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Jacobson DH, Pan S, Fisher J, Secrier M. Multi-scale characterisation of homologous recombination deficiency in breast cancer. Genome Med 2023; 15:90. [PMID: 37919776 PMCID: PMC10621207 DOI: 10.1186/s13073-023-01239-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Homologous recombination is a robust, broadly error-free mechanism of double-strand break repair, and deficiencies lead to PARP inhibitor sensitivity. Patients displaying homologous recombination deficiency can be identified using 'mutational signatures'. However, these patterns are difficult to reliably infer from exome sequencing. Additionally, as mutational signatures are a historical record of mutagenic processes, this limits their utility in describing the current status of a tumour. METHODS We apply two methods for characterising homologous recombination deficiency in breast cancer to explore the features and heterogeneity associated with this phenotype. We develop a likelihood-based method which leverages small insertions and deletions for high-confidence classification of homologous recombination deficiency for exome-sequenced breast cancers. We then use multinomial elastic net regression modelling to develop a transcriptional signature of heterogeneous homologous recombination deficiency. This signature is then applied to single-cell RNA-sequenced breast cancer cohorts enabling analysis of homologous recombination deficiency heterogeneity and differential patterns of tumour microenvironment interactivity. RESULTS We demonstrate that the inclusion of indel events, even at low levels, improves homologous recombination deficiency classification. Whilst BRCA-positive homologous recombination deficient samples display strong similarities to those harbouring BRCA1/2 defects, they appear to deviate in microenvironmental features such as hypoxic signalling. We then present a 228-gene transcriptional signature which simultaneously characterises homologous recombination deficiency and BRCA1/2-defect status, and is associated with PARP inhibitor response. Finally, we show that this signature is applicable to single-cell transcriptomics data and predict that these cells present a distinct milieu of interactions with their microenvironment compared to their homologous recombination proficient counterparts, typified by a decreased cancer cell response to TNFα signalling. CONCLUSIONS We apply multi-scale approaches to characterise homologous recombination deficiency in breast cancer through the development of mutational and transcriptional signatures. We demonstrate how indels can improve homologous recombination deficiency classification in exome-sequenced breast cancers. Additionally, we demonstrate the heterogeneity of homologous recombination deficiency, especially in relation to BRCA1/2-defect status, and show that indications of this feature can be captured at a single-cell level, enabling further investigations into interactions between DNA repair deficient cells and their tumour microenvironment.
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Affiliation(s)
- Daniel H Jacobson
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Shi Pan
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jasmin Fisher
- UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
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102
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Derks LLM, van Boxtel R. Stem cell mutations, associated cancer risk, and consequences for regenerative medicine. Cell Stem Cell 2023; 30:1421-1433. [PMID: 37832550 PMCID: PMC10624213 DOI: 10.1016/j.stem.2023.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Mutation accumulation in stem cells has been associated with cancer risk. However, the presence of numerous mutant clones in healthy tissues has raised the question of what limits cancer initiation. Here, we review recent developments in characterizing mutation accumulation in healthy tissues and compare mutation rates in stem cells during development and adult life with corresponding cancer risk. A certain level of mutagenesis within the stem cell pool might be beneficial to limit the size of malignant clones through competition. This knowledge impacts our understanding of carcinogenesis with potential consequences for the use of stem cells in regenerative medicine.
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Affiliation(s)
- Lucca L M Derks
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands.
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103
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Hart SFM, Yonemitsu MA, Giersch RM, Garrett FES, Beal BF, Arriagada G, Davis BW, Ostrander EA, Goff SP, Metzger MJ. Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia. NATURE CANCER 2023; 4:1561-1574. [PMID: 37783804 PMCID: PMC10663159 DOI: 10.1038/s43018-023-00643-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 08/29/2023] [Indexed: 10/04/2023]
Abstract
Transmissible cancers are infectious parasitic clones that metastasize to new hosts, living past the death of the founder animal in which the cancer initiated. We investigated the evolutionary history of a cancer lineage that has spread though the soft-shell clam (Mya arenaria) population by assembling a chromosome-scale soft-shell clam reference genome and characterizing somatic mutations in transmissible cancer. We observe high mutation density, widespread copy-number gain, structural rearrangement, loss of heterozygosity, variable telomere lengths, mitochondrial genome expansion and transposable element activity, all indicative of an unstable cancer genome. We also discover a previously unreported mutational signature associated with overexpression of an error-prone polymerase and use this to estimate the lineage to be >200 years old. Our study reveals the ability for an invertebrate cancer lineage to survive for centuries while its genome continues to structurally mutate, likely contributing to the evolution of this lineage as a parasitic cancer.
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Affiliation(s)
- Samuel F M Hart
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marisa A Yonemitsu
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | | | | | - Brian F Beal
- Division of Environmental and Biological Sciences, University of Maine at Machias, Machias, ME, USA
- Downeast Institute, Beals, ME, USA
| | - Gloria Arriagada
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine, College Station, TX, USA
- Department of Small Animal Clinical Sciences, Texas A&M University School of Veterinary Medicine, College Station, TX, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Michael J Metzger
- Pacific Northwest Research Institute, Seattle, WA, USA.
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
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104
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Bruzos AL, Santamarina M, García-Souto D, Díaz S, Rocha S, Zamora J, Lee Y, Viña-Feás A, Quail MA, Otero I, Pequeño-Valtierra A, Temes J, Rodriguez-Castro J, Aramburu L, Vidal-Capón A, Villanueva A, Costas D, Rodríguez R, Prieto T, Tomás L, Alvariño P, Alonso J, Cao A, Iglesias D, Carballal MJ, Amaral AM, Balseiro P, Calado R, El Khalfi B, Izagirre U, de Montaudouin X, Pade NG, Probert I, Ricardo F, Ruiz P, Skazina M, Smolarz K, Pasantes JJ, Villalba A, Ning Z, Ju YS, Posada D, Demeulemeester J, Baez-Ortega A, Tubio JMC. Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule. NATURE CANCER 2023; 4:1575-1591. [PMID: 37783803 DOI: 10.1038/s43018-023-00641-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/23/2023] [Indexed: 10/04/2023]
Abstract
Transmissible cancers are malignant cell lineages that spread clonally between individuals. Several such cancers, termed bivalve transmissible neoplasia (BTN), induce leukemia-like disease in marine bivalves. This is the case of BTN lineages affecting the common cockle, Cerastoderma edule, which inhabits the Atlantic coasts of Europe and northwest Africa. To investigate the evolution of cockle BTN, we collected 6,854 cockles, diagnosed 390 BTN tumors, generated a reference genome and assessed genomic variation across 61 tumors. Our analyses confirmed the existence of two BTN lineages with hemocytic origins. Mitochondrial variation revealed mitochondrial capture and host co-infection events. Mutational analyses identified lineage-specific signatures, one of which likely reflects DNA alkylation. Cytogenetic and copy number analyses uncovered pervasive genomic instability, with whole-genome duplication, oncogene amplification and alkylation-repair suppression as likely drivers. Satellite DNA distributions suggested ancient clonal origins. Our study illuminates long-term cancer evolution under the sea and reveals tolerance of extreme instability in neoplastic genomes.
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Affiliation(s)
- Alicia L Bruzos
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Martín Santamarina
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Daniel García-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Wellcome Sanger Institute, Hinxton, UK
| | - Seila Díaz
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Sara Rocha
- CINBIO, Universidade de Vigo, Vigo, Spain
| | - Jorge Zamora
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Yunah Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Alejandro Viña-Feás
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | | | - Iago Otero
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Ana Pequeño-Valtierra
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Javier Temes
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Jorge Rodriguez-Castro
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Leyre Aramburu
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - André Vidal-Capón
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
| | - Antonio Villanueva
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Damián Costas
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Rosana Rodríguez
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Tamara Prieto
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- New York Genome Center, New York, NY, USA
| | - Laura Tomás
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Pilar Alvariño
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Juana Alonso
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - David Iglesias
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - María J Carballal
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - Ana M Amaral
- Centro de Ciencias do Mar do Algarve (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Pablo Balseiro
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- NORCE AS, Bergen, Norway
| | - Ricardo Calado
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Bouchra El Khalfi
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Health and Biotechnology Research Centre, Hassan II University of Casablanca, Casablanca, Morocco
| | - Urtzi Izagirre
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Cell Biology in Environmental Toxicology Research Group, University of the Basque Country (UPV/EHU), Leioa-Bizkaia, Spain
| | | | - Nicolas G Pade
- European Marine Biology Resources Centre (EMBRC-ERIC), Paris, France
| | - Ian Probert
- FR2424 Station Biologique de Roscoff, Sorbonne University/CNRS, Roscoff, France
| | - Fernando Ricardo
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Pamela Ruiz
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Cell Biology in Environmental Toxicology Research Group, University of the Basque Country (UPV/EHU), Leioa-Bizkaia, Spain
| | - Maria Skazina
- Department of Applied Ecology, St Petersburg State University, St Petersburg, Russia
| | - Katarzyna Smolarz
- Department of Marine Ecosystem Functioning, University of Gdańsk, Gdynia, Poland
| | - Juan J Pasantes
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Department of Life Sciences, Universidad de Alcalá, Alcalá de Henares, Spain
| | | | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - David Posada
- CINBIO, Universidade de Vigo, Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jonas Demeulemeester
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- The Francis Crick Institute, London, UK
| | - Adrian Baez-Ortega
- Wellcome Sanger Institute, Hinxton, UK.
- Magdalene College, University of Cambridge, Cambridge, UK.
| | - Jose M C Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
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105
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Olafsson S, Rodriguez E, Lawson ARJ, Abascal F, Huber AR, Suembuel M, Jones PH, Gerdes S, Martincorena I, Weidinger S, Campbell PJ, Anderson CA. Effects of psoriasis and psoralen exposure on the somatic mutation landscape of the skin. Nat Genet 2023; 55:1892-1900. [PMID: 37884686 PMCID: PMC10632143 DOI: 10.1038/s41588-023-01545-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Somatic mutations are hypothesized to play a role in many non-neoplastic diseases. We performed whole-exome sequencing of 1,182 microbiopsies dissected from lesional and nonlesional epidermis from 111 patients with psoriasis to search for evidence that somatic mutations in keratinocytes may influence the disease process. Lesional skin remained highly polyclonal, showing no evidence of large-scale spread of clones carrying potentially pathogenic mutations. The mutation rate of keratinocytes was similarly only modestly affected by the disease. We found evidence of positive selection in previously reported driver genes NOTCH1, NOTCH2, TP53, FAT1 and PPM1D and also identified mutations in four genes (GXYLT1, CHEK2, ZFP36L2 and EEF1A1) that we hypothesize are selected for in squamous epithelium irrespective of disease status. Finally, we describe a mutational signature of psoralens-a class of chemicals previously found in some sunscreens and which are used as part of PUVA (psoralens and ultraviolet-A) photochemotherapy treatment for psoriasis.
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Affiliation(s)
| | - Elke Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Melike Suembuel
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Sascha Gerdes
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Stephan Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
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106
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Chen S, Zhou Z, Li Y, Du Y, Chen G. Application of single-cell sequencing to the research of tumor microenvironment. Front Immunol 2023; 14:1285540. [PMID: 37965341 PMCID: PMC10641410 DOI: 10.3389/fimmu.2023.1285540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Single-cell sequencing is a technique for detecting and analyzing genomes, transcriptomes, and epigenomes at the single-cell level, which can detect cellular heterogeneity lost in conventional sequencing hybrid samples, and it has revolutionized our understanding of the genetic heterogeneity and complexity of tumor progression. Moreover, the tumor microenvironment (TME) plays a crucial role in the formation, development and response to treatment of tumors. The application of single-cell sequencing has ushered in a new age for the TME analysis, revealing not only the blueprint of the pan-cancer immune microenvironment, but also the heterogeneity and differentiation routes of immune cells, as well as predicting tumor prognosis. Thus, the combination of single-cell sequencing and the TME analysis provides a unique opportunity to unravel the molecular mechanisms underlying tumor development and progression. In this review, we summarize the recent advances in single-cell sequencing and the TME analysis, highlighting their potential applications in cancer research and clinical translation.
