (CPTAC). Results Our proposed deep learning method demonstrated high accuracy in identifying clinically relevant biomarkers. For predicting MSI status, the model achieved an accuracy of 0.98, a sensitivity of 0.95, and a specificity of 1.00 on an external validation cohort. For predicting HRD status, the model achieved an accuracy of 0.80, a sensitivity of 0.75, and a specificity of 0.86. Furthermore, the deep learning approach significantly outperformed traditional machine learning methods in both tasks (MSI accuracy, p-value = 5.11×10-18; HRD accuracy, p-value = 1.07×10-10). Using explainability techniques, we demonstrated that the model's predictions are based on biologically meaningful features, aligning with key DNA damage repair mutation signatures. Conclusion We demonstrate that deep learning can identify patterns in unfiltered somatic mutations without the need for manual feature extraction. This approach enhances the detection of actionable targets and paves the way for developing NGS-based biomarkers using minimally processed data.
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Affiliation(s)
- Michaela Unger
- Else Kroener Fresenius Center for Digital Health, University of Technology Dresden, Dresden, Germany
| | - Chiara M L Loeffler
- Else Kroener Fresenius Center for Digital Health, University of Technology Dresden, Dresden, Germany
- Medical Department 1, University Hospital and Faculty of Medicine Carl Gustav Carus, University of Technology Dresden, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Laura Žigutytė
- Else Kroener Fresenius Center for Digital Health, University of Technology Dresden, Dresden, Germany
| | - Srividhya Sainath
- Else Kroener Fresenius Center for Digital Health, University of Technology Dresden, Dresden, Germany
| | - Tim Lenz
- Else Kroener Fresenius Center for Digital Health, University of Technology Dresden, Dresden, Germany
| | - Julien Vibert
- Drug Development Department (DITEP), Gustave Roussy, Villejuif, France
| | - Andreas Mock
- Institute of Pathology, Ludwig-Maximilians-University München, Munich, Germany
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Division of Translational Precision Medicine, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Trevor A Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Zunamys I Carrero
- Else Kroener Fresenius Center for Digital Health, University of Technology Dresden, Dresden, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, University of Technology Dresden, Dresden, Germany
- Medical Department 1, University Hospital and Faculty of Medicine Carl Gustav Carus, University of Technology Dresden, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
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62
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Boysen G, Alexandrov L, Rahbari R, Nookaew I, Ussery D, Chao MR, Hu CW, Cooke M. Investigating the origins of the mutational signatures in cancer. Nucleic Acids Res 2025; 53:gkae1303. [PMID: 39778866 PMCID: PMC11707540 DOI: 10.1093/nar/gkae1303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 12/17/2024] [Accepted: 01/05/2025] [Indexed: 01/11/2025] Open
Abstract
Most of the risk factors associated with chronic and complex diseases, such as cancer, stem from exogenous and endogenous exposures experienced throughout an individual's life, collectively known as the exposome. These exposures can modify DNA, which can subsequently lead to the somatic mutations found in all normal and tumor tissues. Understanding the precise origins of specific somatic mutations has been challenging due to multitude of DNA adducts (i.e. the DNA adductome) and their diverse positions within the genome. Thus far, this limitation has prevented researchers from precisely linking exposures to DNA adducts and DNA adducts to subsequent mutational outcomes. Indeed, many common mutations observed in human cancers appear to originate from error-prone endogenous processes. Consequently, it remains unclear whether these mutations result from exposure-induced DNA adducts, or arise indirectly from endogenous processes or are a combination of both. In this review, we summarize approaches that aim to bridge our understanding of the mechanism by which exposure leads to DNA damage and then to mutation and highlight some of the remaining challenges and shortcomings to fully supporting this paradigm. We emphasize the need to integrate cellular DNA adductomics, long read-based mapping, single-molecule duplex sequencing of native DNA molecules and advanced computational analysis. This proposed holistic approach aims to unveil the causal connections between key DNA modifications and the mutational landscape, whether they originate from external exposures, internal processes or a combination of both, thereby addressing key questions in cancer biology.
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Affiliation(s)
- Gunnar Boysen
- Department of Environmental Health Science, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
- The Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Raheleh Rahbari
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Intawat Nookaew
- Department of BioMedical Informatics, The University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
| | - Dave Ussery
- Department of BioMedical Informatics, The University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
| | - Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Jianguo N Rd, South District, Taichung 40201, Taiwan
- Department of Occupational Medicine, Chung Shan Medical University Hospital, Jianguo N Rd, South District, Taichung 40201, Taiwan
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Jianguo N Rd, South District, Taichung 40201, Taiwan
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, 4202 E. Fowler Avenue, Tampa, FL 33612, USA
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63
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Hwang T, Sitko L, Khoirunnisa R, Navarro-Aguad F, Samuel D, Park H, Cheon B, Mutsnaini L, Lee J, Otlu B, Takeda S, Lee S, Ivanov D, Gartner A. Comprehensive whole-genome sequencing reveals origins of mutational signatures associated with aging, mismatch repair deficiency and temozolomide chemotherapy. Nucleic Acids Res 2025; 53:gkae1122. [PMID: 39656916 PMCID: PMC11724276 DOI: 10.1093/nar/gkae1122] [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: 03/12/2024] [Revised: 10/17/2024] [Accepted: 11/07/2024] [Indexed: 12/17/2024] Open
Abstract
In a comprehensive study to decipher the multi-layered response to the chemotherapeutic agent temozolomide (TMZ), we analyzed 427 genomes and determined mutational patterns in a collection of ∼40 isogenic DNA repair-deficient human TK6 lymphoblast cell lines. We first demonstrate that the spontaneous mutational background is very similar to the aging-associated mutational signature SBS40 and mainly caused by polymerase zeta-mediated translesion synthesis (TLS). MSH2-/- mismatch repair (MMR) knockout in conjunction with additional repair deficiencies uncovers cryptic mutational patterns. We next report how distinct mutational signatures are induced by TMZ upon sequential inactivation of DNA repair pathways, mirroring the acquisition of chemotherapy resistance by glioblastomas. The most toxic adduct induced by TMZ, O6-meG, is directly repaired by the O6-methylguanine-DNA methyltransferase (MGMT). In MGMT-/- cells, MMR leads to cell death and limits mutagenesis. MMR deficiency results in TMZ resistance, allowing the accumulation of ∼105 C > T substitutions corresponding to signature SBS11. Under these conditions, N3-methyladenine (3-meA), processed by base excision repair (BER), limits cell survival. Without BER, 3-meA is read through via error-prone TLS, causing T > A substitutions but not affecting survival. Blocking BER after abasic site formation results in large deletions and TMZ hypersensitization. Our findings reveal potential vulnerabilities of TMZ-resistant tumors.
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Affiliation(s)
- Taejoo Hwang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Lukasz Karol Sitko
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Ratih Khoirunnisa
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Fernanda Navarro-Aguad
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - David M Samuel
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Hajoong Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Banyoon Cheon
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Luthfiyyah Mutsnaini
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Jaewoong Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Burçak Otlu
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Shunichi Takeda
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University Medical School, 1066 Xueyuan Avenue, Shenzhen, Guangdong 518060, China
| | - Semin Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Dmitri Ivanov
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Anton Gartner
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
- Graduate School for Health Sciences and Technology, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
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Luzadder MM, Minko IG, Vartanian VL, Davenport M, Fedorov LM, McCullough AK, Stephen Lloyd R. The Distinct Roles of NEIL1 and XPA in Limiting Aflatoxin B1-Induced Mutagenesis in Mice. Mol Cancer Res 2025; 23:46-58. [PMID: 39387543 PMCID: PMC11695181 DOI: 10.1158/1541-7786.mcr-24-0577] [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: 06/21/2024] [Revised: 09/17/2024] [Accepted: 10/08/2024] [Indexed: 10/15/2024]
Abstract
Dietary exposure to aflatoxin B1 (AFB1) is a risk factor for the development of hepatocellular carcinomas. Following metabolic activation, AFB1 reacts with guanines to form covalent DNA adducts, which induce high-frequency G > T transversions. The molecular signature associated with these mutational events aligns with the single-base substitution signature 24 (SBS24) in the Catalog of Somatic Mutations in Cancer database. Deficiencies in either base excision repair due to the absence of Nei-like DNA glycosylase 1 (NEIL1) or nucleotide excision repair due to the absence of xeroderma complementation group A protein (XPA) contribute to hepatocellular carcinomas in murine models. In the current study, ultra-low error duplex sequencing was used to characterize mutational profiles in liver DNAs of NEIL1-deficient, XPA-deficient, and DNA repair-proficient mice following neonatal injection of 1 mg/kg AFB1. Analyses of AFB1-induced mutations showed high cosine similarity to SBS24 regardless of repair proficiency status. The absence of NEIL1 resulted in an approximately 30% increase in the frequency of mutations, with the distribution suggesting preferential NEIL1-dependent repair of AFB1 lesions in open chromatin regions. A trend of increased mutagenesis was also observed in the absence of XPA. Consistent with the role of XPA in transcription-coupled repair, mutational profiles in XPA-deficient mice showed disruption of the transcriptional bias in mutations associated with SBS24. Implications: Our findings define the roles of DNA repair pathways in AFB1-induced mutagenesis and carcinogenesis in murine models, with these findings having implications in human health for those with base excision repair and nucleotide excision repair deficiencies.
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Affiliation(s)
- Michael M. Luzadder
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, USA
| | - Irina G. Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, USA
| | - Vladimir L. Vartanian
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, USA
| | - Marten Davenport
- Transgenic Mouse Models Shared Resource, Oregon Health & Science University, Portland, Oregon, USA
| | - Lev M. Fedorov
- Transgenic Mouse Models Shared Resource, Oregon Health & Science University, Portland, Oregon, USA
| | - Amanda K. McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
| | - R. Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
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Tremmel R, Hübschmann D, Schaeffeler E, Pirmann S, Fröhling S, Schwab M. Innovation in cancer pharmacotherapy through integrative consideration of germline and tumor genomes. Pharmacol Rev 2025; 77:100014. [PMID: 39952686 DOI: 10.1124/pharmrev.124.001049] [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: 04/03/2024] [Revised: 10/02/2024] [Accepted: 10/04/2024] [Indexed: 01/22/2025] Open
Abstract
Precision cancer medicine is widely established, and numerous molecularly targeted drugs for various tumor entities are approved or are in development. Personalized pharmacotherapy in oncology has so far been based primarily on tumor characteristics, for example, somatic mutations. However, the response to drug treatment also depends on pharmacological processes summarized under the term ADME (absorption, distribution, metabolism, and excretion). Variations in ADME genes have been the subject of intensive research for >5 decades, considering individual patients' genetic makeup, referred to as pharmacogenomics (PGx). The combined impact of a patient's tumor and germline genome is only partially understood and often not adequately considered in cancer therapy. This may be attributed, in part, to the lack of methods for combined analysis of both data layers. Optimized personalized cancer therapies should, therefore, aim to integrate molecular information, which derives from both the tumor and the germline genome, and taking into account existing PGx guidelines for drug therapy. Moreover, such strategies should provide the opportunity to consider genetic variants of previously unknown functional significance. Bioinformatic analysis methods and corresponding algorithms for data interpretation need to be developed to integrate PGx data in cancer therapy with a special meaning for interdisciplinary molecular tumor boards, in which cancer patients are discussed to provide evidence-based recommendations for clinical management based on individual tumor profiles. SIGNIFICANCE STATEMENT: The era of personalized oncology has seen the emergence of drugs tailored to genetic variants associated with cancer biology. However, the full potential of targeted therapy remains untapped owing to the predominant focus on acquired tumor-specific alterations. Optimized cancer care must integrate tumor and patient genomes, guided by pharmacogenomic principles. An essential prerequisite for realizing truly personalized drug treatment of cancer patients is the development of bioinformatic tools for comprehensive analysis of all data layers generated in modern precision oncology programs.
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Affiliation(s)
- Roman Tremmel
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tuebingen, Tuebingen, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between the German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium (DKTK), DKFZ, Core Center Heidelberg, Heidelberg, Germany; Innovation and Service Unit for Bioinformatics and Precision Medicine, DKFZ, Heidelberg, Germany; Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tuebingen, Tuebingen, Germany
| | - Sebastian Pirmann
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between the German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), DKFZ, Core Center Heidelberg, Heidelberg, Germany; Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany; NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany; Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tuebingen, Tuebingen, Germany; Departments of Clinical Pharmacology, and Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany; DKTK, DKFZ, Partner Site Tuebingen, Tuebingen, Germany; NCT SouthWest, a partnership between DKFZ and University Hospital Tuebingen, Tuebingen, Germany.
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66
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Lucas O, Ward S, Zaidi R, Bunkum A, Frankell AM, Moore DA, Hill MS, Liu WK, Marinelli D, Lim EL, Hessey S, Naceur-Lombardelli C, Rowan A, Purewal-Mann SK, Zhai H, Dietzen M, Ding B, Royle G, Aparicio S, McGranahan N, Jamal-Hanjani M, Kanu N, Swanton C, Zaccaria S. Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER. Nat Genet 2025; 57:103-114. [PMID: 39614124 PMCID: PMC11735394 DOI: 10.1038/s41588-024-01989-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/15/2024] [Indexed: 12/01/2024]
Abstract
Proliferation is a key hallmark of cancer, but whether it differs between evolutionarily distinct clones co-existing within a tumor is unknown. We introduce the Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) algorithm that uses single-cell whole-genome DNA sequencing data to enable accurate identification and clone assignment of S- and G2-phase cells, as assessed by generating accurate ground truth data. Applied to a newly generated longitudinal, primary-metastasis-matched dataset of 14,994 non-small cell lung cancer cells, SPRINTER revealed widespread clone proliferation heterogeneity, orthogonally supported by Ki-67 staining, nuclei imaging and clinical imaging. We further demonstrated that high-proliferation clones have increased metastatic seeding potential, increased circulating tumor DNA shedding and clone-specific altered replication timing in proliferation- or metastasis-related genes associated with expression changes. Applied to previously generated datasets of 61,914 breast and ovarian cancer cells, SPRINTER revealed increased single-cell rates of different genomic variants and enrichment of proliferation-related gene amplifications in high-proliferation clones.
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Affiliation(s)
- Olivia Lucas
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- University College London Hospitals, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Genomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Rija Zaidi
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Abigail Bunkum
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
- 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
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Wing Kin Liu
- 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
| | - Daniele Marinelli
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sonya Hessey
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | | | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Haoran Zhai
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Boyue Ding
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Gary Royle
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- University College London Hospitals, London, UK.
| | - Simone Zaccaria
- Computational Cancer Genomics Research Group, 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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67
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Gu L, Zhu Y, Nandi SP, Lee M, Watari K, Bareng B, Ohira M, Liu Y, Sakane S, Carlessi R, Sauceda C, Dhar D, Ganguly S, Hosseini M, Teneche MG, Adams PD, Gonzalez DJ, Kisseleva T, Tirnitz-Parker JEE, Simon MC, Alexandrov LB, Karin M. FBP1 controls liver cancer evolution from senescent MASH hepatocytes. Nature 2025; 637:461-469. [PMID: 39743585 DOI: 10.1038/s41586-024-08317-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/30/2024] [Indexed: 01/04/2025]
Abstract
Hepatocellular carcinoma (HCC) originates from differentiated hepatocytes undergoing compensatory proliferation in livers damaged by viruses or metabolic-dysfunction-associated steatohepatitis (MASH)1. While increasing HCC risk2, MASH triggers p53-dependent hepatocyte senescence3, which we found to parallel hypernutrition-induced DNA breaks. How this tumour-suppressive response is bypassed to license oncogenic mutagenesis and enable HCC evolution was previously unclear. Here we identified the gluconeogenic enzyme fructose-1,6-bisphosphatase 1 (FBP1) as a p53 target that is elevated in senescent-like MASH hepatocytes but suppressed through promoter hypermethylation and proteasomal degradation in most human HCCs. FBP1 first declines in metabolically stressed premalignant disease-associated hepatocytes and HCC progenitor cells4,5, paralleling the protumorigenic activation of AKT and NRF2. By accelerating FBP1 and p53 degradation, AKT and NRF2 enhance the proliferation and metabolic activity of previously senescent HCC progenitors. The senescence-reversing and proliferation-supportive NRF2-FBP1-AKT-p53 metabolic switch, operative in mice and humans, also enhances the accumulation of DNA-damage-induced somatic mutations needed for MASH-to-HCC progression.
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Affiliation(s)
- Li Gu
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA.
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.
- Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Yahui Zhu
- School of Medicine, Chongqing University, Chongqing, China.
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Shuvro P Nandi
- Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA, USA
- Department of Bioengineering, UCSD, La Jolla, CA, USA
- Moores Cancer Center, UCSD, La Jolla, CA, USA
| | - Maiya Lee
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Kosuke Watari
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Breanna Bareng
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Masafumi Ohira
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Yuxiao Liu
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA
| | | | - Rodrigo Carlessi
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Consuelo Sauceda
- Department of Pharmacology, UCSD, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, CA, USA
| | | | | | | | - Marcos G Teneche
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - David J Gonzalez
- Department of Pharmacology, UCSD, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, CA, USA
| | | | - Janina E E Tirnitz-Parker
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA, USA
- Department of Bioengineering, UCSD, La Jolla, CA, USA
- Moores Cancer Center, UCSD, La Jolla, CA, USA
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA.
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Funk JS, Klimovich M, Drangenstein D, Pielhoop O, Hunold P, Borowek A, Noeparast M, Pavlakis E, Neumann M, Balourdas DI, Kochhan K, Merle N, Bullwinkel I, Wanzel M, Elmshäuser S, Teply-Szymanski J, Nist A, Procida T, Bartkuhn M, Humpert K, Mernberger M, Savai R, Soussi T, Joerger AC, Stiewe T. Deep CRISPR mutagenesis characterizes the functional diversity of TP53 mutations. Nat Genet 2025; 57:140-153. [PMID: 39774325 PMCID: PMC11735402 DOI: 10.1038/s41588-024-02039-4] [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: 03/17/2024] [Accepted: 11/20/2024] [Indexed: 01/11/2025]
Abstract
The mutational landscape of TP53, a tumor suppressor mutated in about half of all cancers, includes over 2,000 known missense mutations. To fully leverage TP53 mutation status for personalized medicine, a thorough understanding of the functional diversity of these mutations is essential. We conducted a deep mutational scan using saturation genome editing with CRISPR-mediated homology-directed repair to engineer 9,225 TP53 variants in cancer cells. This high-resolution approach, covering 94.5% of all cancer-associated TP53 missense mutations, precisely mapped the impact of individual mutations on tumor cell fitness, surpassing previous deep mutational scan studies in distinguishing benign from pathogenic variants. Our results revealed even subtle loss-of-function phenotypes and identified promising mutants for pharmacological reactivation. Moreover, we uncovered the roles of splicing alterations and nonsense-mediated messenger RNA decay in mutation-driven TP53 dysfunction. These findings underscore the power of saturation genome editing in advancing clinical TP53 variant interpretation for genetic counseling and personalized cancer therapy.
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Affiliation(s)
- Julianne S Funk
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Maria Klimovich
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | | | - Ole Pielhoop
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Pascal Hunold
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Anna Borowek
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Maxim Noeparast
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | | | - Michelle Neumann
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Frankfurt am Main, Germany
| | - Katharina Kochhan
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Nastasja Merle
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Imke Bullwinkel
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Michael Wanzel
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | | | - Julia Teply-Szymanski
- Institute of Pathology, Philipps-University, Marburg University Hospital, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Philipps-University, Marburg, Germany
| | - Tara Procida
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Marek Bartkuhn
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University, Giessen, Germany
| | - Katharina Humpert
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
- Bioinformatics Core Facility, Philipps-University, Marburg, Germany
| | - Marco Mernberger
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany
| | - Rajkumar Savai
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Giessen, Germany
- Cardio-Pulmonary Institute (CPI), Giessen, Germany
- Lung Microenvironmental Niche in Cancerogenesis, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Thierry Soussi
- Centre de Recherche Saint-Antoine UMRS_938, INSERM, Sorbonne Université, Paris, France
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Frankfurt am Main, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, Marburg, Germany.
- Genomics Core Facility, Philipps-University, Marburg, Germany.
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany.
- Bioinformatics Core Facility, Philipps-University, Marburg, Germany.
- Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Giessen, Germany.
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69
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Shahbaz W, Greif PA. [(Over-)living with cancer: secondary malignancies (incl. genetics)]. Dtsch Med Wochenschr 2025; 150:37-43. [PMID: 39662494 DOI: 10.1055/a-2258-4682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2024]
Abstract
Secondary malignancies (secondary cancers) are malignant diseases that occur at a certain time after cancer treatment. The malignant neoplasms can occur anywhere from 2 months to decades after cancer treatment. In addition, multiple tumor diseases can also develop due to a hereditary tendency to tumors. This article provides an overview of the causes, early detection and individual treatment.
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70
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Wang J, Guo C, Wang J, Zhang X, Qi J, Huang X, Hu Z, Wang H, Hong B. Tumor Mutation Signature Reveals the Risk Factors of Lung Adenocarcinoma with EGFR or KRAS Mutation. Cancer Control 2025; 32:10732748241307363. [PMID: 39760242 DOI: 10.1177/10732748241307363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2025] Open
Abstract
INTRODUCTION EGFR and KRAS mutations are frequently detected in lung adenocarcinoma (LUAD). Tumor mutational signature (TMS) determination is an approach to identify somatic mutational patterns associated with pathogenic factors. In this study, through the analysis of TMS, the underlying pathogenic factors of LUAD with EGFR and KRAS mutations were traced. METHODS This was a retrospective study. TMS of LUAD with KRAS and EGFR mutations from the TCGA, OncoSG, and MSK datasets was determined by two bioinformatics tools, namely the "MutationalPatterns" and "FitMS" packages. Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) of LUAD clinical specimens was analyzed using capillary electrophoresis. RESULTS In LUAD with KRAS mutations, TMS analysis indicated that the smoking-related SBS4 signature was enriched. For LUAD with EGFR L858R mutation, the smoking-related SBS4 signature was enriched in the Western population from the TCGA database; however, the smoking-related SBS4 signature was not obvious in Asian LUAD patients. LUAD with EGFR exon19 deletion (19Del) exhibited stronger SBS15 signature, which was related to defective DNA mismatch repair. Capillary electrophoresis analysis showed that an EMAST locus was frequently instable in LUAD with EGFR 19Del. Different from the Western population, Asian LUAD patients with EGFR mutations exhibited the enrichment of SBS1, SBS2, and SBS13 signatures, which were associated with the endogenous mutation process of cytidine deamination. CONCLUSIONS TMS analysis reveals that smoking is associated with LUAD with KRAS mutations. Defective DNA mismatch repair and endogenous cytidine deamination are associated with LUAD with EGFR mutations, especially for the EGFR 19Del. The endogenous mutational process is stronger in Asian LUAD patients than Western LUAD patients.