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Affiliation(s)
| | | | | | | | - Guoan Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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107
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Chen H, Shu J, Maley CC, Liu L. A Mouse-Specific Model to Detect Genes under Selection in Tumors. Cancers (Basel) 2023; 15:5156. [PMID: 37958330 PMCID: PMC10647215 DOI: 10.3390/cancers15215156] [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: 09/14/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
The mouse is a widely used model organism in cancer research. However, no computational methods exist to identify cancer driver genes in mice due to a lack of labeled training data. To address this knowledge gap, we adapted the GUST (Genes Under Selection in Tumors) model, originally trained on human exomes, to mouse exomes via transfer learning. The resulting tool, called GUST-mouse, can estimate long-term and short-term evolutionary selection in mouse tumors, and distinguish between oncogenes, tumor suppressor genes, and passenger genes using high-throughput sequencing data. We applied GUST-mouse to analyze 65 exomes of mouse primary breast cancer models and 17 exomes of mouse leukemia models. Comparing the predictions between cancer types and between human and mouse tumors revealed common and unique driver genes. The GUST-mouse method is available as an open-source R package on github.
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Affiliation(s)
- Hai Chen
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (H.C.); (J.S.)
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;
| | - Jingmin Shu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (H.C.); (J.S.)
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;
| | - Carlo C. Maley
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85281, USA
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (H.C.); (J.S.)
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85281, USA
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108
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Brown M, Leon A, Kedzierska K, Moore C, Belnoue‐Davis HL, Flach S, Lydon JP, DeMayo FJ, Lewis A, Bosse T, Tomlinson I, Church DN. Functional analysis reveals driver cooperativity and novel mechanisms in endometrial carcinogenesis. EMBO Mol Med 2023; 15:e17094. [PMID: 37589076 PMCID: PMC10565641 DOI: 10.15252/emmm.202217094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023] Open
Abstract
High-risk endometrial cancer has poor prognosis and is increasing in incidence. However, understanding of the molecular mechanisms which drive this disease is limited. We used genetically engineered mouse models (GEMM) to determine the functional consequences of missense and loss of function mutations in Fbxw7, Pten and Tp53, which collectively occur in nearly 90% of high-risk endometrial cancers. We show that Trp53 deletion and missense mutation cause different phenotypes, with the latter a substantially stronger driver of endometrial carcinogenesis. We also show that Fbxw7 missense mutation does not cause endometrial neoplasia on its own, but potently accelerates carcinogenesis caused by Pten loss or Trp53 missense mutation. By transcriptomic analysis, we identify LEF1 signalling as upregulated in Fbxw7/FBXW7-mutant mouse and human endometrial cancers, and in human isogenic cell lines carrying FBXW7 mutation, and validate LEF1 and the additional Wnt pathway effector TCF7L2 as novel FBXW7 substrates. Our study provides new insights into the biology of high-risk endometrial cancer and suggests that targeting LEF1 may be worthy of investigation in this treatment-resistant cancer subgroup.
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Affiliation(s)
- Matthew Brown
- Cancer Genomics and Immunology Group, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation TrustOxfordUK
| | - Alicia Leon
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | - Katarzyna Kedzierska
- Cancer Genomics and Immunology Group, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Charlotte Moore
- Cancer Genomics and Immunology Group, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Hayley L Belnoue‐Davis
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Susanne Flach
- Department of Otorhinolaryngology, Head and Neck SurgeryLMU KlinikumMunichGermany
- German Cancer Consortium (DKTK), Partner SiteMunichGermany
| | - John P Lydon
- Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTXUSA
| | - Francesco J DeMayo
- Reproductive and Developmental Biology LaboratoryNational Institute of Environmental Health SciencesResearch Triangle ParkNCUSA
| | - Annabelle Lewis
- Department of Life Sciences, College of Health, Medicine and Life SciencesBrunel University LondonUxbridgeUK
| | - Tjalling Bosse
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | - Ian Tomlinson
- Institute of Genetics and CancerThe University of EdinburghEdinburghUK
| | - David N Church
- Cancer Genomics and Immunology Group, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation TrustOxfordUK
- Oxford Cancer Centre, Churchill HospitalOxford University Hospitals Foundation NHS TrustOxfordUK
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109
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Aldea M, Friboulet L, Apcher S, Jaulin F, Mosele F, Sourisseau T, Soria JC, Nikolaev S, André F. Precision medicine in the era of multi-omics: can the data tsunami guide rational treatment decision? ESMO Open 2023; 8:101642. [PMID: 37769400 PMCID: PMC10539962 DOI: 10.1016/j.esmoop.2023.101642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/30/2023] Open
Abstract
Precision medicine for cancer is rapidly moving to an approach that integrates multiple dimensions of the biology in order to model mechanisms of cancer progression in each patient. The discovery of multiple drivers per tumor challenges medical decision that faces several treatment options. Drug sensitivity depends on the actionability of the target, its clonal or subclonal origin and coexisting genomic alterations. Sequencing has revealed a large diversity of drivers emerging at treatment failure, which are potential targets for clinical trials or drug repurposing. To effectively prioritize therapies, it is essential to rank genomic alterations based on their proven actionability. Moving beyond primary drivers, the future of precision medicine necessitates acknowledging the intricate spatial and temporal heterogeneity inherent in cancer. The advent of abundant complex biological data will make artificial intelligence algorithms indispensable for thorough analysis. Here, we will discuss the advancements brought by the use of high-throughput genomics, the advantages and limitations of precision medicine studies and future perspectives in this field.
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Affiliation(s)
- M Aldea
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif.
| | | | - S Apcher
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Jaulin
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Mosele
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif
| | | | - J-C Soria
- Paris Saclay University, Orsay; Drug Development Department, Gustave Roussy, Villejuif, France
| | - S Nikolaev
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F André
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif; Paris Saclay University, Orsay
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110
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Li Y, Zhang SW, Xie MY, Zhang T. PhenoDriver: interpretable framework for studying personalized phenotype-associated driver genes in breast cancer. Brief Bioinform 2023; 24:bbad291. [PMID: 37738403 DOI: 10.1093/bib/bbad291] [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: 04/02/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 09/24/2023] Open
Abstract
Identifying personalized cancer driver genes and further revealing their oncogenic mechanisms is critical for understanding the mechanisms of cell transformation and aiding clinical diagnosis. Almost all existing methods primarily focus on identifying driver genes at the cohort or individual level but fail to further uncover their underlying oncogenic mechanisms. To fill this gap, we present an interpretable framework, PhenoDriver, to identify personalized cancer driver genes, elucidate their roles in cancer development and uncover the association between driver genes and clinical phenotypic alterations. By analyzing 988 breast cancer patients, we demonstrate the outstanding performance of PhenoDriver in identifying breast cancer driver genes at the cohort level compared to other state-of-the-art methods. Otherwise, our PhenoDriver can also effectively identify driver genes with both recurrent and rare mutations in individual patients. We further explore and reveal the oncogenic mechanisms of some known and unknown breast cancer driver genes (e.g. TP53, MAP3K1, HTT, etc.) identified by PhenoDriver, and construct their subnetworks for regulating clinical abnormal phenotypes. Notably, most of our findings are consistent with existing biological knowledge. Based on the personalized driver profiles, we discover two existing and one unreported breast cancer subtypes and uncover their molecular mechanisms. These results intensify our understanding for breast cancer mechanisms, guide therapeutic decisions and assist in the development of targeted anticancer therapies.
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Affiliation(s)
- Yan Li
- School of Automation from Northwestern Polytechnical University, China
| | - Shao-Wu Zhang
- School of Automation from Northwestern Polytechnical University, China
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, China
| | - Ming-Yu Xie
- School of Automation from Northwestern Polytechnical University, China
| | - Tong Zhang
- School of Automation from Northwestern Polytechnical University, China
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111
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Liu Z, Liu M, Liu Y, Zhou R, Abliz A, Yuan W, Guo C, Zhang L, He W, Zheng H, Huang Y, Pan Y, Liu F, Hu Z, Chen H, Cai H, He Z, Ke Y. Absence of Lugol staining indicates initiation of esophageal squamous cell carcinoma: A combined genomic and epidemiologic study. Cell Rep Med 2023; 4:101168. [PMID: 37625408 PMCID: PMC10518598 DOI: 10.1016/j.xcrm.2023.101168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023]
Abstract
The genomic characteristics during the carcinogenic process of esophageal squamous cell carcinoma (ESCC) remain largely unknown. We report here the genomic characteristics of 106 esophageal tissues of various stages from a population-based screening cohort in China ("Endoscopic Screening for Esophageal Cancer in China" trial) and 57 ESCC tissues from a local hospital. A significant increase in somatic mutation and copy number alterations is observed in the non-dysplastic Lugol unstaining lesions (ND-LULs). Extensive clonal expansion has emerged in the ND-LULs to an extent similar to that in higher-stage lesions. The burden of genomic alterations correlates with the size of LULs in the ND-LULs. 8-year follow-up shows that ND-LULs harbor an increased risk of progression to ESCC (adjusted IRR6-10 mm vs. none = 4.66, adjusted IRR>10 mm vs. none = 40.70), and the risk is correlated with LUL size for both non-dysplastic and dysplastic lesions. Lugol unstaining can be the initial stage in the carcinogenic process of ESCC.
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Affiliation(s)
- Zhen Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Mengfei Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ren Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Amir Abliz
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China; Department of Biochemistry and Molecular Biology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Wenqing Yuan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China; Department of Education, Peking University Third Hospital, Beijing, China
| | - Chuanhai Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lixin Zhang
- Anyang Cancer Hospital, Anyang, Henan, China
| | - Wei He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hongchen Zheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yi Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yaqi Pan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Fangfang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhe Hu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Huanyu Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hong Cai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhonghu He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China.
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China.
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112
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Borgsmüller N, Valecha M, Kuipers J, Beerenwinkel N, Posada D. Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues. CELL GENOMICS 2023; 3:100380. [PMID: 37719146 PMCID: PMC10504633 DOI: 10.1016/j.xgen.2023.100380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 09/19/2023]
Abstract
Cell lineages accumulate somatic mutations during organismal development, potentially leading to pathological states. The rate of somatic evolution within a cell population can vary due to multiple factors, including selection, a change in the mutation rate, or differences in the microenvironment. Here, we developed a statistical test called the Poisson Tree (PT) test to detect varying evolutionary rates among cell lineages, leveraging the phylogenetic signal of single-cell DNA sequencing (scDNA-seq) data. We applied the PT test to 24 healthy and cancer samples, rejecting a constant evolutionary rate in 11 out of 15 cancer and five out of nine healthy scDNA-seq datasets. In six cancer datasets, we identified subclonal mutations in known driver genes that could explain the rate accelerations of particular cancer lineages. Our findings demonstrate the efficacy of scDNA-seq for studying somatic evolution and suggest that cell lineages often evolve at different rates within cancer and healthy tissues.
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Affiliation(s)
- Nico Borgsmüller
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Monica Valecha
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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113
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Deng M, Guo J, Ling Z, Zhang C, He L, Fan Z, Cheng B, Xia J. KRAS mutations upregulate Runx1 to promote occurrence of head and neck squamous cell carcinoma. Mol Carcinog 2023; 62:1284-1294. [PMID: 37222390 DOI: 10.1002/mc.23563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/23/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023]
Abstract
Gene mutations play an important role in head and neck squamous cell carcinoma (HNSCC) by not only promoting the occurrence and progression of HNSCC but also affecting sensitivity to treatment and prognosis. KRAS is one of the most frequently mutated oncogenes, which has been reported to have a mutation rate from 1.7% to 12.7% and may lead to poor prognosis in HNSCC, but its role remains unclear. Here, we found that the KRAS mutation can promote HNSCC generation through synergism with 4-Nitroquinoline-1-Oxide(4NQO). Mechanistically, KRAS mutations can significantly upregulate Runx1 to promote oral epithelial cell proliferation and migration and inhibit apoptosis. Runx1 inhibitor Ro 5-3335 can effectively inhibit KRAS-mutated HNSCC progression both in vitro and in vivo. These findings suggest that the KRAS mutation plays an important role in HNSCC and that Runx1 may be a novel therapeutic target for KRAS-mutated HNSCC.