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Affiliation(s)
- Jialiang Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
| | - Chang Guo
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
| | - Jiexiao Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
| | - Xiaopeng Zhang
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
| | - Jian Qi
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
| | - Xiang Huang
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
| | - Zongtao Hu
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
| | - Hongzhi Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
| | - Bo Hong
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei, China
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71
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Karihtala P, Kilpivaara O, Porvari K. Mutational signatures and their association with cancer survival and gene expression in multiple cancer types. Int J Cancer 2025; 156:114-129. [PMID: 39194330 DOI: 10.1002/ijc.35148] [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: 03/21/2024] [Revised: 06/19/2024] [Accepted: 07/15/2024] [Indexed: 08/29/2024]
Abstract
Different endogenous and exogenous mutational processes cause specific patterns of somatic mutations and mutational signatures. Although their biological research has been intensive, there are only rare studies assessing the possible prognostic role of mutational signatures. We used data from The Cancer Genome Atlas to study the associations between the activity of the mutational signatures and four survival endpoints in 18 types of malignancies. We further explored the prognostic differences according to, for example, the HPV status in head and neck squamous cell carcinomas and smoking status in lung cancers. The predictive power of the signatures over time was evaluated with a dynamic area under the curve model, and the links between mutational signature activities and differences in gene expression patterns were analyzed. In 12 of 18 studied cancer types, we identified at least one mutational signature whose activity predicted survival outcomes after adjusting for the established prognostic factors. For example, overall survival was associated with the activity of mutational signatures in nine cancer types and disease-specific survival in seven cancer types. The clock-like signatures SBS5 and SBS40 were most commonly associated with survival endpoints. The genes of the myosin binding protein and melanoma antigen families were among the most substantially dysregulated genes between the signatures of low and high activity. The differences in gene expression also revealed various enriched pathways. Based on these data, specific mutational signatures associate with the gene expression and have the potential to serve as strong prognostic factors in several cancer types.
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Affiliation(s)
- Peeter Karihtala
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center and University of Helsinki, Helsinki, Finland
- Department of Oncology and Radiotherapy, Oulu University Hospital, Oulu, Finland
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- K. Albin Johansson Cancer Research Fellow, Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Katja Porvari
- Department of Pathology, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
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Lu WT, Zalmas LP, Bailey C, Black JRM, Martinez-Ruiz C, Pich O, Gimeno-Valiente F, Usaite I, Magness A, Thol K, Webber TA, Jiang M, Saunders RE, Liu YH, Biswas D, Ige EO, Aerne B, Grönroos E, Venkatesan S, Stavrou G, Karasaki T, Al Bakir M, Renshaw M, Xu H, Schneider-Luftman D, Sharma N, Tovini L, Jamal-Hanjani M, McClelland SE, Litchfield K, Birkbak NJ, Howell M, Tapon N, Fugger K, McGranahan N, Bartek J, Kanu N, Swanton C. TRACERx analysis identifies a role for FAT1 in regulating chromosomal instability and whole-genome doubling via Hippo signalling. Nat Cell Biol 2025; 27:154-168. [PMID: 39738653 PMCID: PMC11735399 DOI: 10.1038/s41556-024-01558-w] [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: 07/07/2023] [Accepted: 10/16/2024] [Indexed: 01/02/2025]
Abstract
Chromosomal instability (CIN) is common in solid tumours and fuels evolutionary adaptation and poor prognosis by increasing intratumour heterogeneity. Systematic characterization of driver events in the TRACERx non-small-cell lung cancer (NSCLC) cohort identified that genetic alterations in six genes, including FAT1, result in homologous recombination (HR) repair deficiencies and CIN. Using orthogonal genetic and experimental approaches, we demonstrate that FAT1 alterations are positively selected before genome doubling and associated with HR deficiency. FAT1 ablation causes persistent replication stress, an elevated mitotic failure rate, nuclear deformation and elevated structural CIN, including chromosome translocations and radial chromosomes. FAT1 loss contributes to whole-genome doubling (a form of numerical CIN) through the dysregulation of YAP1. Co-depletion of YAP1 partially rescues numerical CIN caused by FAT1 loss but does not relieve HR deficiencies, nor structural CIN. Importantly, overexpression of constitutively active YAP15SA is sufficient to induce numerical CIN. Taken together, we show that FAT1 loss in NSCLC attenuates HR and exacerbates CIN through two distinct downstream mechanisms, leading to increased tumour heterogeneity.
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Affiliation(s)
| | | | | | - James R M Black
- The Francis Crick Institute, London, UK
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | - Carlos Martinez-Ruiz
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | | | - Francisco Gimeno-Valiente
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | - Ieva Usaite
- The Francis Crick Institute, London, UK
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | | | - Kerstin Thol
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | | | | | | | - Yun-Hsin Liu
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- The Francis Crick Institute, London, UK
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | | | | | | | - Subramanian Venkatesan
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | - Georgia Stavrou
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | - Takahiro Karasaki
- The Francis Crick Institute, London, UK
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
- Department of Thoracic Surgery, Respiratory Center, Toranomon Hospital, Tokyo, Japan
| | - Maise Al Bakir
- The Francis Crick Institute, London, UK
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | | | - Hang Xu
- The Francis Crick Institute, London, UK
| | | | - Natasha Sharma
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | - Laura Tovini
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Mariam Jamal-Hanjani
- The Francis Crick Institute, London, UK
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | | | - Kevin Litchfield
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | - Kasper Fugger
- University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- CRUK Lung Cancer Centre of Excellence, London, UK
- University College London Cancer Institute, London, UK
| | - Jiri Bartek
- Danish Cancer Society Research Centre, Copenhagen, Denmark.
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Laboratory, Karolinska Institutet, Solna, Sweden.
| | - Nnennaya Kanu
- CRUK Lung Cancer Centre of Excellence, London, UK.
- University College London Cancer Institute, London, UK.
| | - Charles Swanton
- The Francis Crick Institute, London, UK.
- CRUK Lung Cancer Centre of Excellence, London, UK.
- University College London Cancer Institute, London, UK.
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de Groot D, Spanjaard A, Shah R, Kreft M, Morris B, Lieftink C, Catsman JJI, Ormel S, Ayidah M, Pilzecker B, Buoninfante OA, van den Berk PCM, Beijersbergen RL, Jacobs H. Molecular dependencies and genomic consequences of a global DNA damage tolerance defect. Genome Biol 2024; 25:323. [PMID: 39741332 DOI: 10.1186/s13059-024-03451-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 11/29/2024] [Indexed: 01/02/2025] Open
Abstract
BACKGROUND DNA damage tolerance (DDT) enables replication to continue in the presence of fork stalling lesions. In mammalian cells, DDT is regulated by two independent pathways, controlled by the polymerase REV1 and ubiquitinated PCNA, respectively. RESULTS To determine the molecular and genomic impact of a global DDT defect, we studied PcnaK164R/-;Rev1-/- compound mutants in mouse cells. Double-mutant cells display increased replication stress, hypersensitivity to genotoxic agents, replication speed, and repriming. A whole-genome CRISPR-Cas9 screen revealed a strict reliance of double-mutant cells on the CST complex, where CST promotes fork stability. Whole-genome sequencing indicated that this double-mutant DDT defect favors the generation of large, replication-stress inducible deletions of 0.4-4.0 kbp, defined as type 3 deletions. Junction break sites of these deletions reveal microhomology preferences of 1-2 base pairs, differing from the smaller type 1 and type 2 deletions. These differential characteristics suggest the existence of molecularly distinct deletion pathways. Type 3 deletions are abundant in human tumors, can dominate the deletion landscape, and are associated with DNA damage response status and treatment modality. CONCLUSIONS Our data highlight the essential contribution of the DDT system to genome maintenance and type 3 deletions as mutational signature of replication stress. The unique characteristics of type 3 deletions implicate the existence of a novel deletion pathway in mice and humans that is counteracted by DDT.
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Affiliation(s)
- Daniel de Groot
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Ronak Shah
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Maaike Kreft
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Joyce J I Catsman
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Shirley Ormel
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Matilda Ayidah
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Bas Pilzecker
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Olimpia Alessandra Buoninfante
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Paul C M van den Berk
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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74
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Murat P, Guilbaud G, Sale JE. DNA replication initiation drives focal mutagenesis and rearrangements in human cancers. Nat Commun 2024; 15:10850. [PMID: 39738026 DOI: 10.1038/s41467-024-55148-3] [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: 04/10/2024] [Accepted: 12/03/2024] [Indexed: 01/01/2025] Open
Abstract
The rate and pattern of mutagenesis in cancer genomes is significantly influenced by DNA accessibility and active biological processes. Here we show that efficient sites of replication initiation drive and modulate specific mutational processes in cancer. Sites of replication initiation impede nucleotide excision repair in melanoma and are off-targets for activation-induced deaminase (AICDA) activity in lymphomas. Using ductal pancreatic adenocarcinoma as a cancer model, we demonstrate that the initiation of DNA synthesis is error-prone at G-quadruplex-forming sequences in tumours displaying markers of replication stress, resulting in a previously recognised but uncharacterised mutational signature. Finally, we demonstrate that replication origins serve as hotspots for genomic rearrangements, including structural and copy number variations. These findings reveal replication origins as functional determinants of tumour biology and demonstrate that replication initiation both passively and actively drives focal mutagenesis in cancer genomes.
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Affiliation(s)
- Pierre Murat
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Wellcome Sanger Institute, Hinxton, CB10 1RQ, UK.
| | - Guillaume Guilbaud
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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75
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Zhuravleva E, Lewinska M, O'Rourke CJ, Pea A, Rashid A, Hsing AW, Taranta A, Chang D, Gao YT, Koshiol J, Oliveira RC, Andersen JB. Mutational signatures define immune and Wnt-associated subtypes of ampullary carcinoma. Gut 2024:gutjnl-2024-333368. [PMID: 39725462 DOI: 10.1136/gutjnl-2024-333368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 11/21/2024] [Indexed: 12/28/2024]
Abstract
BACKGROUND AND OBJECTIVE Ampullary carcinoma (AMPAC) taxonomy is based on morphology and immunohistochemistry. This classification lacks prognostic reliability and unique genetic associations. We applied an approach of integrative genomics characterising patients with AMPAC exploring molecular subtypes that may guide personalised treatments. DESIGN We analysed the mutational landscapes of 170 patients with AMPAC. The discovery included 110 tumour/normal pairs and the validation comprised 60 patients. In a tumour subset, we interrogated the transcriptomes and DNA methylomes. Patients were stratified based on mutational signatures and associated with molecular and clinical features. To evaluate tumour and immune cellularity, 22 tumours were independently assessed histomorphologically and by digital pathology. RESULTS We defined three patient clusters by mutational signatures independent of histomorphology. Cluster 1 (C1) was defined by spontaneous deamination of DNA 5-methylcytosine and defective mismatch repair. C2 and C3 were related to the activity of transcription-coupled nucleotide excision repair but C3 was further defined by the polymerase eta mutational process. C1-2 showed enrichment of Wnt pathway alterations, aberrant DNA methylation profiles, immune cell exclusion and patients with poor prognosis. These features were associated with a hypermutator phenotype caused by C>T alterations at CpGs. C3 patients with improved overall survival were associated with activation of immune-related pathways, immune infiltration and elevated expression of immunoinhibitory checkpoint genes. CONCLUSION Immunogenicity and Wnt pathway associations, emphasised by the mutational signatures, defined patients with prospective sensitivity to either immunotherapy or Wnt pathway inhibitors. This emphasises a novel mutational signature-based AMPAC classification with prognostic potential, suggesting prospective implications for subgroup-specific management of patients with AMPAC.
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Affiliation(s)
- Ekaterina Zhuravleva
- Biotech Research and Innovation Center (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Monika Lewinska
- Biotech Research and Innovation Center (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colm J O'Rourke
- Biotech Research and Innovation Center (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Pea
- University of Glasgow, Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, Glasgow, UK
- University of Verona, Verona, Italy
| | - Asif Rashid
- Department of Pathology, Division of Pathology/Lab Medicine, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
| | - Ann W Hsing
- Stanford Cancer Institute and Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford University, Palo Alto, California, USA
| | - Andrzej Taranta
- Biotech Research and Innovation Center (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Chang
- University of Glasgow, Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, Glasgow, UK
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, Shanghai, China
| | - Jill Koshiol
- Division of Cancer Epidemiology and Genetics, NIH, Rockville, Maryland, USA
| | | | - Jesper B Andersen
- Biotech Research and Innovation Center (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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76
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Ahmed F, Zhong J. Advances in DNA/RNA Sequencing and Their Applications in Acute Myeloid Leukemia (AML). Int J Mol Sci 2024; 26:71. [PMID: 39795930 PMCID: PMC11720148 DOI: 10.3390/ijms26010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 11/24/2024] [Accepted: 12/19/2024] [Indexed: 01/13/2025] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive malignancy that poses significant challenges due to high rates of relapse and resistance to treatment, particularly in older populations. While therapeutic advances have been made, survival outcomes remain suboptimal. The evolution of DNA and RNA sequencing technologies, including whole-genome sequencing (WGS), whole-exome sequencing (WES), and RNA sequencing (RNA-Seq), has significantly enhanced our understanding of AML at the molecular level. These technologies have led to the discovery of driver mutations and transcriptomic alterations critical for improving diagnosis, prognosis, and personalized therapy development. Furthermore, single-cell RNA sequencing (scRNA-Seq) has uncovered rare subpopulations of leukemia stem cells (LSCs) contributing to disease progression and relapse. However, widespread clinical integration of these tools remains limited by costs, data complexity, and ethical challenges. This review explores recent advancements in DNA/RNA sequencing in AML and highlights both the potential and limitations of these techniques in clinical practice.
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Affiliation(s)
| | - Jiang Zhong
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA;
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77
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Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA. Contributing factors to the oxidation-induced mutational landscape in human cells. Nat Commun 2024; 15:10722. [PMID: 39715760 DOI: 10.1038/s41467-024-55497-z] [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: 05/09/2024] [Accepted: 12/10/2024] [Indexed: 12/25/2024] Open
Abstract
8-oxoguanine (8-oxoG) is a common oxidative DNA lesion that causes G > T substitutions. Determinants of local and regional differences in 8-oxoG-induced mutability across genomes are currently unknown. Here, we show DNA oxidation induces G > T substitutions and insertion/deletion (INDEL) mutations in human cells and cancers. Potassium bromate (KBrO3)-induced 8-oxoGs occur with similar sequence preferences as their derived substitutions, indicating that the reactivity of specific oxidants dictates mutation sequence specificity. While 8-oxoG occurs uniformly across chromatin, 8-oxoG-induced mutations are elevated in compact genomic regions, within nucleosomes, and at inward facing guanines within strongly positioned nucleosomes. Cryo-electron microscopy structures of OGG1-nucleosome complexes indicate that these effects originate from OGG1's ability to flip outward positioned 8-oxoG lesions into the catalytic pocket while inward facing lesions are occluded by the histone octamer. Mutation spectra from human cells with DNA repair deficiencies reveals contributions of a DNA repair network limiting 8-oxoG mutagenesis, where OGG1- and MUTYH-mediated base excision repair is supplemented by the replication-associated factors Pol η and HMCES. Transcriptional asymmetry of KBrO3-induced mutations in OGG1- and Pol η-deficient cells also demonstrates transcription-coupled repair can prevent 8-oxoG-induced mutation. Thus, oxidant chemistry, chromatin structures, and DNA repair processes combine to dictate the oxidative mutational landscape in human genomes.
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Affiliation(s)
- Cameron Cordero
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA
- University of Vermont Cancer Center, University of Vermont, Burlington, VT, 05405, USA
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Kavi P M Mehta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53706, USA.
| | - Tyler M Weaver
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- University of Kansas Cancer Center, Kansas City, KS, 66160, USA
| | - Justin A Ling
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- University of Kansas Cancer Center, Kansas City, KS, 66160, USA.
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
| | - Steven A Roberts
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA.
- University of Vermont Cancer Center, University of Vermont, Burlington, VT, 05405, USA.
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA.
- Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
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78
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Mallawaarachchi AC, Hort Y, Wedd L, Lo K, Senum S, Toumari M, Chen W, Utsiwegota M, Mawson J, Leslie S, Laurence J, Anderson L, Snelling P, Salomon R, Rangan GK, Furlong T, Shine J, Cowley MJ. Somatic mutation in autosomal dominant polycystic kidney disease revealed by deep sequencing human kidney cysts. NPJ Genom Med 2024; 9:69. [PMID: 39702469 DOI: 10.1038/s41525-024-00452-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/02/2024] [Indexed: 12/21/2024] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) results in progressive cysts that lead to kidney failure, and is caused by heterozygous germline variants in PKD1 or PKD2. Cyst pathogenesis is not definitively understood. Somatic second-hit mutations have been implicated in cyst pathogenesis, though technical sequencing challenges have limited investigation. We used unique molecular identifiers, high-depth massively parallel sequencing and custom analysis techniques to identify somatic second-hit mutations in 24 whole cysts from disparate regions of six human ADPKD kidneys, utilising replicate samples and orthogonal confirmation. Average depth of coverage of 1166 error-corrected reads for PKD1 and 539 reads for PKD2 was obtained. 58% (14/24) of cysts had a detectable PKD1 somatic variant, with 5/6 participants having at least one cyst with a somatic variant. We demonstrate that low-frequency somatic mutations are detectable in a proportion of cysts from end-stage ADPKD human kidneys. Further studies are required to understand the drivers of this somatic mutation.
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Affiliation(s)
- Amali C Mallawaarachchi
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, Sydney, NSW, Australia.
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
| | - Yvonne Hort
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Laura Wedd
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Kitty Lo
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Sarah Senum
- Department of Artificial Intelligence & Informatics, Mayo Clinic, Rochester, MN, USA
| | - Mojgan Toumari
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Wenhan Chen
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Mike Utsiwegota
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Jane Mawson
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Scott Leslie
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- RPA Institute of Academic Surgery, University of Sydney, Sydney, NSW, Australia
- Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Jerome Laurence
- RPA Institute of Academic Surgery, University of Sydney, Sydney, NSW, Australia
| | - Lyndal Anderson
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Sydney, NSW, Australia
| | - Paul Snelling
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Robert Salomon
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Gopala K Rangan
- Department of Renal Medicine, Westmead Hospital, Sydney, NSW, Australia
- Michael Stern Laboratory for Polycystic Kidney Disease, Centre for Transplant and Renal Research, Westmead Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Timothy Furlong
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - John Shine
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, Sydney, NSW, Australia
| | - Mark J Cowley
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, Sydney, NSW, Australia.
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.
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Mitsiades IR, Onozato M, Iafrate AJ, Hicks D, Gülhan DC, Sgroi DC, Rheinbay E. ERBB2/HOXB13 co-amplification with interstitial loss of BRCA1 defines a unique subset of breast cancers. Breast Cancer Res 2024; 26:185. [PMID: 39695741 DOI: 10.1186/s13058-024-01943-1] [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: 08/08/2024] [Accepted: 12/03/2024] [Indexed: 12/20/2024] Open
Abstract
BACKGROUND The HOXB13/IL17RB gene expression biomarker has been shown to predict response to adjuvant and extended endocrine therapy in patients with early-stage ER+ HER2- breast tumors. HOXB13 gene expression is the primary determinant driving the prognostic and endocrine treatment-predictive performance of the biomarker. Currently, there is limited data on HOXB13 expression in HER2+ and ER- breast cancers. Herein, we studied the expression of HOXB13 in large cohorts of HER2+ and ER- breast cancers. METHODS We investigated gene expression, genomic copy number, mutational signatures, and clinical outcome data in the TGGA and METABRIC breast cancer cohorts. Genomic-based gene amplification data was validated with tri-colored fluorescence in situ hybridization. RESULTS In the TCGA breast cancer cohort, HOXB13 gene expression was significantly higher in HER2+ versus HER2- breast cancers, and its expression was also significantly higher in the ER- versus ER+ breast cancers. HOXB13 is frequently co-gained or co-amplified with ERBB2. Joint copy gains of HOXB13 and ERBB2 occurred with low-level co-gains or high-level co-amplifications (co-amp), the latter of which is associated with an interstitial loss that includes the tumor suppressor BRCA1. ERBB2/HOXB13 co-amp tumors with interstitial BRCA1 loss exhibit a mutational signature associated with APOBEC deaminase activity and copy number signatures associated with chromothripsis and genomic instability. Among ERBB2-amplified tumors of different tissue origins, ERBB2/HOXB13 co-amp with a BRCA1 loss appeared to be enriched in breast cancer compared to other tumor types. Lastly, patients with ERBB2/HOXB13 co-amplified and BRCA1 lost tumors displayed a significantly shorter progression-free survival (PFS) than those with ERBB2-only amplifications. The difference in PFS was restricted to the ER- subset patients and this difference in PFS was not solely driven by HOXB13 gene expression. CONCLUSIONS HOXB13 is frequently co-gained with ERBB2 at both low-copy number level or as complex high-level amplification with relative BRCA1 loss. ERBB2/HOXB13 amplified, BRCA1-lost tumors are strongly enriched in breast cancer, and patients with such breast tumors experience a shortened PFS.
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Affiliation(s)
- Irene Rin Mitsiades
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, 02129, USA
| | - Maristela Onozato
- Vertex Pharmaceuticals, Preclinical Safety Assessment, Pathology, 316 Northern Ave, Boston, MA, 02210, USA
| | - A John Iafrate
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, 02129, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Hicks
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, 02129, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - Doğa C Gülhan
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, 02129, USA
- The Broad Institute or MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Dennis C Sgroi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, 02129, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
| | - Esther Rheinbay
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, 02129, USA.