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Affiliation(s)
- Miao Deng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P. R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jiaxin Guo
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P. R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Zihang Ling
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P. R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Chi Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P. R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Lihong He
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P. R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Zhaona Fan
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P. R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Bin Cheng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P. R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Juan Xia
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P. R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P. R. China
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114
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Takahashi K, Tanaka T. Clonal evolution and hierarchy in myeloid malignancies. Trends Cancer 2023; 9:707-715. [PMID: 37302922 PMCID: PMC10766088 DOI: 10.1016/j.trecan.2023.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Myeloid malignancies, a group of hematopoietic disorders that includes acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myeloproliferative neoplasms (MPNs), are caused by the accumulation of genetic and epigenetic changes in hematopoietic stem and progenitor cells (HSPCs) over time. Despite the relatively low number of genomic drivers compared with other forms of cancer, the process by which these changes shape the genomic architecture of myeloid malignancies remains elusive. Recent advancements in clonal hematopoiesis research and the use of cutting-edge single cell technologies have shed new light on the developmental process of myeloid malignancies. In this review, we delve into the intricacies of clonal evolution in myeloid malignancies and its implications for the development of new diagnostic and therapeutic approaches.
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Affiliation(s)
- Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Tomoyuki Tanaka
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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115
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King C, Fowler JC, Abnizova I, Sood RK, Hall MWJ, Szeverényi I, Tham M, Huang J, Young SM, Hall BA, Birgitte Lane E, Jones PH. Somatic mutations in facial skin from countries of contrasting skin cancer risk. Nat Genet 2023; 55:1440-1447. [PMID: 37537257 PMCID: PMC10484783 DOI: 10.1038/s41588-023-01468-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
The incidence of keratinocyte cancer (basal cell and squamous cell carcinomas of the skin) is 17-fold lower in Singapore than the UK1-3, despite Singapore receiving 2-3 times more ultraviolet (UV) radiation4,5. Aging skin contains somatic mutant clones from which such cancers develop6,7. We hypothesized that differences in keratinocyte cancer incidence may be reflected in the normal skin mutational landscape. Here we show that, compared to Singapore, aging facial skin from populations in the UK has a fourfold greater mutational burden, a predominant UV mutational signature, increased copy number aberrations and increased mutant TP53 selection. These features are shared by keratinocyte cancers from high-incidence and low-incidence populations8-13. In Singaporean skin, most mutations result from cell-intrinsic processes; mutant NOTCH1 and NOTCH2 are more strongly selected than in the UK. Aging skin in a high-incidence country has multiple features convergent with cancer that are not found in a low-risk country. These differences may reflect germline variation in UV-protective genes.
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Affiliation(s)
| | | | | | | | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- Department of Oncology, University of Cambridge, Hutchinson Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Ildikó Szeverényi
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agricultural and Life Sciences, Keszthely, Hungary
| | - Muly Tham
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jingxiang Huang
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - E Birgitte Lane
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Oncology, University of Cambridge, Hutchinson Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
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116
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Hou M, Shi J, Gong Z, Wen H, Lan Y, Deng X, Fan Q, Li J, Jiang M, Tang X, Wu CI, Li F, Ruan Y. Intra- vs. Interhost Evolution of SARS-CoV-2 Driven by Uncorrelated Selection-The Evolution Thwarted. Mol Biol Evol 2023; 40:msad204. [PMID: 37707487 PMCID: PMC10521905 DOI: 10.1093/molbev/msad204] [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: 07/01/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
In viral evolution, a new mutation has to proliferate within the host (Stage I) in order to be transmitted and then compete in the host population (Stage II). We now analyze the intrahost single nucleotide variants (iSNVs) in a set of 79 SARS-CoV-2 infected patients with most transmissions tracked. Here, every mutation has two measures: 1) iSNV frequency within each individual host in Stage I; 2) occurrence among individuals ranging from 1 (private), 2-78 (public), to 79 (global) occurrences in Stage II. In Stage I, a small fraction of nonsynonymous iSNVs are sufficiently advantageous to rise to a high frequency, often 100%. However, such iSNVs usually fail to become public mutations. Thus, the selective forces in the two stages of evolution are uncorrelated and, possibly, antagonistic. For that reason, successful mutants, including many variants of concern, have to avoid being eliminated in Stage I when they first emerge. As a result, they may not have the transmission advantage to outcompete the dominant strains and, hence, are rare in the host population. Few of them could manage to slowly accumulate advantageous mutations to compete in Stage II. When they do, they would appear suddenly as in each of the six successive waves of SARS-CoV-2 strains. In conclusion, Stage I evolution, the gate-keeper, may contravene the long-term viral evolution and should be heeded in viral studies.
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Affiliation(s)
- Mei Hou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jingrong Shi
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zanke Gong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yun Lan
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xizi Deng
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qinghong Fan
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiaojiao Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Mengling Jiang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoping Tang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Feng Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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117
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Wong K, Abascal F, Ludwig L, Aupperle-Lellbach H, Grassinger J, Wright CW, Allison SJ, Pinder E, Phillips RM, Romero LP, Gal A, Roady PJ, Pires I, Guscetti F, Munday JS, Peleteiro MC, Pinto CA, Carvalho T, Cota J, Du Plessis EC, Constantino-Casas F, Plog S, Moe L, de Brot S, Bemelmans I, Amorim RL, Georgy SR, Prada J, Del Pozo J, Heimann M, de Carvalho Nunes L, Simola O, Pazzi P, Steyl J, Ubukata R, Vajdovich P, Priestnall SL, Suárez-Bonnet A, Roperto F, Millanta F, Palmieri C, Ortiz AL, Barros CSL, Gava A, Söderström ME, O'Donnell M, Klopfleisch R, Manrique-Rincón A, Martincorena I, Ferreira I, Arends MJ, Wood GA, Adams DJ, van der Weyden L. Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer. Genome Biol 2023; 24:191. [PMID: 37635261 PMCID: PMC10464500 DOI: 10.1186/s13059-023-03026-4] [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: 12/02/2022] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND In humans, muscle-invasive bladder cancer (MIBC) is highly aggressive and associated with a poor prognosis. With a high mutation load and large number of altered genes, strategies to delineate key driver events are necessary. Dogs and cats develop urothelial carcinoma (UC) with histological and clinical similarities to human MIBC. Cattle that graze on bracken fern also develop UC, associated with exposure to the carcinogen ptaquiloside. These species may represent relevant animal models of spontaneous and carcinogen-induced UC that can provide insight into human MIBC. RESULTS Whole-exome sequencing of domestic canine (n = 87) and feline (n = 23) UC, and comparative analysis with human MIBC reveals a lower mutation rate in animal cases and the absence of APOBEC mutational signatures. A convergence of driver genes (ARID1A, KDM6A, TP53, FAT1, and NRAS) is discovered, along with common focally amplified and deleted genes involved in regulation of the cell cycle and chromatin remodelling. We identify mismatch repair deficiency in a subset of canine and feline UCs with biallelic inactivation of MSH2. Bovine UC (n = 8) is distinctly different; we identify novel mutational signatures which are recapitulated in vitro in human urinary bladder UC cells treated with bracken fern extracts or purified ptaquiloside. CONCLUSION Canine and feline urinary bladder UC represent relevant models of MIBC in humans, and cross-species analysis can identify evolutionarily conserved driver genes. We characterize mutational signatures in bovine UC associated with bracken fern and ptaquiloside exposure, a human-linked cancer exposure. Our work demonstrates the relevance of cross-species comparative analysis in understanding both human and animal UC.
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Affiliation(s)
- Kim Wong
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Federico Abascal
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Latasha Ludwig
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Heike Aupperle-Lellbach
- Laboklin GmbH & Co. KG, Bad Kissingen, Germany and Institute of Pathology, Department Comparative Experimental Pathology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Grassinger
- Laboklin GmbH & Co. KG, Bad Kissingen, Germany and Institute of Pathology, Department Comparative Experimental Pathology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Colin W Wright
- School of Pharmacy and Medical Sciences, University of Bradford, West Yorkshire, UK
| | - Simon J Allison
- Department of Pharmacy, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Emma Pinder
- Department of Pharmacy, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Roger M Phillips
- Department of Pharmacy, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Laura P Romero
- Departmento de Patología, Facultad de Medicina Veterinaria Y Zootecnia, Universidad Nacional Autónoma de México (UNAM), CDMX, Mexico City, México
| | - Arnon Gal
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patrick J Roady
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Isabel Pires
- Department of Veterinary Science, CECAV-Veterinary and Animal Research Center, University of Trás-Os-Montes and Alto Douro, Vila Real, Portugal
| | - Franco Guscetti
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - John S Munday
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Maria C Peleteiro
- Faculty of Veterinary Medicine, Centre for Interdisciplinary Research in Animal Health (CIISA), University of Lisbon, Lisbon, Portugal
| | - Carlos A Pinto
- Faculty of Veterinary Medicine, Centre for Interdisciplinary Research in Animal Health (CIISA), University of Lisbon, Lisbon, Portugal
| | | | - João Cota
- Faculty of Veterinary Medicine, Centre for Interdisciplinary Research in Animal Health (CIISA), University of Lisbon, Lisbon, Portugal
| | | | | | | | - Lars Moe
- Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Simone de Brot
- Institute of Animal Pathology, COMPATH, University of Bern, Bern, Switzerland
| | | | - Renée Laufer Amorim
- Veterinary Clinic Department, School of Veterinary Medicine and Animal Science, São Paulo State University, Botucatu, Brazil
| | - Smitha R Georgy
- Department of Anatomic Pathology, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Justina Prada
- Department of Veterinary Science, CECAV-Veterinary and Animal Research Center, University of Trás-Os-Montes and Alto Douro, Vila Real, Portugal
| | - Jorge Del Pozo
- Royal Dick School of Veterinary Sciences, University of Edinburgh, Roslin, Scotland, UK
| | | | | | | | - Paolo Pazzi
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Johan Steyl
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Rodrigo Ubukata
- E+ Especialidades Veterinárias - Veterinary Oncology, São Paulo, Brazil
| | - Peter Vajdovich
- Department of Clinical Pathology and Oncology, University of Veterinary Medicine Budapest, Budapest, Hungary
| | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Alejandro Suárez-Bonnet
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Franco Roperto
- Dipartimento Di Biologia, Università Degli Studi Di Napoli Federico II, Napoli, Italy
| | | | - Chiara Palmieri
- School of Veterinary Science, The University of Queensland, Brisbane, QLD, Australia
| | - Ana L Ortiz
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Claudio S L Barros
- Faculdade de Medicina Veterinária E Zootecnia, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | - Aldo Gava
- Pathology Laboratory of the Centro de Ciencias Agro-Veterinarias, Universidade Do Estado de Santa Catarina, Lages, SC, Brazil
| | - Minna E Söderström
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Marie O'Donnell
- Department of Pathology, Western General Hospital, Edinburgh, Scotland, UK
| | - Robert Klopfleisch
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Andrea Manrique-Rincón
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Inigo Martincorena
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ingrid Ferreira
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Cancer Research UK Edinburgh Cancer Centre, Institute of Genetics & Cancer, Edinburgh, Scotland, UK
| | - Geoffrey A Wood
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Louise van der Weyden
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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118
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Machado HE, Øbro NF, Williams N, Tan S, Boukerrou AZ, Davies M, Belmonte M, Mitchell E, Baxter EJ, Mende N, Clay A, Ancliff P, Köglmeier J, Killick SB, Kulasekararaj A, Meyer S, Laurenti E, Campbell PJ, Kent DG, Nangalia J, Warren AJ. Convergent somatic evolution commences in utero in a germline ribosomopathy. Nat Commun 2023; 14:5092. [PMID: 37608017 PMCID: PMC10444798 DOI: 10.1038/s41467-023-40896-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/14/2023] [Indexed: 08/24/2023] Open
Abstract
Clonal tracking of cells using somatic mutations permits exploration of clonal dynamics in human disease. Here, we perform whole genome sequencing of 323 haematopoietic colonies from 10 individuals with the inherited ribosomopathy Shwachman-Diamond syndrome to reconstruct haematopoietic phylogenies. In ~30% of colonies, we identify mutually exclusive mutations in TP53, EIF6, RPL5, RPL22, PRPF8, plus chromosome 7 and 15 aberrations that increase SBDS and EFL1 gene dosage, respectively. Target gene mutations commence in utero, resulting in a profusion of clonal expansions, with only a few haematopoietic stem cell lineages (mean 8, range 1-24) contributing ~50% of haematopoietic colonies across 8 individuals (range 4-100% clonality) by young adulthood. Rapid clonal expansion during disease transformation is associated with biallelic TP53 mutations and increased mutation burden. Our study highlights how convergent somatic mutation of the p53-dependent nucleolar surveillance pathway offsets the deleterious effects of germline ribosomopathy but increases opportunity for TP53-mutated cancer evolution.
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Affiliation(s)
| | - Nina F Øbro
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Shengjiang Tan
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge, UK
| | - Ahmed Z Boukerrou
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge, UK
| | - Megan Davies
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Miriam Belmonte
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Emily Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - E Joanna Baxter
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Nicole Mende
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anna Clay
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Philip Ancliff
- Department of Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jutta Köglmeier
- Department of Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sally B Killick
- University Hospitals Dorset NHS Foundation Trust, The Royal Bournemouth Hospital, Bournemouth, UK
| | - Austin Kulasekararaj
- Department of Haematological Medicine, King's College Hospital NHS Foundation Trust and King's College London, London, UK
| | - Stefan Meyer
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester, UK
- Department of Paediatric Haematology and Oncology, Royal Manchester Children's Hospital, Manchester Foundation Trust, Manchester, Oxford Road, Manchester, UK
- Teenage and Adolescent Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK
| | - Elisa Laurenti
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - David G Kent
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- York Biomedical Research Institute, Department of Biology, University of York, York, UK.
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Alan J Warren
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge, UK.
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119
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Pál C, Papp B. How selection shapes the short- and long-term dynamics of molecular evolution. Proc Natl Acad Sci U S A 2023; 120:e2311012120. [PMID: 37531373 PMCID: PMC10433269 DOI: 10.1073/pnas.2311012120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023] Open
Affiliation(s)
- Csaba Pál
- Synthetic and System Biology Unit, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network, SzegedHU-6726, Hungary
| | - Balázs Papp
- Synthetic and System Biology Unit, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network, SzegedHU-6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Research Group, SzegedHU-6726, Hungary
- National Laboratory for Health Security, Biological Research Centre, Eötvös Loránd Research Network, SzegedHU-6726, Hungary
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120
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Desai H, Ofori S, Boatner L, Yu F, Villanueva M, Ung N, Nesvizhskii AI, Backus K. Multi-omic stratification of the missense variant cysteinome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.12.553095. [PMID: 37645963 PMCID: PMC10461992 DOI: 10.1101/2023.08.12.553095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Cancer genomes are rife with genetic variants; one key outcome of this variation is gain-ofcysteine, which is the most frequently acquired amino acid due to missense variants in COSMIC. Acquired cysteines are both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain uncharacterized. Here, we pair cysteine chemoproteomics-a technique that enables proteome-wide pinpointing of functional, redox sensitive, and potentially druggable residues-with genomics to reveal the hidden landscape of cysteine acquisition. For both cancer and healthy genomes, we find that cysteine acquisition is a ubiquitous consequence of genetic variation that is further elevated in the context of decreased DNA repair. Our chemoproteogenomics platform integrates chemoproteomic, whole exome, and RNA-seq data, with a customized 2-stage false discovery rate (FDR) error controlled proteomic search, further enhanced with a user-friendly FragPipe interface. Integration of CADD predictions of deleteriousness revealed marked enrichment for likely damaging variants that result in acquisition of cysteine. By deploying chemoproteogenomics across eleven cell lines, we identify 116 gain-of-cysteines, of which 10 were liganded by electrophilic druglike molecules. Reference cysteines proximal to missense variants were also found to be pervasive, 791 in total, supporting heretofore untapped opportunities for proteoform-specific chemical probe development campaigns. As chemoproteogenomics is further distinguished by sample-matched combinatorial variant databases and compatible with redox proteomics and small molecule screening, we expect widespread utility in guiding proteoform-specific biology and therapeutic discovery.
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Affiliation(s)
- Heta Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Samuel Ofori
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Lisa Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Nicholas Ung
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Keriann Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
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121
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Wu S, Wagner G. Computational inference of eIF4F complex function and structure in human cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552450. [PMID: 37609226 PMCID: PMC10441403 DOI: 10.1101/2023.08.10.552450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The canonical eukaryotic initiation factor 4F (eIF4F) complex, composed of eIF4G1, eIF4A1, and the cap-binding protein eIF4E, plays a crucial role in cap-dependent translation initiation in eukaryotic cells (1). However, cap-independent initiation can occur through internal ribosomal entry sites (IRESs), involving only eIF4G1 and eIF4A1 present, which is considered to be a complementary process to cap-dependent initiation in tumors under stress conditions (2). The selection and molecular mechanism of specific translation initiation in human cancers remains poorly understood. Thus, we analyzed gene copy number variations (CNVs) in TCGA tumor samples and found frequent amplification of genes involved in translation initiation. Copy number gains in EIF4G1 and EIF3E frequently co-occur across human cancers. Additionally, EIF4G1 expression strongly correlates with genes from cancer cell survival pathways including cell cycle and lipogenesis, in tumors with EIF4G1 amplification or duplication. Furthermore, we revealed that eIF4G1 and eIF4A1 protein levels strongly co-regulate with ribosomal subunits, eIF2, and eIF3 complexes, while eIF4E co-regulates with 4E-BP1, ubiquitination, and ESCRT proteins. Using Alphafold predictions, we modeled the eIF4F structure with and without eIF4G1-eIF4E binding. The modeling for cap-dependent initiation suggests that eIF4G1 interacts with eIF4E through its N-terminal eIF4E-binding domain, bringing eIF4E near the eIF4A1 mRNA binding cavity and closing the cavity with both eIF4G1 HEAT-2 domain and eIF4E. In the cap-independent mechanism, α-helix 5 of eIF4G1 HEAT-2 domain instead directly interacts with the eIF4A1 N-terminal domain to close the mRNA binding cavity without eIF4E involvement, resulting in a stronger interaction between eIF4G1 and eIF4A1. Significance Statement Translation initiation is primarily governed by eIF4F, employing a "cap-dependent" mechanism, but eIF4F dysregulation may lead to a "cap-independent" mechanism in stressed cancer cells. We found frequent amplification of translation initiation genes, and co-occurring copy number gains of EIF4G1 and EIF3E genes in human cancers. EIF4G1 amplification or duplication may be positively selected for its beneficial impact on the overexpression of cancer survival genes. The co-regulation of eIF4G1 and eIF4A1, distinctly from eIF4E, reveals eIF4F dysregulation favoring cap-independent initiation. Alphafold predicts changes in the eIF4F complex assembly to accommodate both initiation mechanisms. These findings have significant implications for evaluating cancer cell vulnerability to eIF4F inhibition and developing treatments that target cancer cells with dependency on the translation initiation mechanism.
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122
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Hasan AMM, Cremaschi P, Wetterskog D, Jayaram A, Wong SQ, Williams S, Pasam A, Trigos A, Trujillo B, Grist E, Friedrich S, Vainauskas O, Parry M, Ismail M, Devlies W, Wingate A, Linch M, Naceur-Lombardelli C, Swanton C, Jamal-Hanjani M, Lise S, Sandhu S, Attard G. Copy number architectures define treatment-mediated selection of lethal prostate cancer clones. Nat Commun 2023; 14:4823. [PMID: 37563129 PMCID: PMC10415299 DOI: 10.1038/s41467-023-40315-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Despite initial responses to hormone treatment, metastatic prostate cancer invariably evolves to a lethal state. To characterize the intra-patient evolutionary relationships of metastases that evade treatment, we perform genome-wide copy number profiling and bespoke approaches targeting the androgen receptor (AR) on 167 metastatic regions from 11 organs harvested post-mortem from 10 men who died from prostate cancer. We identify diverse and patient-unique alterations clustering around the AR in metastases from every patient with evidence of independent acquisition of related genomic changes within an individual and, in some patients, the co-existence of AR-neutral clones. Using the genomic boundaries of pan-autosome copy number changes, we confirm a common clone of origin across metastases and diagnostic biopsies, and identified in individual patients, clusters of metastases occupied by dominant clones with diverged autosomal copy number alterations. These autosome-defined clusters are characterized by cluster-specific AR gene architectures, and in two index cases are topologically more congruent than by chance (p-values 3.07 × 10-8 and 6.4 × 10-4). Integration with anatomical sites suggests patterns of spread and points of genomic divergence. Here, we show that copy number boundaries identify treatment-selected clones with putatively distinct lethal trajectories.
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Affiliation(s)
| | | | | | - Anuradha Jayaram
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Scott Williams
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Anupama Pasam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna Trigos
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Blanca Trujillo
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Emily Grist
- University College London Cancer Institute, London, UK
| | | | | | - Marina Parry
- University College London Cancer Institute, London, UK
| | | | - Wout Devlies
- University College London Cancer Institute, London, UK
| | - Anna Wingate
- University College London Cancer Institute, London, UK
| | - Mark Linch
- University College London Cancer Institute, London, UK
- University College London Hospitals, 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
- Department of Oncology, University College London Hospitals, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Stefano Lise
- University College London Cancer Institute, London, UK
| | | | - Gerhardt Attard
- University College London Cancer Institute, London, UK.
- University College London Hospitals, London, UK.
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123
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Majic P, Payne JL. Developmental Selection and the Perception of Mutation Bias. Mol Biol Evol 2023; 40:msad179. [PMID: 37556606 PMCID: PMC10443735 DOI: 10.1093/molbev/msad179] [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: 04/05/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023] Open
Abstract
The notion that mutations are random relative to their fitness effects is central to the Neo-Darwinian view of evolution. However, a recent interpretation of the patterns of mutation accumulation in the genome of Arabidopsis thaliana has challenged this notion, arguing for the presence of a targeted DNA repair mechanism that causes a nonrandom association of mutation rates and fitness effects. Specifically, this mechanism was suggested to cause a reduction in the rates of mutations on essential genes, thus lowering the rates of deleterious mutations. Central to this argument were attempts to rule out selection at the population level. Here, we offer an alternative and parsimonious interpretation of the patterns of mutation accumulation previously attributed to mutation bias, showing how they can instead or additionally be caused by developmental selection, that is selection occurring at the cellular level during the development of a multicellular organism. Thus, the depletion of deleterious mutations in A. thaliana may indeed be the result of a selective process, rather than a bias in mutation. More broadly, our work highlights the importance of considering development in the interpretation of population-genetic analyses of multicellular organisms, and it emphasizes that efforts to identify mechanisms involved in mutational biases should explicitly account for developmental selection.
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Affiliation(s)
- Paco Majic
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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124
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Chapdelaine AG, Sun G. Challenges and Opportunities in Developing Targeted Therapies for Triple Negative Breast Cancer. Biomolecules 2023; 13:1207. [PMID: 37627272 PMCID: PMC10452226 DOI: 10.3390/biom13081207] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
Triple negative breast cancer (TNBC) is a heterogeneous group of breast cancers characterized by their lack of estrogen receptors, progesterone receptors, and the HER2 receptor. They are more aggressive than other breast cancer subtypes, with a higher mean tumor size, higher tumor grade, the worst five-year overall survival, and the highest rates of recurrence and metastasis. Developing targeted therapies for TNBC has been a major challenge due to its heterogeneity, and its treatment still largely relies on surgery, radiation therapy, and chemotherapy. In this review article, we review the efforts in developing targeted therapies for TNBC, discuss insights gained from these efforts, and highlight potential opportunities going forward. Accumulating evidence supports TNBCs as multi-driver cancers, in which multiple oncogenic drivers promote cell proliferation and survival. In such multi-driver cancers, targeted therapies would require drug combinations that simultaneously block multiple oncogenic drivers. A strategy designed to generate mechanism-based combination targeted therapies for TNBC is discussed.