- The Broad Institute or MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
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Delgado-de la Mora J, Al Assaad M, Quitian S, Levine MF, Deshpande A, Sigouros M, Manohar J, Medina-Martínez JS, Sboner A, Elemento O, Jessurun J, Hissong E, Mosquera JM. Novel structural variants that impact cell cycle genes are elucidated in metastatic gastrointestinal stromal tumors. Pathol Res Pract 2024; 266:155782. [PMID: 39708519 DOI: 10.1016/j.prp.2024.155782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 12/17/2024] [Indexed: 12/23/2024]
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasm of the digestive tract. Despite multiple therapeutic advances, patients with advanced disease frequently develop resistance to tyrosine kinase inhibitors (TKIs), and therefore represent a therapeutic challenge. We employed whole genome sequencing (WGS) on three metastatic GISTs refractory to various TKIs and explored a publicly available cohort of 499 GISTs. This study sheds light on the clinical importance of alterations in cell cycle genes such as cyclin-dependent kinase 2 A (CDKN2A), and cyclin-dependent kinase 2B (CDKN2B), their frequent alteration in metastatic GISTs and their potential role in tumor progression of this neoplasm. Likewise, new structural variations were identified in cyclin-dependent kinase 12 (CDK12). Whole genome profiling of metastatic GIST provides new insights to advance precision care of the disease, focusing on new therapeutic possibilities, especially for emerging targets such as CDK12.
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Affiliation(s)
- Jesús Delgado-de la Mora
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY 10021, USA
| | - Majd Al Assaad
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY 10021, USA
| | - Stephanie Quitian
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA
| | - Max F Levine
- Isabl Inc., 175 Greenwich Street, Fl 38, New York, NY 10007, USA
| | - Aditya Deshpande
- Isabl Inc., 175 Greenwich Street, Fl 38, New York, NY 10007, USA
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY 10021, USA
| | - Jyothi Manohar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY 10021, USA
| | | | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, 1305 York Avenue, New York, NY 10021, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, 1305 York Avenue, New York, NY 10021, USA
| | - José Jessurun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA
| | - Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY 10021, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY 10021, USA.
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81
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Shelley CS, Galiègue-Zouitina S, Andritsos LA, Epperla N, Troussard X. The role of the JunD-RhoH axis in the pathogenesis of hairy cell leukemia and its ability to identify existing therapeutics that could be repurposed to treat relapsed or refractory disease. Leuk Lymphoma 2024:1-19. [PMID: 39689307 DOI: 10.1080/10428194.2024.2438800] [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: 07/17/2024] [Revised: 11/19/2024] [Accepted: 12/01/2024] [Indexed: 12/19/2024]
Abstract
Hairy cell leukemia (HCL) is an indolent malignancy of mature B-lymphocytes. While existing front-line therapies achieve excellent initial results, a significant number of patients relapse and become increasingly treatment resistant. A major molecular driver of HCL is aberrant interlocking expression of the transcription factor JunD and the intracellular signaling molecule RhoH. Here we discuss the molecular basis of how the JunD-RhoH axis contributes to HCL pathogenesis. We also discuss how leveraging the JunD-RhoH axis identifies CD23, CD38, CD66a, CD115, CD269, integrin β7, and MET as new potential therapeutic targets. Critically, preclinical studies have already demonstrated that targeting CD38 with isatuximab effectively treats preexisiting HCL. Isatuximab and therapeutics directed against each of the other six new HCL targets are currently in clinical use to treat other disorders. Consequently, leveraging the JunD-RhoH axis has identified a battery of therapies that could be repurposed as new means of treating relapsed or refractory HCL.
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Affiliation(s)
| | | | - Leslie A Andritsos
- Division of Hematology Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, USA
| | - Narendranath Epperla
- Division of Hematology, University of Utah Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Xavier Troussard
- Hematology CHU Caen Normandie, INSERM1245, MICAH, Normandie University of Caen and Rouen, UNIROUEN, UNICAEN, Hematology Institute, University Hospital Caen, Caen, France
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82
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Zhang L, Deng T, Liufu Z, Liu X, Chen B, Hu Z, Liu C, Tracy ME, Lu X, Wen HJ, Wu CI. The theory of massively repeated evolution and full identifications of cancer-driving nucleotides (CDNs). eLife 2024; 13:RP99340. [PMID: 39688960 DOI: 10.7554/elife.99340] [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] [Indexed: 12/19/2024] Open
Abstract
Tumorigenesis, like most complex genetic traits, is driven by the joint actions of many mutations. At the nucleotide level, such mutations are cancer-driving nucleotides (CDNs). The full sets of CDNs are necessary, and perhaps even sufficient, for the understanding and treatment of each cancer patient. Currently, only a small fraction of CDNs is known as most mutations accrued in tumors are not drivers. We now develop the theory of CDNs on the basis that cancer evolution is massively repeated in millions of individuals. Hence, any advantageous mutation should recur frequently and, conversely, any mutation that does not is either a passenger or deleterious mutation. In the TCGA cancer database (sample size n=300-1000), point mutations may recur in i out of n patients. This study explores a wide range of mutation characteristics to determine the limit of recurrences (i*) driven solely by neutral evolution. Since no neutral mutation can reach i*=3, all mutations recurring at i≥3 are CDNs. The theory shows the feasibility of identifying almost all CDNs if n increases to 100,000 for each cancer type. At present, only <10% of CDNs have been identified. When the full sets of CDNs are identified, the evolutionary mechanism of tumorigenesis in each case can be known and, importantly, gene targeted therapy will be far more effective in treatment and robust against drug resistance.
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Affiliation(s)
- Lingjie Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tong Deng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhongqi Liufu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Genetic Resources and Evolution/Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
| | - Xueyu Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chenli Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Miles E Tracy
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution/Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
| | - Hai-Jun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Innovation Center for Evolutionary Synthetic Biology, Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Innovation Center for Evolutionary Synthetic Biology, Sun Yat-sen University, Guangzhou, China
- Department of Ecology and Evolution, University of Chicago, Chicago, United States
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83
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Fixman B, Díaz-Gay M, Qiu C, Margaryan T, Lee B, Chen XS. Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures. J Mol Biol 2024; 436:168854. [PMID: 39510348 PMCID: PMC11637894 DOI: 10.1016/j.jmb.2024.168854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 10/30/2024] [Accepted: 10/31/2024] [Indexed: 11/15/2024]
Abstract
Mutational signature analysis gained significant attention for providing critical insights into the underlying mutational processes for various DNA single base substitution (SBS) signatures and their associations with different cancer types. Recently, RNA single base substitution (RNA-SBS) signatures were defined and described by decomposing RNA variants found in non-small cell lung cancer. Through statistical association, they attributed Apolipoprotein B mRNA Editing Enzyme, Catalytic Polypeptide 3A (APOBEC3A) mutagenesis to the RNA-SBS2 signature. Here, we provide the first validation of an RNA-SBS mutational signature by decomposing novel exogenous and endogenous APOBEC3A RNA editing signatures into COSMICv3.4 RNA-SBS reference signatures. Additionally, we have identified novel RNA-SBS signatures for APOBEC1, APOBEC3B, and APOBEC3G.
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Affiliation(s)
- Benjamin Fixman
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Connor Qiu
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Tamara Margaryan
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Brian Lee
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, USA; Norris Comprehensive Cancer Center, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA.
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84
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Oelschläger L, Künstner A, Frey F, Leitner T, Leypoldt L, Reimer N, Gebauer N, Bastian L, Weisel K, Sailer VW, Röcken C, Klapper W, Konukiewitz B, Murga Penas EM, Forster M, Schub N, Ahmed HMM, Kirfel J, von Bubnoff NCC, Busch H, Khandanpour C. Whole-Exome Sequencing, Mutational Signature Analysis, and Outcome in Multiple Myeloma-A Pilot Study. Int J Mol Sci 2024; 25:13418. [PMID: 39769182 PMCID: PMC11680055 DOI: 10.3390/ijms252413418] [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: 10/31/2024] [Revised: 12/02/2024] [Accepted: 12/09/2024] [Indexed: 01/11/2025] Open
Abstract
The complex and heterogeneous genomic landscape of multiple myeloma (MM) and many of its clinical and prognostic implications remains to be understood. In other cancers, such as breast cancer, using whole-exome sequencing (WES) and molecular signatures in clinical practice has revolutionized classification, prognostic prediction, and patient management. However, such integration is still in its early stages in MM. In this study, we analyzed WES data from 35 MM patients to identify potential mutational signatures and driver mutations correlated with clinical and cytogenetic characteristics. Our findings confirm the complex mutational spectrum and its impact on previously described ontogenetic and epigenetic pathways. They show TYW1 as a possible new potential driver gene and find no significant associations of mutational signatures with clinical findings. Further studies are needed to strengthen the role of mutational signatures in the clinical context of patients with MM to improve patient management.
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Affiliation(s)
- Lorenz Oelschläger
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH), University Cancer Center Schleswig-Holstein (UCCSH), Campus Lübeck, 23538 Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, 23538 Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, 23538 Lübeck, Germany
| | - Friederike Frey
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH), University Cancer Center Schleswig-Holstein (UCCSH), Campus Lübeck, 23538 Lübeck, Germany
| | - Theo Leitner
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH), University Cancer Center Schleswig-Holstein (UCCSH), Campus Lübeck, 23538 Lübeck, Germany
| | - Lisa Leypoldt
- Department of Hematology, Oncology and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, 20521 Hamburg, Germany
| | - Niklas Reimer
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, 23538 Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, 23538 Lübeck, Germany
| | - Niklas Gebauer
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH), University Cancer Center Schleswig-Holstein (UCCSH), Campus Lübeck, 23538 Lübeck, Germany
| | - Lorenz Bastian
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, 23538 Lübeck, Germany
- Division for Stem Cell Transplantation and Immunotherapy, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Katja Weisel
- Department of Hematology, Oncology and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, 20521 Hamburg, Germany
| | - Verena-Wilbeth Sailer
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, 23538 Lübeck, Germany
- Department of Pathology, University of Lübeck, 23538 Lübeck, Germany
| | - Christoph Röcken
- Department of Pathology, University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany
| | - Wolfram Klapper
- Department of Pathology, University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany
| | - Björn Konukiewitz
- Department of Pathology, University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany
| | - Eva Maria Murga Penas
- Institute of Human Genetics, University Hospital Schleswig-Holstein (UKSH)/Christian-Albrechts University Kiel (CAU), 24105 Kiel, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts University, 24105 Kiel, Germany
| | - Natalie Schub
- Division for Stem Cell Transplantation and Immunotherapy, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Helal M. M. Ahmed
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH), University Cancer Center Schleswig-Holstein (UCCSH), Campus Lübeck, 23538 Lübeck, Germany
| | - Jutta Kirfel
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, 23538 Lübeck, Germany
- Department of Pathology, University of Lübeck, 23538 Lübeck, Germany
| | - Nikolas Christian Cornelius von Bubnoff
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH), University Cancer Center Schleswig-Holstein (UCCSH), Campus Lübeck, 23538 Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, 23538 Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, 23538 Lübeck, Germany
| | - Cyrus Khandanpour
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH), University Cancer Center Schleswig-Holstein (UCCSH), Campus Lübeck, 23538 Lübeck, Germany
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85
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Avsievich E, Salimgereeva D, Maluchenko A, Antysheva Z, Voloshin M, Feidorov I, Glazova O, Abramov I, Maksimov D, Kaziakhmedova S, Bodunova N, Karnaukhov N, Volchkov P, Krupinova J. Pancreatic Neuroendocrine Tumor: The Case Report of a Patient with Germline FANCD2 Mutation and Tumor Analysis Using Single-Cell RNA Sequencing. J Clin Med 2024; 13:7621. [PMID: 39768544 PMCID: PMC11728285 DOI: 10.3390/jcm13247621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 11/18/2024] [Accepted: 11/21/2024] [Indexed: 01/16/2025] Open
Abstract
Background: Neuroendocrine neoplasms are a rare and heterogeneous group of neoplasms. Small-sized (≤2 cm) pancreatic neuroendocrine tumors (PanNETs) are of particular interest as they are often associated with aggressive behavior, with no specific prognostic or progression markers. METHODS This article describes a clinical case characterized by a progressive growth of nonfunctional PanNET requiring surgical treatment in a patient with a germline FANCD2 mutation, previously not reported in PanNETs. The patient underwent whole exome sequencing and single-cell RNA sequencing. RESULTS The patient underwent surgical treatment. We confirmed the presence of the germline mutation FANCD2 and also detected the germline mutation WNT10A. The cellular composition of the PanNET was analyzed using single-cell sequencing, and the main cell clusters were identified. We analyzed the tumor genomics, and used the data to define the effect the germline FANCD2 mutation had. CONCLUSIONS Analysis of the mutational status of patients with PanNET may provide additional data that may influence treatment tactics, refine the plan for monitoring such patients, and provide more information about the pathogenesis of PanNET. PanNET research using scRNA-seq data may help in predicting the effect of therapy on neuroendocrine cells with FANCD2 mutations.