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Affiliation(s)
| | - Gongqin Sun
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA;
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125
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Iizuka A, Akiyama Y, Sakura N, Kanematsu A, Kikuchi Y, Nagashima T, Urakami K, Shimoda Y, Ohshima K, Shiomi A, Ohde Y, Terashima M, Uesaka K, Mukaigawa T, Hirashima Y, Yoshikawa S, Katagiri H, Sugino T, Takahashi M, Kenmotsu H, Yamaguchi K. Generation of novel complete HLA class I monoallelic cell lines used in an MHC stabilization assay for neoantigen evaluation. Oncol Lett 2023; 26:324. [PMID: 37415627 PMCID: PMC10320429 DOI: 10.3892/ol.2023.13910] [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: 01/17/2023] [Accepted: 05/16/2023] [Indexed: 07/08/2023] Open
Abstract
Immunogenic neoantigens derived from somatic mutations in cancer have been identified through clinical studies with the cloning of tumor-infiltrating T cells, and cancer driver gene mutation-derived epitopes have been reported; however, these are rare. At present, the validation of epitopes predicted in silico is difficult as human T-cell clonal diversity cannot be reproduced in vitro or in experimental animal models. To confirm the epitope peptides presented by human leukocyte antigen (HLA) class I molecules predicted in silico, biochemical methods such as major histocompatibility complex (MHC) stabilization assays and mass spectrometry-mediated identification have been developed based on HLA-A*02:01 monoallelic T2 cells and HLA-C*01:02 monoallelic LCL721.221 cells. Therefore, in the present study, to prevent confusion due to peptide cross-presentation among HLA molecules, HLA class I monoallelic B-cell clones were generated from the TISI cell line by knocking out HLA-ABC and TAP2, and knocking in HLA alleles. To explore cancer driver mutations as potential targets for immunotherapy, exome sequencing data from 5,143 patients with cancer enrolled in a comprehensive genome analysis project at the Shizuoka Cancer Center were used to identify somatic amino acid substituted mutations and the 50 most frequent mutations in five genes, TP53, EGFR, PIK3CA, KRAS and BRAF, were identified. Using NetMHC4.1, the present study predicted whether epitopes derived from these mutations are presented on major HLA-ABC alleles in Japanese individuals and synthesized 138 peptides for MHC stabilization assays. The authors also attempted to examine the candidate epitopes at physiological temperatures by using antibody clone G46-2.6, which can detect HLA-ABC, independent of β2-microglobulin association. In the assays, although the peptide-induced HLA expression levels were associated with the predicted affinities, the respective HLA alleles exhibited varying degrees of responsiveness, and unexpectedly, p53-mutant epitopes with predicted weak affinities exhibited strong responses. These results suggested that MHC stabilization assays using completely monoallelic HLA-expressing B-cell lines are useful for evaluating the presentation of neoantigen epitopes.
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Affiliation(s)
- Akira Iizuka
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Naoki Sakura
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Akari Kanematsu
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Yasufumi Kikuchi
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
- SRL, Inc., Tokyo 163-0409, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Yasuhisa Ohde
- Division of Thoracic Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Masanori Terashima
- Division of Gastric Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Takashi Mukaigawa
- Division of Head and Neck Surgery, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Yasuyuki Hirashima
- Division of Gynecology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Shusuke Yoshikawa
- Division of Dermatology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Hirohisa Katagiri
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Mitsuru Takahashi
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, Shizuoka 411-8777, Japan
| | - Ken Yamaguchi
- Office of The President, Shizuoka Cancer Center, Shizuoka 411-8777, Japan
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126
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Nishimura T, Kakiuchi N, Yoshida K, Sakurai T, Kataoka TR, Kondoh E, Chigusa Y, Kawai M, Sawada M, Inoue T, Takeuchi Y, Maeda H, Baba S, Shiozawa Y, Saiki R, Nakagawa MM, Nannya Y, Ochi Y, Hirano T, Nakagawa T, Inagaki-Kawata Y, Aoki K, Hirata M, Nanki K, Matano M, Saito M, Suzuki E, Takada M, Kawashima M, Kawaguchi K, Chiba K, Shiraishi Y, Takita J, Miyano S, Mandai M, Sato T, Takeuchi K, Haga H, Toi M, Ogawa S. Evolutionary histories of breast cancer and related clones. Nature 2023; 620:607-614. [PMID: 37495687 PMCID: PMC10432280 DOI: 10.1038/s41586-023-06333-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 06/15/2023] [Indexed: 07/28/2023]
Abstract
Recent studies have documented frequent evolution of clones carrying common cancer mutations in apparently normal tissues, which are implicated in cancer development1-3. However, our knowledge is still missing with regard to what additional driver events take place in what order, before one or more of these clones in normal tissues ultimately evolve to cancer. Here, using phylogenetic analyses of multiple microdissected samples from both cancer and non-cancer lesions, we show unique evolutionary histories of breast cancers harbouring der(1;16), a common driver alteration found in roughly 20% of breast cancers. The approximate timing of early evolutionary events was estimated from the mutation rate measured in normal epithelial cells. In der(1;16)(+) cancers, the derivative chromosome was acquired from early puberty to late adolescence, followed by the emergence of a common ancestor by the patient's early 30s, from which both cancer and non-cancer clones evolved. Replacing the pre-existing mammary epithelium in the following years, these clones occupied a large area within the premenopausal breast tissues by the time of cancer diagnosis. Evolution of multiple independent cancer founders from the non-cancer ancestors was common, contributing to intratumour heterogeneity. The number of driver events did not correlate with histology, suggesting the role of local microenvironments and/or epigenetic driver events. A similar evolutionary pattern was also observed in another case evolving from an AKT1-mutated founder. Taken together, our findings provide new insight into how breast cancer evolves.
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Affiliation(s)
- Tomomi Nishimura
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Next-generation Clinical Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Cancer Evolution, National Cancer Center Research Institute, Tokyo, Japan
| | - Takaki Sakurai
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
- Department of Diagnostic Pathology, Osaka Red Cross Hospital, Osaka, Japan
| | - Tatsuki R Kataoka
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
- Department of Pathology, Iwate Medical University, Iwate, Japan
| | - Eiji Kondoh
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Obstetrics and Gynecology Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshitsugu Chigusa
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Kawai
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | - Yasuhide Takeuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Hirona Maeda
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Satoko Baba
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryunosuke Saiki
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro M Nakagawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Next-generation Clinical Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Hematopoietic Disease Control, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomonori Hirano
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tomoe Nakagawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yukiko Inagaki-Kawata
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Aoki
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Kosaku Nanki
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Mami Matano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Megumu Saito
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Company, Limited, Osaka, Japan
| | - Eiji Suzuki
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Breast Surgery Department, Kobe City Medical Center General Hospital, Hyogo, Japan
| | - Masahiro Takada
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Kawashima
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Kawaguchi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoru Miyano
- Department of Integrated Analytics, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Masakazu Toi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden.
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127
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Franch-Expósito S, Mehine M, Ptashkin RN, Bolton KL, Bandlamudi C, Srinivasan P, Zhang L, Goodell MA, Gedvilaite E, Menghrajani K, Sánchez-Vela P, Mandelker D, Comen E, Norton L, Benayed R, Gao T, Papaemmanuil E, Taylor B, Levine R, Offit K, Stadler Z, Berger MF, Zehir A. Associations Between Cancer Predisposition Mutations and Clonal Hematopoiesis in Patients With Solid Tumors. JCO Precis Oncol 2023; 7:e2300070. [PMID: 37561983 PMCID: PMC10581611 DOI: 10.1200/po.23.00070] [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: 02/10/2023] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
PURPOSE Clonal hematopoiesis (CH), the expansion of clones in the hematopoietic system, has been linked to different internal and external features such as aging, genetic ancestry, smoking, and oncologic treatment. However, the interplay between mutations in known cancer predisposition genes and CH has not been thoroughly examined in patients with solid tumors. METHODS We used prospective tumor-blood paired sequencing data from 46,906 patients who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) testing to interrogate the associations between CH and rare pathogenic or likely pathogenic (P/LP) germline variants. RESULTS We observed an enrichment of CH-positive patients among those carrying P/LP germline mutations and identified a significant association between P/LP germline variants in ATM and CH. Germline and CH comutation patterns in ATM, TP53, and CHEK2 suggested biallelic inactivation as a potential mediator of clonal expansion. Moreover, we observed that CH-PPM1D mutations, similar to somatic tumor-associated PPM1D mutations, were depleted in patients with P/LP germline mutations in the DNA damage response (DDR) genes ATM, CHEK2, and TP53. Patients with solid tumors and harboring P/LP germline mutations, CH mutations, and mosaicism chromosomal alterations might be at an increased risk of developing secondary leukemia while germline variants in TP53 were identified as an independent risk factor (hazard ratio, 36; P < .001) for secondary leukemias. CONCLUSION Our results suggest a close relationship between inherited variants and CH mutations within the DDR genes in patients with solid tumors. Associations identified in this study might translate into enhanced clinical surveillance for CH and associated comorbidities in patients with cancer harboring these germline mutations.
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Affiliation(s)
- Sebastià Franch-Expósito
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Miika Mehine
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- C2i Genomics, New York, NY
| | - Kelly L. Bolton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Natera Inc, San Carlos, CA
| | - Linda Zhang
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Margaret A. Goodell
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamal Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pablo Sánchez-Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Comen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
| | - Teng Gao
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Elli Papaemmanuil
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barry Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
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128
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Moesslacher CS, Auernig E, Woodsmith J, Feichtner A, Jany-Luig E, Jehle S, Worseck JM, Heine CL, Stefan E, Stelzl U. Missense variant interaction scanning reveals a critical role of the FERM domain for tumor suppressor protein NF2 conformation and function. Life Sci Alliance 2023; 6:e202302043. [PMID: 37280085 PMCID: PMC10244618 DOI: 10.26508/lsa.202302043] [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: 03/16/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023] Open
Abstract
NF2 (moesin-ezrin-radixin-like [MERLIN] tumor suppressor) is frequently inactivated in cancer, where its NF2 tumor suppressor functionality is tightly coupled to protein conformation. How NF2 conformation is regulated and how NF2 conformation influences tumor suppressor activity is a largely open question. Here, we systematically characterized three NF2 conformation-dependent protein interactions utilizing deep mutational scanning interaction perturbation analyses. We identified two regions in NF2 with clustered mutations which affected conformation-dependent protein interactions. NF2 variants in the F2-F3 subdomain and the α3H helix region substantially modulated NF2 conformation and homomerization. Mutations in the F2-F3 subdomain altered proliferation in three cell lines and matched patterns of disease mutations in NF2 related-schwannomatosis. This study highlights the power of systematic mutational interaction perturbation analysis to identify missense variants impacting NF2 conformation and provides insight into NF2 tumor suppressor function.
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Affiliation(s)
- Christina S Moesslacher
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Elisabeth Auernig
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Jonathan Woodsmith
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Evelyne Jany-Luig
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Stefanie Jehle
- Max-Planck Institute for Molecular Genetics (MPIMG), Otto-Warburg-Laboratory, Berlin, Germany
| | - Josephine M Worseck
- Max-Planck Institute for Molecular Genetics (MPIMG), Otto-Warburg-Laboratory, Berlin, Germany
| | - Christian L Heine
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
- Institute of Molecular Biology, Innsbruck, Austria
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
- Max-Planck Institute for Molecular Genetics (MPIMG), Otto-Warburg-Laboratory, Berlin, Germany
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
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129
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Maura F, Coffey DG, Stein CK, Braggio E, Ziccheddu B, Sharik ME, Du M, Alvarado YT, Shi CX, Zhu YX, Meermeier EW, Morgan GJ, Landgren O, Leif Bergsagel P, Chesi M. The Vk*MYC Mouse Model recapitulates human multiple myeloma evolution and genomic diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550482. [PMID: 37546905 PMCID: PMC10402028 DOI: 10.1101/2023.07.25.550482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Despite advancements in profiling multiple myeloma (MM) and its precursor conditions, there is limited information on mechanisms underlying disease progression. Clincal efforts designed to deconvolute such mechanisms are challenged by the long lead time between monoclonal gammopathy and its transformation to MM. MM mouse models represent an opportunity to overcome this temporal limitation. Here, we profile the genomic landscape of 118 genetically engineered Vk*MYC MM and reveal that it recapitulates the genomic heterogenenity and life history of human MM. We observed recurrent copy number alterations, structural variations, chromothripsis, driver mutations, APOBEC mutational activity, and a progressive decrease in immunoglobulin transcription that inversely correlates with proliferation. Moreover, we identified frequent insertional mutagenesis by endogenous retro-elements as a murine specific mechanism to activate NF-kB and IL6 signaling pathways shared with human MM. Despite the increased genomic complexity associated with progression, advanced tumors remain dependent on MYC expression, that drives the progression of monoclonal gammopathy to MM.
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130
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Hall MWJ, Shorthouse D, Alcraft R, Jones PH, Hall BA. Mutations observed in somatic evolution reveal underlying gene mechanisms. Commun Biol 2023; 6:753. [PMID: 37468606 PMCID: PMC10356810 DOI: 10.1038/s42003-023-05136-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Highly sensitive DNA sequencing techniques have allowed the discovery of large numbers of somatic mutations in normal tissues. Some mutations confer a competitive advantage over wild-type cells, generating expanding clones that spread through the tissue. Competition between mutant clones leads to selection. This process can be considered a large scale, in vivo screen for mutations increasing cell fitness. It follows that somatic missense mutations may offer new insights into the relationship between protein structure, function and cell fitness. We present a flexible statistical method for exploring the selection of structural features in data sets of somatic mutants. We show how this approach can evidence selection of specific structural features in key drivers in aged tissues. Finally, we show how drivers may be classified as fitness-enhancing and fitness-suppressing through different patterns of mutation enrichment. This method offers a route to understanding the mechanism of protein function through in vivo mutant selection.
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Affiliation(s)
| | - David Shorthouse
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London, WC1E 6BT, UK
| | - Rachel Alcraft
- Advanced Research Computing, University College London, London, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London, WC1E 6BT, UK.
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131
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Abbas S, Pich O, Devonshire G, Zamani SA, Katz-Summercorn A, Killcoyne S, Cheah C, Nutzinger B, Grehan N, Lopez-Bigas N, Fitzgerald RC, Secrier M. Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma. Nat Commun 2023; 14:4239. [PMID: 37454136 PMCID: PMC10349863 DOI: 10.1038/s41467-023-39957-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
A variety of mutational processes drive cancer development, but their dynamics across the entire disease spectrum from pre-cancerous to advanced neoplasia are poorly understood. We explore the mutagenic processes shaping oesophageal adenocarcinoma tumorigenesis in 997 instances comprising distinct stages of this malignancy, from Barrett Oesophagus to primary tumours and advanced metastatic disease. The mutational landscape is dominated by the C[T > C/G]T substitution enriched signatures SBS17a/b, which are linked with TP53 mutations, increased proliferation, genomic instability and disease progression. The APOBEC mutagenesis signature is a weak but persistent signal amplified in primary tumours. We also identify prevalent alterations in DNA damage repair pathways, with homologous recombination, base and nucleotide excision repair and translesion synthesis mutated in up to 50% of the cohort, and surprisingly uncoupled from transcriptional activity. Among these, the presence of base excision repair deficiencies show remarkably poor prognosis in the cohort. In this work, we provide insights on the mutational aetiology and changes enabling the transition from pre-neoplastic to advanced oesophageal adenocarcinoma.
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Affiliation(s)
- Sujath Abbas
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Sarah Killcoyne
- Early Cancer Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Calvin Cheah
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | | | - Nicola Grehan
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK.
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132
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Wang Y, Zhu H, Xu H, Qiu Y, Zhu Y, Wang X. Senescence-related gene c-Myc affects bladder cancer cell senescence by interacting with HSP90B1 to regulate cisplatin sensitivity. Aging (Albany NY) 2023; 15:7408-7423. [PMID: 37433010 PMCID: PMC10457043 DOI: 10.18632/aging.204863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/19/2023] [Indexed: 07/13/2023]
Abstract
Patients with advanced bladder cancer gradually become less sensitive to chemotherapeutic agents, leading to tumor recurrence. Initiating the senescence program in solid tumors may be an important means of improving short-term drug sensitivity. The important role of c-Myc in bladder cancer cell senescence was determined using bioinformatics methods. The response to cisplatin chemotherapy in bladder cancer sample was analyzed according to the Genomics of Drug Sensitivity in Cancer database. Cell Counting Kit-8 assay, clone formation assay, and senescence-associated β-galactosidase staining were used to assess bladder cancer cell growth, senescence, and sensitivity to cisplatin, respectively. Western blot and immunoprecipitation were performed to understand the regulation of p21 by c-Myc/HSP90B1. Bioinformatic analysis showed that c-Myc, a cellular senescence gene, was significantly associated with bladder cancer prognosis and sensitivity to cisplatin chemotherapy. c-Myc and HSP90B1 expression were highly correlated in bladder cancer. Reducing the level of c-Myc significantly inhibited bladder cancer cell proliferation, promoted cellular senescence, and enhanced cisplatin chemosensitivity. Immunoprecipitation assays confirmed that HSP90B1 interacted with c-Myc. Western blot analysis showed that reducing the level of HSP90B1 could redeem the p21 overexpression caused by c-Myc overexpression. Further studies showed that reducing HSP90B1 expression could alleviate the rapid growth and accelerate cellular senescence of bladder cancer cells caused by c-Myc overexpression, and that reducing HSP90B1 levels could also improve cisplatin sensitivity in bladder cancer cells. HSP90B1/c-Myc interaction regulates the p21 signaling pathway, which affects cisplatin chemosensitivity by modulating bladder cancer cell senescence.
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Affiliation(s)
- Yaxuan Wang
- Department of Urology, Affiliated Tumor Hospital of Nantong University and Nantong Tumor Hospital, Nantong 226361, China
| | - Haixia Zhu
- Department of Central Laboratory, Affiliated Tumor Hospital of Nantong University and Nantong Tumor Hospital, Nantong 226361, China
| | - Haifei Xu
- Department of Urology, Affiliated Tumor Hospital of Nantong University and Nantong Tumor Hospital, Nantong 226361, China
| | - Yifan Qiu
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Yonghong Zhu
- Department of Urology, Affiliated Tumor Hospital of Nantong University and Nantong Tumor Hospital, Nantong 226361, China
| | - Xiaolin Wang
- Department of Urology, Affiliated Tumor Hospital of Nantong University and Nantong Tumor Hospital, Nantong 226361, China
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133
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Rane JK, Frankell AM, Weeden CE, Swanton C. Clonal Evolution in Healthy and Premalignant Tissues: Implications for Early Cancer Interception Strategies. Cancer Prev Res (Phila) 2023; 16:369-378. [PMID: 36930945 PMCID: PMC7614725 DOI: 10.1158/1940-6207.capr-22-0469] [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: 01/13/2023] [Revised: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023]
Abstract
Histologically normal human tissues accumulate significant mutational burden with age. The extent and spectra of mutagenesis are comparable both in rapidly proliferating and post-mitotic tissues and in stem cells compared with their differentiated progeny. Some of these mutations provide increased fitness, giving rise to clones which, at times, can replace the entire surface area of tissues. Compared with cancer, somatic mutations in histologically normal tissues are primarily single-nucleotide variations. Interestingly though, the presence of these mutations and positive clonal selection in isolation remains a poor indicator of potential future cancer transformation in solid tissues. Common clonally expanded mutations in histologically normal tissues also do not always represent the most frequent early mutations in cancers of corresponding tissues, indicating differences in selection pressures. Preliminary evidence implies that stroma and immune system co-evolve with age, which may impact selection dynamics. In this review, we will explore the mutational landscape of histologically normal and premalignant human somatic tissues in detail and discuss cell-intrinsic and environmental factors that can determine the fate of positively selected mutations within them. Precisely pinpointing these determinants of cancer transformation would aid development of early cancer interventional and prevention strategies.
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Affiliation(s)
- Jayant K. Rane
- University College London Cancer Institute, London, UK
- Department of Clinical Oncology, University College London Hospitals, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M. Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare E. Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
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134
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Tabata M, Sato Y, Kogure Y, McClure MB, Oshikawa-Kumade Y, Saito Y, Shingaki S, Ito Y, Yuasa M, Koya J, Yoshida K, Kohno T, Miyama Y, Morikawa T, Chiba K, Okada A, Ogawa S, Ushiku T, Shiraishi Y, Kume H, Kataoka K. Inter- and intra-tumor heterogeneity of genetic and immune profiles in inherited renal cell carcinoma. Cell Rep 2023; 42:112736. [PMID: 37405915 DOI: 10.1016/j.celrep.2023.112736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/04/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Patients with von Hippel-Lindau disease (vHL) are at risk of developing spatially and temporally multiple clear cell renal cell carcinomas (ccRCCs), which offers a valuable opportunity to analyze inter- and intra-tumor heterogeneity of genetic and immune profiles within the same patient. Here, we perform whole-exome and RNA sequencing, digital gene expression, and immunohistochemical analyses for 81 samples from 51 ccRCCs of 10 patients with vHL. Inherited ccRCCs are clonally independent and have less genomic alterations than sporadic ccRCCs. Hierarchical clustering of transcriptome profiles shows two clusters with distinct immune signatures: immune hot and cold clusters. Interestingly, not only samples from the same tumors but also different tumors from the same patients tend to show a similar immune signature, whereas samples from different patients frequently exhibit different signatures. Our findings reveal the genetic and immune landscape of inherited ccRCCs, demonstrating the relevance of host factors in shaping anti-tumor immunity.
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Affiliation(s)
- Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yusuke Sato
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Marni B McClure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuji Oshikawa-Kumade
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima 771-0182, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuta Ito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Clinical Oncology and Hematology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Mitsuhiro Yuasa
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kazushi Yoshida
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yu Miyama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Teppei Morikawa
- Department of Diagnostic Pathology, NTT Medical Center Tokyo, Tokyo 141-8625, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm 17177, Sweden
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan.
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135
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de Joode K, van de Geer WS, van Leenders GJLH, Hamberg P, Westgeest HM, Beeker A, Oosting SF, van Rooijen JM, Beerepoot LV, Labots M, Mathijssen RHJ, Lolkema MP, Cuppen E, Sleijfer S, van de Werken HJG, van der Veldt AAM. The genomic and transcriptomic landscape of advanced renal cell cancer for individualized treatment strategies. Sci Rep 2023; 13:10720. [PMID: 37400554 DOI: 10.1038/s41598-023-37764-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
Differences in the clinical course and treatment responses in individual patients with advanced renal cell carcinoma (RCC) can largely be explained by the different genomics of this disease. To improve the personalized treatment strategy and survival outcomes for patients with advanced RCC, the genomic make-up in patients with advanced RCC was investigated to identify putative actionable variants and signatures. In this prospective multicenter study (NCT01855477), whole-genome sequencing (WGS) data of locally advanced and metastatic tissue biopsies and matched whole-blood samples were collected from 91 patients with histopathologically confirmed RCC. WGS data were analyzed for small somatic variants, copy-number alterations and structural variants. For a subgroup of patients, RNA sequencing (RNA-Seq) data could be analyzed. RNA-Seq data were clustered on immunogenic and angiogenic gene expression patterns according to a previously developed angio-immunogenic gene signature. In all patients with papillary and clear cell RCC, putative actionable drug targets were detected by WGS, of which 94% were on-label available. RNA-Seq data of clear cell and papillary RCC were clustered using a previously developed angio-immunogenic gene signature. Analyses of driver mutations and RNA-Seq data revealed clear differences among different RCC subtypes, showing the added value of WGS and RNA-Seq over clinicopathological data. By improving both histological subtyping and the selection of treatment according to actionable targets and immune signatures, WGS and RNA-Seq may improve therapeutic decision making for most patients with advanced RCC, including patients with non-clear cell RCC for whom no standard treatment is available to data. Prospective clinical trials are needed to evaluate the impact of genomic and transcriptomic diagnostics on survival outcome for advanced RCC patients.