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Affiliation(s)
- Ekaterina Avsievich
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
- Federal Research Center for Innovator, Emerging Biomedical and Pharmaceutical Technologies, Moscow 125315, Russia
| | - Diana Salimgereeva
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
| | - Alesia Maluchenko
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
| | - Zoia Antysheva
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
- Federal Research Center for Innovator, Emerging Biomedical and Pharmaceutical Technologies, Moscow 125315, Russia
| | - Mark Voloshin
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
| | - Ilia Feidorov
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
| | - Olga Glazova
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
| | - Ivan Abramov
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
- Federal Research Center for Innovator, Emerging Biomedical and Pharmaceutical Technologies, Moscow 125315, Russia
| | - Denis Maksimov
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
- Federal Research Center for Innovator, Emerging Biomedical and Pharmaceutical Technologies, Moscow 125315, Russia
| | - Samira Kaziakhmedova
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
| | - Natalia Bodunova
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
| | - Nikolay Karnaukhov
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
| | - Pavel Volchkov
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
- Federal Research Center for Innovator, Emerging Biomedical and Pharmaceutical Technologies, Moscow 125315, Russia
| | - Julia Krupinova
- Moscow Clinical Scientific Center N.A. A.S. Loginov, Moscow 111123, Russia; (E.A.); (D.S.); (M.V.); (I.F.); (O.G.); (I.A.); (N.B.); (N.K.); (P.V.)
- Moscow Center for Advanced Studies, Kulakova Street 20, Moscow 123592, Russia; (A.M.); (Z.A.); (D.M.); (S.K.)
- Federal Research Center for Innovator, Emerging Biomedical and Pharmaceutical Technologies, Moscow 125315, Russia
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86
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Teodoro L, Carreira ACO, Sogayar MC. Exploring the Complexity of Pan-Cancer: Gene Convergences and in silico Analyses. BREAST CANCER (DOVE MEDICAL PRESS) 2024; 16:913-934. [PMID: 39691553 PMCID: PMC11651076 DOI: 10.2147/bctt.s489246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 11/06/2024] [Indexed: 12/19/2024]
Abstract
Cancer is a complex and multifaceted group of diseases characterized by highly intricate mechanisms of tumorigenesis and tumor progression, which complicates diagnosis, prognosis, and treatment. In recent years, targeted therapies have gained prominence by focusing on specific mutations and molecular features unique to each tumor type, offering more effective and personalized treatment options. However, it is equally critical to explore the genetic commonalities across different types of cancer, which has led to the rise of pan-cancer studies. These approaches help identify shared therapeutic targets across various tumor types, enabling the development of broader and potentially more widely applicable treatment strategies. This review aims to provide a comprehensive overview of key concepts related to tumors, including tumorigenesis processes, the tumor microenvironment, and the role of extracellular vesicles in tumor biology. Additionally, we explore the molecular interactions and mechanisms driving tumor progression, with a particular focus on the pan-cancer perspective. To achieve this, we conducted an in silico analysis using publicly available datasets, which facilitated the identification of both common and divergent genetic and molecular patterns across different tumor types. By integrating these diverse areas, this review offers a clearer and deeper understanding of the factors influencing tumorigenesis and highlights potential therapeutic targets.
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Affiliation(s)
- Leandro Teodoro
- Cell and Molecular Therapy NUCEL Group, School of Medicine, University of São Paulo, São Paulo, São Paulo, 01246-903, Brazil
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, São Paulo, 05508-900, Brazil
| | - Ana Claudia O Carreira
- Cell and Molecular Therapy NUCEL Group, School of Medicine, University of São Paulo, São Paulo, São Paulo, 01246-903, Brazil
- Center of Human and Natural Sciences, Federal University of ABC, Santo André, São Paulo, 09280-560, Brazil
| | - Mari C Sogayar
- Cell and Molecular Therapy NUCEL Group, School of Medicine, University of São Paulo, São Paulo, São Paulo, 01246-903, Brazil
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, São Paulo, 05508-900, Brazil
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87
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Braza MKE, Demir Ö, Ahn SH, Morris CK, Calvó-Tusell C, McGuire KL, de la Peña Avalos B, Carpenter MA, Chen Y, Casalino L, Aihara H, Herzik MA, Harris RS, Amaro RE. Regulatory interactions between APOBEC3B N- and C-terminal domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.11.628032. [PMID: 39713448 PMCID: PMC11661193 DOI: 10.1101/2024.12.11.628032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
APOBEC3B (A3B) is implicated in DNA mutations that facilitate tumor evolution. Although structures of its individual N- and C-terminal domains (NTD and CTD) have been resolved through X-ray crystallography, the full-length A3B (fl-A3B) structure remains elusive, limiting understanding of its dynamics and mechanisms. In particular, the APOBEC3B C-terminal domain (A3Bctd) active site is frequently closed in models and structures. In this study, we built several new models of fl-A3B using integrative structural biology methods and selected a top model for further dynamical investigation. We compared dynamics of the truncated (A3Bctd) to the fl-A3B via conventional and Gaussian accelerated molecular dynamics (MD) simulations. Subsequently, we employed weighted ensemble methods to explore the fl-A3B active site opening mechanism, finding that interactions at the NTD-CTD interface enhance the opening frequency of the fl-A3B active site. Our findings shed light on the structural dynamics of fl-A3B, which may offer new avenues for therapeutic intervention in cancer.
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Affiliation(s)
- Mac Kevin E Braza
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California, Davis, Davis, CA
| | - Clare K Morris
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Carla Calvó-Tusell
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Kelly L McGuire
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Bárbara de la Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX
| | - Michael A Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX
| | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX
| | - Lorenzo Casalino
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Mark A Herzik
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA
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88
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Kadam A, Shilo S, Naor H, Wainstein A, Brilon Y, Feldman T, Minden M, Kaushansky N, Chapal-Ilani N, Shlush L. Utilizing insights of DNA repair machinery to discover MMEJ deletions and novel mechanisms. Nucleic Acids Res 2024; 52:e106. [PMID: 39607705 DOI: 10.1093/nar/gkae1132] [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: 09/12/2023] [Revised: 10/17/2024] [Accepted: 10/30/2024] [Indexed: 11/29/2024] Open
Abstract
We developed Del-read, an algorithm targeting medium-sized deletions (6-100 bp) in short-reads, which are challenging for current variant callers relying on alignment. Our focus was on Micro-Homolog mediated End Joining deletions (MMEJ-dels), prevalent in myeloid malignancies. MMEJ-dels follow a distinct pattern, occurring between two homologies, allowing us to generate a comprehensive list of MMEJ-dels in the exome. Using Del-read, we identified numerous novel germline and somatic MMEJ-dels in BEAT-AML and TCGA-breast datasets. Validation in 672 healthy individuals confirmed their presence. These novel MMEJ-dels were linked to genomic features associated with replication stress, like G-quadruplexes and minisatellite. Additionally, we observed a new category of MMEJ-dels with an imperfect-match at the flanking sequences of the homologies, suggesting a mechanism involving mispairing in homology alignment. We demonstrated robustness of the repair system despite CRISPR/Cas9-induced mismatches in the homologies. Further analysis of the canonical ASXL1 deletion revealed a diverse array of these imperfect-matches. This suggests a potentially more flexible and error-prone MMEJ repair system than previously understood. Our findings highlight Del-read's potential in uncovering previously undetected deletions and deepen our understanding of repair mechanisms.
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Affiliation(s)
- Aditee Kadam
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Shay Shilo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Hadas Naor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Alexander Wainstein
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Yardena Brilon
- Sequentify Ltd., 10 Moti Kind St., 5th Floor, Rehovot 7638519, Israel
| | - Tzah Feldman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Mark Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Department of Medical Oncology & Hematology, Toronto, ON M5G 2C4, Canada
| | - Nathali Kaushansky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Noa Chapal-Ilani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Liran Shlush
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
- Molecular Hematology Clinic Maccabi Healthcare Services, Tel Aviv 6812509, Israel
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89
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Schuster D, LeBlanc DPM, Zhou G, Meier MJ, Dodge AE, White PA, Long AS, Williams A, Hobbs C, Diesing A, Smith-Roe SL, Salk JJ, Marchetti F, Yauk CL. Dose-Related Mutagenic and Clastogenic Effects of Benzo[ b]fluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:21450-21463. [PMID: 39602390 PMCID: PMC11636207 DOI: 10.1021/acs.est.4c07236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 10/06/2024] [Accepted: 11/09/2024] [Indexed: 11/29/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are common environmental pollutants that originate from the incomplete combustion of organic materials. We investigated the clastogenicity and mutagenicity of benzo[b]fluoranthene (BbF), one of 16 priority PAHs, in MutaMouse males after a 28 day oral exposure. BbF causes robust dose-dependent increases in micronucleus frequency in peripheral blood, indicative of chromosome damage. Duplex sequencing (DS), an error-corrected sequencing technology, reveals that BbF induces dose-dependent increases in mutation frequencies in bone marrow (BM) and liver. Mutagenicity is increased in intergenic relative to genic regions, suggesting a role for transcription-coupled repair of BbF-induced DNA damage. At higher doses, the maximum mutagenic response to BbF is higher in liver, which has a lower mitotic index but higher metabolic capacity than BM; however, mutagenic potency is comparable between the two tissues. BbF induces primarily C:G > A:T mutations, followed by C:G > T:A and C:G > G:C, indicating that BbF metabolites mainly target guanines and cytosines. The mutation spectrum of BbF correlates with cancer mutational signatures associated with tobacco exposure, supporting its contribution to the carcinogenicity of combustion-derived PAHs in humans. Overall, BbF's mutagenic effects are similar to benzo[a]pyrene, a well-studied mutagenic PAH. Our work showcases the utility of DS for effective mutagenicity assessment of environmental pollutants.
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Affiliation(s)
| | | | - Gu Zhou
- Environmental
Health Science and Research Bureau, Health
Canada, Ottawa K1A 0K9, Canada
| | - Matthew J. Meier
- Environmental
Health Science and Research Bureau, Health
Canada, Ottawa K1A 0K9, Canada
| | - Annette E. Dodge
- Department
of Biology, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Paul A. White
- Department
of Biology, University of Ottawa, Ottawa K1N 6N5, Canada
- Environmental
Health Science and Research Bureau, Health
Canada, Ottawa K1A 0K9, Canada
| | - Alexandra S. Long
- Existing
Substances Risk Assessment Bureau, Health
Canada, Ottawa K1A 0K9, Canada
| | - Andrew Williams
- Environmental
Health Science and Research Bureau, Health
Canada, Ottawa K1A 0K9, Canada
| | - Cheryl Hobbs
- Integrated
Laboratory Systems, LLC, an Inotiv Company, Research Triangle Park 27560, North Carolina, United States
| | - Alex Diesing
- Integrated
Laboratory Systems, LLC, an Inotiv Company, Research Triangle Park 27560, North Carolina, United States
| | - Stephanie L. Smith-Roe
- Division
of Translational Toxicology, National Institute
of Environmental Health Sciences, Research Triangle Park 27709, North Carolina, United States
| | - Jesse J. Salk
- Department
of Medicine, Division of Hematology and Oncology, University of Washington School of Medicine, Seattle 98195, Washington, United
States
| | - Francesco Marchetti
- Environmental
Health Science and Research Bureau, Health
Canada, Ottawa K1A 0K9, Canada
- Department
of Biology, Carleton University, Ottawa K1N6N5, Canada
| | - Carole L. Yauk
- Department
of Biology, University of Ottawa, Ottawa K1N 6N5, Canada
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90
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Yi Z, Feng K, Lv D, Guan Y, Shao Y, Ma F, Xu B. Genomic landscape of circulating tumor DNA in HER2-low metastatic breast cancer. Signal Transduct Target Ther 2024; 9:345. [PMID: 39648226 PMCID: PMC11625825 DOI: 10.1038/s41392-024-02047-0] [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: 02/26/2024] [Revised: 10/30/2024] [Accepted: 11/04/2024] [Indexed: 12/10/2024] Open
Abstract
The large population of HER2-low breast cancer patients necessitates further research to provide enhanced clinical guidance. In this study, we retrospectively analyzed 1071 metastatic breast cancer (MBC) patients and the circulating tumor DNA (ctDNA) to investigate clinicopathological and genetic alterations of HER2-low MBC patients. The effect of HER2-low status on different treatment modalities was explored in two prospective clinical trials (NCT03412383, NCT01917279) and a retrospective study. Our findings suggest TP53, PIK3CA, and ESR1 are frequently mutated genes in HER2-low MBC. Compared to the HER2-0 group, mutations observed in the HER2-low group are more closely associated with metabolic pathway alterations. Additionally, among patients with ERBB2 mutations and treated with pyrotinib, the HER2-low group may experience superior prognosis when compared to the HER2-0 group. Notably, we did not find any statistically significant disparity in the response to chemotherapy, endocrine therapy, or CDK4/6 inhibitor therapy between HER2-0 and HER2-low breast cancer patients. Interestingly, within the subgroup of individuals with metabolic pathway-related gene mutations, we found that HER2-low group exhibited a more favorable response to these treatments compared to HER2-0 group. Additionally, dynamic analysis showed the HER2-low MBC patients whose molecular tumor burden index decreased or achieved early clearance of ctDNA after the initial two treatment cycles, exhibited prolonged survival. Moreover, we classified HER2-low MBC into three clusters, providing a reference for subsequent treatment with enhanced precision. Our study offers valuable insights into the biology of HER2-low MBC and may provide reference for personalized treatment strategies.
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Affiliation(s)
- Zongbi Yi
- Department of Radiation and Medical Oncology, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaixiang Feng
- Department of Radiation and Medical Oncology, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Breast and Thyroid Surgery, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dan Lv
- Department of Medical Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, China
| | | | - Youcheng Shao
- Department of Pathology and Pathophysiology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Binghe Xu
- Department of Radiation and Medical Oncology, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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91
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Seed G, Beije N, Yuan W, Bertan C, Goodall J, Lundberg A, Tyler M, Figueiredo I, Pereira R, Baker C, Bogdan D, Gallagher L, Cieslik JP, Greening S, Lambros M, Neves R, Magraner-Pardo L, Fowler G, Ebbs B, Miranda S, Flohr P, Bianchini D, Rescigno P, Porta N, Hall E, Gurel B, Tunariu N, Sharp A, Pettit S, Stoecklein NH, Sandhu S, Quigley D, Lord CJ, Mateo J, Carreira S, de Bono J. Elucidating acquired PARP inhibitor resistance in advanced prostate cancer. Cancer Cell 2024; 42:2113-2123.e4. [PMID: 39577422 DOI: 10.1016/j.ccell.2024.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/16/2024] [Accepted: 10/28/2024] [Indexed: 11/24/2024]
Abstract
PARP inhibition (PARPi) has anti-tumor activity against castration-resistant prostate cancer (CRPC) with homologous recombination repair (HRR) defects. However, mechanisms underlying PARPi resistance are not fully understood. While acquired mutations restoring BRCA genes are well documented, their clinical relevance, frequency, and mechanism of generation remain unclear. Moreover, how resistance emerges in BRCA2 homozygously deleted (HomDel) CRPC is unknown. Evaluating samples from patients with metastatic CRPC treated in the TOPARP-B trial, we identify reversion mutations in most BRCA2/PALB2-mutated tumors (79%) by end of treatment. Among reversions mediated by frameshift deletions, 60% are flanked by DNA microhomologies, implicating POLQ-mediated repair. The number of reversions and time of their detection associate with radiological progression-free survival and overall survival (p < 0.01). For BRCA2 HomDels, selection for rare subclones without BRCA2-HomDel is observed following PARPi, confirmed by single circulating-tumor-cell genomics, biopsy fluorescence in situ hybridization (FISH), and RNAish. These data support the need for restored HRR function in PARPi resistance.
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Affiliation(s)
- George Seed
- The Institute of Cancer Research, London, UK
| | - Nick Beije
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - Wei Yuan
- The Institute of Cancer Research, London, UK
| | | | | | | | | | | | | | - Chloe Baker
- The Institute of Cancer Research, London, UK
| | | | | | | | | | | | - Rui Neves
- Heinrich Heine University, Düsseldorf, Germany
| | | | | | - Berni Ebbs
- The Institute of Cancer Research, London, UK
| | | | - Penny Flohr
- The Institute of Cancer Research, London, UK
| | | | | | - Nuria Porta
- The Institute of Cancer Research, London, UK
| | - Emma Hall
- The Institute of Cancer Research, London, UK
| | - Bora Gurel
- The Institute of Cancer Research, London, UK
| | - Nina Tunariu
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Adam Sharp
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | | | | | | | | | | | - Joaquin Mateo
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Johann de Bono
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK.
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92
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Tandukar B, Deivendran D, Chen L, Cruz-Pacheco N, Sharma H, Xu A, Bandari AK, Chen DB, George C, Marty A, Cho RJ, Cheng J, Saylor D, Gerami P, Arron ST, Bastian BC, Shain AH. Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604673. [PMID: 39091884 PMCID: PMC11291049 DOI: 10.1101/2024.07.23.604673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic keratoses, and squamous cell carcinomas to understand the molecular transitions during skin carcinogenesis. Single-cell mutational analyses of normal skin cells showed that most keratinocytes have remarkably low mutation burdens, despite decades of sun exposure, however keratinocytes with TP53 or NOTCH1 mutations had substantially higher mutation burdens. These observations suggest that wild-type keratinocytes (i.e. without pathogenic mutations) are able to withstand high dosages of cumulative UV radiation, but certain pathogenic mutations break these adaptive mechanisms, priming keratinocytes for transformation by increasing their mutation rate. Mutational profiling of squamous cell carcinomas adjacent to actinic keratoses revealed TERT promoter and CDKN2A mutations emerging in actinic keratoses, whereas additional mutations inactivating ARID2 and activating the MAPK-pathway delineated the transition to squamous cell carcinomas. Surprisingly, actinic keratoses were often not related to their neighboring squamous cell carcinoma, indicating that collisions of unrelated neoplasms are common in the skin. Spatial variation in gene expression patterns was common in both tumor and immune cells, with high expression of checkpoint molecules at the invasive front of tumors. In conclusion, this study catalogues the key events during the evolution of cutaneous squamous cell carcinoma.
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Affiliation(s)
- Bishal Tandukar
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Human Tumor Atlas Network (HTAN), National Cancer Institute, Bethesda, MD, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Human Tumor Atlas Network (HTAN), National Cancer Institute, Bethesda, MD, USA
| | - Limin Chen
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Human Tumor Atlas Network (HTAN), National Cancer Institute, Bethesda, MD, USA
| | - Harsh Sharma
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Human Tumor Atlas Network (HTAN), National Cancer Institute, Bethesda, MD, USA
| | - Albert Xu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Aravind K. Bandari
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Daniel B. Chen
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Christopher George
- Department of Dermatology, Erasmus MC, Rotterdam, Netherlands
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Dermatology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Annika Marty
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Raymond J. Cho
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey Cheng
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Drew Saylor
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Boris C. Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Human Tumor Atlas Network (HTAN), National Cancer Institute, Bethesda, MD, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - A. Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Human Tumor Atlas Network (HTAN), National Cancer Institute, Bethesda, MD, USA
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93
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Srivatsa A, Schwartz R. Optimizing design of genomics studies for clonal evolution analysis. BIOINFORMATICS ADVANCES 2024; 4:vbae193. [PMID: 39678206 PMCID: PMC11645549 DOI: 10.1093/bioadv/vbae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 11/06/2024] [Accepted: 11/29/2024] [Indexed: 12/17/2024]
Abstract
Motivation Genomic biotechnology has rapidly advanced, allowing for the inference and modification of genetic and epigenetic information at the single-cell level. While these tools hold enormous potential for basic and clinical research, they also raise difficult issues of how to design studies to deploy them most effectively. In designing a genomic study, a modern researcher might combine many sequencing modalities and sampling protocols, each with different utility, costs, and other tradeoffs. This is especially relevant for studies of somatic variation, which may involve highly heterogeneous cell populations whose differences can be probed via an extensive set of biotechnological tools. Efficiently deploying genomic technologies in this space will require principled ways to create study designs that recover desired genomic information while minimizing various measures of cost. Results The central problem this paper attempts to address is how one might create an optimal study design for a genomic analysis, with particular focus on studies involving somatic variation that occur most often with application to cancer genomics. We pose the study design problem as a stochastic constrained nonlinear optimization problem. We introduce a Bayesian optimization framework that iteratively optimizes for an objective function using surrogate modeling combined with pattern and gradient search. We demonstrate our procedure on several test cases to derive resource and study design allocations optimized for various goals and criteria, demonstrating its ability to optimize study designs efficiently across diverse scenarios. Availability and implementation https://github.com/CMUSchwartzLab/StudyDesignOptimization.