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Affiliation(s)
- K de Joode
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - W S van de Geer
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Internal Postal Address NA-1218, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | | | - P Hamberg
- Department of Internal Medicine, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - H M Westgeest
- Department of Internal Medicine, Amphia Hospital, Breda, The Netherlands
| | - A Beeker
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - S F Oosting
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J M van Rooijen
- Department of Internal Medicine, Martini Hospital, Groningen, The Netherlands
| | - L V Beerepoot
- Department of Internal Medicine, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - M Labots
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - R H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - M P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - E Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - S Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - H J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Internal Postal Address NA-1218, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.
- Department of Immunology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.
| | - A A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
- Departments of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands.
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136
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Kim YS, Bang CH, Chung YJ. Mutational Landscape of Normal Human Skin: Clues to Understanding Early-Stage Carcinogenesis in Keratinocyte Neoplasia. J Invest Dermatol 2023; 143:1187-1196.e9. [PMID: 36716918 DOI: 10.1016/j.jid.2023.01.006] [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: 09/24/2022] [Revised: 12/15/2022] [Accepted: 01/07/2023] [Indexed: 01/29/2023]
Abstract
Normal skin contains numerous clones carrying cancer driver mutations. However, the mutational landscape of normal skin and its clonal relationship with skin cancer requires further elucidation. The aim of our study was to investigate the mutational landscape of normal human skin. We performed whole-exome sequencing using physiologically normal skin tissues and the matched peripheral blood (n = 39) and adjacent-matched skin cancers from a subset of patients (n = 10). Exposed skin harbored a median of 530 mutations (10.4/mb, range = 51-2,947), whereas nonexposed skin majorly exhibited significantly fewer mutations (median = 13, 0.25/mb, range = 1-166). Patient age was significantly correlated with the mutational burden. Mutations in six driver genes (NOTCH1, FAT1, TP53, PPM1D, KMT2D, and ASXL1) were identified. De novo mutational signature analysis identified a single signature with components of UV- and aging-related signatures. Normal skin harbored only three instances of copy-neutral loss of heterozygosity in 9q (n = 2) and 6q (n = 1). The mutational burden of normal skin was not correlated with that of matched skin cancers, and no protein-coding mutations were shared. In conclusion, we revealed the mutational landscape of normal skin, highlighting the role of driver genes in the malignant progression of normal skin.
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Affiliation(s)
- Yoon-Seob Kim
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chul Hwan Bang
- Department of Dermatology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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137
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Shih J, Sarmashghi S, Zhakula-Kostadinova N, Zhang S, Georgis Y, Hoyt SH, Cuoco MS, Gao GF, Spurr LF, Berger AC, Ha G, Rendo V, Shen H, Meyerson M, Cherniack AD, Taylor AM, Beroukhim R. Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature 2023; 619:793-800. [PMID: 37380777 PMCID: PMC10529820 DOI: 10.1038/s41586-023-06266-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Aneuploidies-whole-chromosome or whole-arm imbalances-are the most prevalent alteration in cancer genomes1,2. However, it is still debated whether their prevalence is due to selection or ease of generation as passenger events1,2. Here we developed a method, BISCUT, that identifies loci subject to fitness advantages or disadvantages by interrogating length distributions of telomere- or centromere-bounded copy-number events. These loci were significantly enriched for known cancer driver genes, including genes not detected through analysis of focal copy-number events, and were often lineage specific. BISCUT identified the helicase-encoding gene WRN as a haploinsufficient tumour-suppressor gene on chromosome 8p, which is supported by several lines of evidence. We also formally quantified the role of selection and mechanical biases in driving aneuploidy, finding that rates of arm-level copy-number alterations are most highly correlated with their effects on cellular fitness1,2. These results provide insight into the driving forces behind aneuploidy and its contribution to tumorigenesis.
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Affiliation(s)
- Juliann Shih
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Tufts University School of Medicine, Boston, MA, USA
- Department of Internal Medicine, Kirk Kerkorian School of Medicine at the University of Nevada, Las Vegas, NV, USA
| | - Shahab Sarmashghi
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nadja Zhakula-Kostadinova
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shu Zhang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yohanna Georgis
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Stephanie H Hoyt
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael S Cuoco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Galen F Gao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Liam F Spurr
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashton C Berger
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gavin Ha
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Veronica Rendo
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Matthew Meyerson
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alison M Taylor
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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138
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Robb TJ, Ward Z, Houseman P, Woodhouse B, Patel R, Fitzgerald S, Tsai P, Lawrence B, Parker K, Print CG, Blenkiron C. Chromosomal Aberrations Accumulate during Metastasis of Virus-Negative Merkel Cell Carcinoma. J Invest Dermatol 2023; 143:1168-1177.e2. [PMID: 36736454 DOI: 10.1016/j.jid.2023.01.015] [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: 10/20/2022] [Revised: 12/13/2022] [Accepted: 01/01/2023] [Indexed: 02/04/2023]
Abstract
Merkel cell carcinoma is a rare, aggressive skin tumor initiated by polyomavirus integration or UV light DNA damage. In New Zealand, there is a propensity toward the UV-driven form (31 of 107, 29% virus positive). Using archival formalin-fixed, paraffin-embedded tissues, we report targeted DNA sequencing covering 246 cancer genes on 71 tumor tissues and 38 nonmalignant tissues from 37 individuals, with 33 of 37 being negative for the virus. Somatic variants of New Zealand virus-negative Merkel cell carcinomas partially overlapped with those reported overseas, including TP53 variants in all tumors and RB1, LRP1B, NOTCH1, and EPHA3/7 variants each found in over half of the cohort. Variants in genes not analyzed or reported in previous studies were also found. Cataloging variants in TP53 and RB1 from published datasets revealed a broad distribution across these genes. Chr 1p gain and Chr 3p loss were identified in around 50% of New Zealand virus-negative Merkel cell carcinomas, and RB1 loss of heterozygosity was found in 90% of cases. Copy number variants accumulate in most metastases. Virus-negative Merkel cell carcinomas have complex combinations of somatic DNA-sequence variants and copy number variants. They likely carry the small genomic changes permissive for metastasis from early tumor development; however, chromosomal alterations may contribute to driving metastatic progression.
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Affiliation(s)
- Tamsin J Robb
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Hosted by the University of Auckland, Auckland, New Zealand
| | - Zoe Ward
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Pascalene Houseman
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Braden Woodhouse
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Department of Oncology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Rachna Patel
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Sandra Fitzgerald
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Hosted by the University of Auckland, Auckland, New Zealand
| | - Peter Tsai
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Hosted by the University of Auckland, Auckland, New Zealand
| | - Ben Lawrence
- Maurice Wilkins Centre for Molecular Biodiscovery, Hosted by the University of Auckland, Auckland, New Zealand; Department of Oncology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Kate Parker
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Department of Oncology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Cristin G Print
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Hosted by the University of Auckland, Auckland, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Hosted by the University of Auckland, Auckland, New Zealand; Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
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139
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Ban D, Housley SN, McDonald JF. The Clinical Significance of Genetic Variation in Ovarian Cancer. Int J Mol Sci 2023; 24:10823. [PMID: 37446001 DOI: 10.3390/ijms241310823] [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: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Genetic variation is a well-known contributor to the onset and progression of cancer. The goal of this study is to provide a comprehensive examination of the nucleotide and chromosomal variation associated with the onset and progression of serous ovarian cancer. Using a variety of computational and statistical methods, we examine the exome sequence profiles of genetic variants present in the primary tumors of 432 ovarian cancer patient samples to compute: (1) the tumor mutational burden for all genes and (2) the chromosomal copy number alterations associated with the onset/progression of ovarian cancer. Tumor mutational burden is reduced in the late vs. early stages, with the highest levels being associated with loss-of-function mutations in DNA-repair genes. Nucleotide variation and copy number alterations associated with known cancer driver genes are selectively favored over ovarian cancer development. The results indicate that genetic variation is a significant contributor to the onset and progression of ovarian cancer. The measurement of the relative levels of genetic variation associated with individual ovarian cancer patient tumors may be a clinically valuable predictor of potential tumor aggressiveness and resistance to chemotherapy. Tumors found to be associated with high levels of genetic variation may help in the clinical identification of high-risk ovarian cancer patients who could benefit from more frequent monitoring.
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Affiliation(s)
- Dongjo Ban
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - Stephen N Housley
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - John F McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
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140
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Qiu MZ, Chen Q, Zheng DY, Zhao Q, Wu QN, Zhou ZW, Yang LQ, Luo QY, Sun YT, Lai MY, Yuan SS, Wang FH, Luo HY, Wang F, Li YH, Zhang HZ, Xu RH. Precise microdissection of gastric mixed adeno-neuroendocrine carcinoma dissects its genomic landscape and evolutionary clonal origins. Cell Rep 2023; 42:112576. [PMID: 37285266 DOI: 10.1016/j.celrep.2023.112576] [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: 09/22/2022] [Revised: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 06/09/2023] Open
Abstract
Gastric mixed adenoneuroendocrine carcinoma (MANEC) is a clinically aggressive and heterogeneous tumor composed of adenocarcinoma (ACA) and neuroendocrine carcinoma (NEC). The genomic properties and evolutionary clonal origins of MANEC remain unclear. We conduct whole-exome and multiregional sequencing on 101 samples from 33 patients to elucidate their evolutionary paths. We identify four significantly mutated genes, TP53, RB1, APC, and CTNNB1. MANEC resembles chromosomal instability stomach adenocarcinoma in that whole-genome doubling in MANEC is predominant and occurs earlier than most copy-number losses. All tumors are of monoclonal origin, and NEC components show more aggressive genomic properties than their ACA counterparts. The phylogenetic trees show two tumor divergence patterns, including sequential and parallel divergence. Furthermore, ACA-to-NEC rather than NEC-to-ACA transition is confirmed by immunohistochemistry on 6 biomarkers in ACA- and NEC-dominant regions. These results provide insights into the clonal origin and tumor differentiation of MANEC.
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Affiliation(s)
- Miao-Zhen Qiu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Qingjian Chen
- Department of Basic Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China; State Key Laboratory of Systems Medicine for Cancer, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Dan-Yang Zheng
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China; Department of Clinical Oncology, LKS Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Qi Zhao
- Department of Basic Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Qi-Nian Wu
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Zhi-Wei Zhou
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Li-Qiong Yang
- Department of Basic Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Qiu-Yun Luo
- Department of Basic Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Yu-Ting Sun
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Ming-Yu Lai
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Sha-Sha Yuan
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Feng-Hua Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Hui-Yan Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Feng Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Yu-Hong Li
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Hui-Zhong Zhang
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China.
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141
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Alfieri F, Caravagna G, Schaefer MH. Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions. Nat Commun 2023; 14:3594. [PMID: 37328455 PMCID: PMC10276008 DOI: 10.1038/s41467-023-39313-8] [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: 09/27/2022] [Accepted: 06/01/2023] [Indexed: 06/18/2023] Open
Abstract
Cancers evolve under the accumulation of thousands of somatic mutations and chromosomal aberrations. While most coding mutations are deleterious, almost all protein-coding genes lack detectable signals of negative selection. This raises the question of how tumors tolerate such large amounts of deleterious mutations. Using 8,690 tumor samples from The Cancer Genome Atlas, we demonstrate that copy number amplifications frequently cover haploinsufficient genes in mutation-prone regions. This could increase tolerance towards the deleterious impact of mutations by creating safe copies of wild-type regions and, hence, protecting the genes therein. Our findings demonstrate that these potential buffering events are highly influenced by gene functions, essentiality, and mutation impact and that they occur early during tumor evolution. We show how cancer type-specific mutation landscapes drive copy number alteration patterns across cancer types. Ultimately, our work paves the way for the detection of novel cancer vulnerabilities by revealing genes that fall within amplifications likely selected during evolution to mitigate the effect of mutations.