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Affiliation(s)
- Arjun Srivatsa
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Russell Schwartz
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, United States
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94
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Kwon SG, Bae GH, Hong JH, Choi JW, Choi JH, Lim NS, Jeon C, Mali NM, Jun MS, Shin J, Kim J, Cho ES, Han MH, Oh JW. Comprehensive analysis of somatic mutations and structural variations in domestic pig. Mamm Genome 2024; 35:645-656. [PMID: 39177814 DOI: 10.1007/s00335-024-10058-z] [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: 06/14/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024]
Abstract
Understanding somatic mutations and structural variations in domestic pigs (Sus scrofa domestica) is critical due to their increasing importance as model organisms in biomedical research. In this study, we conducted a comprehensive analysis through whole-genome sequencing of skin, organs, and blood samples. By examining two pig pedigrees, we investigated the inheritance and sharedness of structural variants among fathers, mothers, and offsprings. Utilizing single-cell clonal expansion techniques, we observed significant variations in the number of somatic mutations across different tissues. An in-house developed pipeline enabled precise filtering and analysis of these mutations, resulting in the construction of individual phylogenetic trees for two pigs. These trees explored the developmental relationships between different tissues, revealing insights into clonal expansions from various anatomical locations. This study enhances the understanding of pig genomes, affirming their increasing value in clinical and genomic research, and provides a foundation for future studies in other animals, paralleling previous studies in mice and humans. This approach not only deepens our understanding of mammalian genomic variations but also strengthens the role of pigs as a crucial model in human health and disease research.
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Affiliation(s)
- Seong Gyu Kwon
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Geon Hue Bae
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Joo Hee Hong
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jeong-Woo Choi
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - June Hyug Choi
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Nam Seop Lim
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - CheolMin Jeon
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Nanda Maya Mali
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Mee Sook Jun
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - JaeEun Shin
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - JinSoo Kim
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Eun-Seok Cho
- Department of Livestock Resource Development, National Institute of Animal Science, Jeonbuk, Republic of Korea
| | - Man-Hoon Han
- Department of Pathology, Kyungpook National University Hospital, Daegu, Republic of Korea.
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
| | - Ji Won Oh
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Absolute DNA, Inc., Daegu, Republic of Korea.
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95
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Bedeir A, Ghani H, Oster C, Crymes A, Ibe I, Yamamoto M, Elliott A, Bryant DA, Oberley MJ, Evans MG. Detection of human papillomavirus (HPV) in malignant melanoma. Ann Diagn Pathol 2024; 73:152361. [PMID: 39032381 DOI: 10.1016/j.anndiagpath.2024.152361] [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: 06/11/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
The most common type of melanoma is cutaneous melanoma (CM). The predominant mutational signature is that of ultraviolet radiation (UVR) exposure. The Cancer Genome Atlas (TCGA) molecular classification includes four major subtypes of CM based on common genetic alterations involving the following genes: BRAF, NRAS, and NF1, with a small fraction being "triple" wild-type. The two main signaling pathway abnormalities in CM are the mitogen-activated protein kinase (MAPK) pathway and the phosphoinositol-3-kinase (PI3K) pathway. Other less common types include mucosal melanomas (MM) and uveal melanoma (UM), which have a significantly different genomic landscape. Although few studies reported rare cases with HPV-positive (HPV+) melanoma, the clinicopathological and molecular characteristic of this entity has not been well-described. Among the 2084 melanoma cases queried at our institution, we identified seven patients diagnosed with HPV+ melanoma (prevalence 0.03 %), including five instances of CM and two of MM. The majority of cases were positive for HPV16 (n = 6). Most of the patients were elderly and with advanced disease (n = 6), although this finding may be attributed to the relative frequency of our institution testing advanced-stage tumors. Histologically, most cases showed high degree of pleomorphism and high mitotic count (5 or more mitoses/mm2) (n = 6). UVR signature was present in the CM, but not in the MM cases. Alterations in either MAPK and/or PI3K pathways were detected in the majority of cases (n = 6). The most common genetic abnormalities detected in this study occurred in the TERT promoter (TERTp) (n = 5), a finding that has been reported to be associated with aggressive disease. Our data shows that while HPV+ melanoma is rare, identifying this disease entity could help guide therapy given the demonstrated genomic alterations.
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Affiliation(s)
- Adam Bedeir
- Basis Phoenix High School, Phoenix, AZ, United States of America
| | - Hassan Ghani
- Caris Life Sciences, Phoenix, AZ, United States of America
| | - Cyrus Oster
- Caris Life Sciences, Phoenix, AZ, United States of America
| | - Anthony Crymes
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Ifegwu Ibe
- University of California Irvine School of Medicine, Irvine, CA, United States of America
| | - Maki Yamamoto
- University of California Irvine School of Medicine, Irvine, CA, United States of America
| | - Andrew Elliott
- Caris Life Sciences, Phoenix, AZ, United States of America
| | - David A Bryant
- Caris Life Sciences, Phoenix, AZ, United States of America
| | | | - Mark G Evans
- Caris Life Sciences, Phoenix, AZ, United States of America.
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96
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van der Werf't Lam AS, Helderman NC, Boot A, Terlouw D, Morreau H, Mei H, Esveldt-van Lange REE, Lakeman IMM, van Asperen CJ, Aten E, Hofland N, de Koning Gans PAM, Rayner E, Tops C, de Wind N, van Wezel T, Nielsen M. Assessing pathogenicity of mismatch repair variants of uncertain significance by molecular tumor analysis. Exp Mol Pathol 2024; 140:104940. [PMID: 39437510 DOI: 10.1016/j.yexmp.2024.104940] [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] [Revised: 09/27/2024] [Accepted: 10/16/2024] [Indexed: 10/25/2024]
Abstract
Functional analyses are the main method to classify mismatch repair (MMR) gene variants of uncertain significance (VUSs). However, the pathogenicity remains unclear for many variants because of conflicting results between clinical, molecular, and functional data. In this study, we evaluated whether whole exome sequencing (WES) could add another layer of evidence to elucidate the pathogenicity of MMR variants with conflicting interpretations. WES was performed on formalin-fixed paraffin-embedded tumor tissue of eight patients with a constitutional MMR VUS (seven families), including eight colorectal and two endometrial carcinomas and one ovarian carcinoma. Cell-free CIMRA assays were performed to assign Odds of Pathogenicity to these VUSs. In four families, seven tumors showed MMR deficiency-associated mutational signatures, supporting the pathogenicity of the VUS. Moreover, somatic (second) MMR hits identified in the WES data were found to explain MMR staining patterns when the MMR staining was discordant with the reported germline MMR gene variant. In conclusion, WES did not significantly reclassify VUS in these cases but clarified some phenotypic aspects such as age of onset and explanations in case of discordant MMR stainings.
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Affiliation(s)
| | - Noah C Helderman
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Diantha Terlouw
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailian Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Inge M M Lakeman
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nandy Hofland
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Pia A M de Koning Gans
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Emily Rayner
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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97
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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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98
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Lukose G, Al Assaad M, Driskill JH, Levine MF, Gundem G, Semaan A, Wilkes DC, Spigland NA, Medina-Martínez JS, Sboner A, Elemento O, Jessurun J, Mosquera JM. Whole genome profiling of rare pediatric thoracic tumors elucidates a YAP1::LEUTX fusion in an unclassified biphasic embryonal neoplasm. Pathol Res Pract 2024; 264:155726. [PMID: 39566337 DOI: 10.1016/j.prp.2024.155726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Accepted: 11/13/2024] [Indexed: 11/22/2024]
Abstract
Malignant biphasic tumors of the lungs are rare, more so in the pediatric population. Here, we present the whole-genome characterization of a pleuropulmonary blastoma Type III and an unclassified biphasic thoracic embryonal neoplasm. The pleuropulmonary blastoma harbored pathogenic DICER1 germline and somatic mutations, and additional somatic variants in TP53 and BCOR. The other malignant tumor demonstrated a t(11;19) balanced translocation with a YAP1::LEUTX fusion that was confirmed by fluorescence in situ hybridization. No DICER1 germline or somatic mutation was present. YAP1 and LEUTX have been implicated in tumorigenesis of various neoplasms, and YAP1 fusion genes are an emerging oncogenic entity in a variety of malignancies. In this study we highlight the importance of whole-genome characterization of rare and unclassified tumors to identify biologic mechanisms and potential therapeutic targets.
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Affiliation(s)
- Georgi Lukose
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Majd Al Assaad
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jordan H Driskill
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Alissa Semaan
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - David C Wilkes
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nitsana A Spigland
- Department of Surgery, Division of Pediatric Surgery, Weill Cornell Medicine / NewYork-Presbyterian Hospital, New York, NY, USA
| | | | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - José Jessurun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
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99
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Deng X, Xiang K, He X, Chen S, Guo Q, Wu H, Liu X, Wen Q, Yang H. Good response of stage IV melanoma to high‑dose radiation therapy combined with immunotherapy: A case report. Oncol Lett 2024; 28:598. [PMID: 39493434 PMCID: PMC11529377 DOI: 10.3892/ol.2024.14731] [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: 01/15/2024] [Accepted: 08/22/2024] [Indexed: 11/05/2024] Open
Abstract
Patients with advanced malignant melanoma (MM) often do not receive satisfactory treatment. The present study reports the case of a 51-year-old female patient with stage IV MM of unknown primary. After undergoing immune checkpoint inhibitor therapy, the patient received multiple doses of hypofractionated radiotherapy (HFRT) for the left inguinal lymph node and single-fraction high-dose-rate brachytherapy for the left and right lung metastases. After combination treatment, the patient experienced almost complete remission of the inguinal target area, significant relief of pain and discomfort and an improved quality of life. The time of lung radiotherapy lesion control was 8 months. Meanwhile, the observed lesions (observation lesions 1, 2, 3 and 5) adjacent to the target lesion received lower doses of scattering (0.9-1.8 Gy) and the time of control for these lung observation lesions was 9 months. In addition, restarting targeted therapy after cessation of other treatments due to myelosuppression resulted in a progression-free survival time of 6 months. Nevertheless, the patient developed new metastases in the brain and abdomen. The present case report demonstrates that high-dose radiotherapy combined with immunotherapy may be effective for local lesions and that multiple doses of HFRT may be superior to single-fraction high-dose-rate brachytherapy for certain patients. Low-dose scattering also shows improvement for local lesions. Furthermore, restarting targeted therapy may be effective in the presence of target sites. Thus, the present case report provides a possible therapeutic option for the treatment of advanced melanoma.
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Affiliation(s)
- Xuemei Deng
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Kewei Xiang
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xingting He
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Shuang Chen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Qingxi Guo
- Department Pathology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Hong Wu
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xiaolong Liu
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Qinglian Wen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Hongru Yang
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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100
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Pfeifer GP, Jin SG. Methods and applications of genome-wide profiling of DNA damage and rare mutations. Nat Rev Genet 2024; 25:846-863. [PMID: 38918545 PMCID: PMC11563917 DOI: 10.1038/s41576-024-00748-4] [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] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
DNA damage is a threat to genome integrity and can be a cause of many human diseases, owing to either changes in the chemical structure of DNA or conversion of the damage into a mutation, that is, a permanent change in DNA sequence. Determining the exact positions of DNA damage and ensuing mutations in the genome are important for identifying mechanisms of disease aetiology when characteristic mutations are prevalent and probably causative in a particular disease. However, this approach is challenging particularly when levels of DNA damage are low, for example, as a result of chronic exposure to environmental agents or certain endogenous processes, such as the generation of reactive oxygen species. Over the past few years, a comprehensive toolbox of genome-wide methods has been developed for the detection of DNA damage and rare mutations at single-nucleotide resolution in mammalian cells. Here, we review and compare these methods, describe their current applications and discuss future research questions that can now be addressed.
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Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
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