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Affiliation(s)
- Fabio Alfieri
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, 34127, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, 20139, Italy.
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142
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Martínez-Jiménez F, Movasati A, Brunner SR, Nguyen L, Priestley P, Cuppen E, Van Hoeck A. Pan-cancer whole-genome comparison of primary and metastatic solid tumours. Nature 2023; 618:333-341. [PMID: 37165194 PMCID: PMC10247378 DOI: 10.1038/s41586-023-06054-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Metastatic cancer remains an almost inevitably lethal disease1-3. A better understanding of disease progression and response to therapies therefore remains of utmost importance. Here we characterize the genomic differences between early-stage untreated primary tumours and late-stage treated metastatic tumours using a harmonized pan-cancer analysis (or reanalysis) of two unpaired primary4 and metastatic5 cohorts of 7,108 whole-genome-sequenced tumours. Metastatic tumours in general have a lower intratumour heterogeneity and a conserved karyotype, displaying only a modest increase in mutations, although frequencies of structural variants are elevated overall. Furthermore, highly variable tumour-specific contributions of mutational footprints of endogenous (for example, SBS1 and APOBEC) and exogenous mutational processes (for example, platinum treatment) are present. The majority of cancer types had either moderate genomic differences (for example, lung adenocarcinoma) or highly consistent genomic portraits (for example, ovarian serous carcinoma) when comparing early-stage and late-stage disease. Breast, prostate, thyroid and kidney renal clear cell carcinomas and pancreatic neuroendocrine tumours are clear exceptions to the rule, displaying an extensive transformation of their genomic landscape in advanced stages. Exposure to treatment further scars the tumour genome and introduces an evolutionary bottleneck that selects for known therapy-resistant drivers in approximately half of treated patients. Our data showcase the potential of pan-cancer whole-genome analysis to identify distinctive features of late-stage tumours and provide a valuable resource to further investigate the biological basis of cancer and resistance to therapies.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Ali Movasati
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sascha Remy Brunner
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Luan Nguyen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Peter Priestley
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Edwin Cuppen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
- Hartwig Medical Foundation, Amsterdam, The Netherlands.
| | - Arne Van Hoeck
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
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143
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Huang SC, Chang IYF, Chang CJ, Liu H, Chen KH, Liu TT, Hsieh TY, Chuang HC, Chen CC, Lin IC, Ng KF, Huang HY, Chen TC. Association between hepatic angiosarcoma and end-stage renal disease: nationwide population-based evidence and enriched mutational signature of aristolochic acid exposure. J Pathol 2023; 260:165-176. [PMID: 36815532 DOI: 10.1002/path.6072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 01/31/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Hepatic angiosarcoma (HAS) is an aggressive mesenchymal malignancy that remains underexplored with respect to its etiology and mutational landscapes. To clarify the association between HAS and end-stage renal disease (ESRD), we used nationwide data of the National Health Insurance Research Database (NHIRD) in Taiwan, covering ~99% of the population, from 2001 to 2016. To investigate molecular signatures, we performed whole-exome sequencing (WES) in 27 surgical specimens, including nine ESRD-associated cases. The NHIRD analysis demonstrated that HAS ranked second among all angiosarcomas in Taiwan, with the incidence rates of HAS being 0.08, 2.49, and 5.71 per 100,000 person-years in the general population, chronic kidney disease (CKD), and ESRD patients, respectively. The standardized incidence ratios of HAS in CKD and ESRD patients were 29.99 and 68.77, respectively. In comparison with nonhepatic angiosarcoma, the multivariate regression analysis of our institutional cohort confirmed CKD/ESRD as an independent risk factor for HAS (odds ratio: 9.521, 95% confidence interval: 2.995-30.261, p < 0.001). WES identified a high tumor mutation burden (TMB; median: 8.66 variants per megabase) and dominant A:T-to-T:A transversion in HAS with frequent TP53 (81%) and ATRX (41%) mutations, KDR amplifications/gains (56%), and CDKN2A/B deletions (48%). Notably, ESRD-associated HAS had a significantly higher TMB (17.62 variants per megabase, p = 0.01) and enriched mutational signatures of aristolochic acid exposure (COSMIC SBS22, p < 0.001). In summary, a significant proportion of HAS in Taiwan is associated with ESRD and harbors a distinctive mutational signature, which concomitantly links nephrotoxicity and mutagenesis resulting from exposure to aristolochic acid or related compounds. A high TMB may support the eligibility for immunotherapy in treating ESRD-associated HAS. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Shih-Chiang Huang
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Neurosurgery, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Chee-Jen Chang
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Services Center for Health Information, Chang Gung University, Taoyuan, Taiwan
- Clinical Informatics and Medical Statistics Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Department of Cardiology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsuan Liu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Kuang-Hua Chen
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Ting-Ting Liu
- Department of Anatomical Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
- Department of Medical Laboratory Science, I-Shou University, Kaohsiung, Taiwan
| | - Tsan-Yu Hsieh
- Department of Anatomic Pathology, Keelung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Keelung, Taiwan
| | - Huei-Chieh Chuang
- Department of Anatomic Pathology, Chiayi Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Chiayi, Taiwan
| | - Chien-Cheng Chen
- Department of Radiology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - I-Chieh Lin
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Kwai-Fong Ng
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsuan-Ying Huang
- Department of Anatomical Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
| | - Tse-Ching Chen
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
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144
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Kumar S, Gerstein M. Unified views on variant impact across many diseases. Trends Genet 2023; 39:442-450. [PMID: 36858880 PMCID: PMC10192142 DOI: 10.1016/j.tig.2023.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 03/03/2023]
Abstract
Genomic studies of human disorders are often performed by distinct research communities (i.e., focused on rare diseases, common diseases, or cancer). Despite underlying differences in the mechanistic origin of different disease categories, these studies share the goal of identifying causal genomic events that are critical for the clinical manifestation of the disease phenotype. Moreover, these studies face common challenges, including understanding the complex genetic architecture of the disease, deciphering the impact of variants on multiple scales, and interpreting noncoding mutations. Here, we highlight these challenges in depth and argue that properly addressing them will require a more unified vocabulary and approach across disease communities. Toward this goal, we present a unified perspective on relating variant impact to various genomic disorders.
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Affiliation(s)
- Sushant Kumar
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics & Data Science, Yale University, New Haven, CT 06520, USA.
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145
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Dehner CA, Geiersbach K, Rowsey R, Murugan P, Broski SM, Meis JM, Rosenberg AE, Folpe AL. Rhabdomyosarcoma Arising in Inflammatory Rhabdomyoblastic Tumor: A Genetically Distinctive Subtype of Rhabdomyosarcoma. Mod Pathol 2023; 36:100131. [PMID: 36966552 DOI: 10.1016/j.modpat.2023.100131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/05/2023] [Indexed: 03/03/2023]
Abstract
"Inflammatory rhabdomyoblastic tumor" (IRMT) is a recently coined name for a distinctive soft tissue neoplasm characterized by slow growth, a dense histiocytic infiltrate, scattered, bizarre-appearing tumor cells with morphologic and immunohistochemical evidence of skeletal muscle differentiation, a near-haploid karyotype with retained biparental disomy of chromosomes 5 and 22, and usually indolent behavior. There are 2 reports of rhabdomyosarcoma (RMS) arising in IRMT. We studied the clinicopathologic and cytogenomic features of 6 cases of IRMT with progression to RMS. Tumors occurred in the extremities of 5 men and 1 woman (median patient age, 50 years; median tumor size, 6.5 cm). Clinical follow-up (6 patients: median, 11 months; range 4-163 months) documented local recurrence and distant metastases in 1 and 5 of 6 patients, respectively. Therapy included complete surgical resection (4 patients) and adjuvant/neoadjuvant chemo/radiotherapy (6 patients). One patient died of disease, 4 were alive with metastatic disease, and one was without evidence of disease. All primary tumors contained conventional IRMT. Progression to RMS appeared as follows: (1) overgrowth of monomorphic rhabdomyoblasts with diminished histiocytes, (2) monomorphic spindle cell morphology with variably pleomorphic rhabdomyoblasts and low mitotic activity, or (3) morphologically undifferentiated spindle cell and epithelioid sarcoma. All but one were diffusely desmin-positive, with more limited MyoD1/myogenin expression. All RMS arising in IRMT, either primary or metastatic, demonstrated widespread loss of heterozygosity with retained heterozygosity of chromosomes 5 and 20, and all but one displayed additional gains and losses involving loci containing oncogenes/ tumor suppressor genes, most often CDKN2A and CDKN2B. RMS arising in IRMT have unique clinicopathologic and cytogenomic features, warranting classification as a distinct, potentially aggressive RMS subtype. It should be distinguished from other RMSs, particularly fusion-driven spindle cell RMS and pleomorphic RMS.
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Affiliation(s)
- Carina A Dehner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Katherine Geiersbach
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ross Rowsey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | | | - Jeanne M Meis
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew E Rosenberg
- Department of Pathology, Miller School of Medicine, University of Miami, Miami Florida
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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146
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Zhu X, Zhao W, Zhou Z, Gu X. Unraveling the Drivers of Tumorigenesis in the Context of Evolution: Theoretical Models and Bioinformatics Tools. J Mol Evol 2023:10.1007/s00239-023-10117-0. [PMID: 37246992 DOI: 10.1007/s00239-023-10117-0] [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: 12/30/2022] [Accepted: 05/09/2023] [Indexed: 05/30/2023]
Abstract
Cancer originates from somatic cells that have accumulated mutations. These mutations alter the phenotype of the cells, allowing them to escape homeostatic regulation that maintains normal cell numbers. The emergence of malignancies is an evolutionary process in which the random accumulation of somatic mutations and sequential selection of dominant clones cause cancer cells to proliferate. The development of technologies such as high-throughput sequencing has provided a powerful means to measure subclonal evolutionary dynamics across space and time. Here, we review the patterns that may be observed in cancer evolution and the methods available for quantifying the evolutionary dynamics of cancer. An improved understanding of the evolutionary trajectories of cancer will enable us to explore the molecular mechanism of tumorigenesis and to design tailored treatment strategies.
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Affiliation(s)
- Xunuo Zhu
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenyi Zhao
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China.
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China.
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
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147
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Zhang W, Xiang X, Zhao B, Huang J, Yang L, Zeng Y. Identifying Cancer Driver Pathways Based on the Mouth Brooding Fish Algorithm. ENTROPY (BASEL, SWITZERLAND) 2023; 25:841. [PMID: 37372185 DOI: 10.3390/e25060841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/05/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Identifying the driver genes of cancer progression is of great significance in improving our understanding of the causes of cancer and promoting the development of personalized treatment. In this paper, we identify the driver genes at the pathway level via an existing intelligent optimization algorithm, named the Mouth Brooding Fish (MBF) algorithm. Many methods based on the maximum weight submatrix model to identify driver pathways attach equal importance to coverage and exclusivity and assign them equal weight, but those methods ignore the impact of mutational heterogeneity. Here, we use principal component analysis (PCA) to incorporate covariate data to reduce the complexity of the algorithm and construct a maximum weight submatrix model considering different weights of coverage and exclusivity. Using this strategy, the unfavorable effect of mutational heterogeneity is overcome to some extent. Data involving lung adenocarcinoma and glioblastoma multiforme were tested with this method and the results compared with the MDPFinder, Dendrix, and Mutex methods. When the driver pathway size was 10, the recognition accuracy of the MBF method reached 80% in both datasets, and the weight values of the submatrix were 1.7 and 1.89, respectively, which are better than those of the compared methods. At the same time, in the signal pathway enrichment analysis, the important role of the driver genes identified by our MBF method in the cancer signaling pathway is revealed, and the validity of these driver genes is demonstrated from the perspective of their biological effects.
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Affiliation(s)
- Wei Zhang
- College of Computer Science and Engineering, Changsha University, Changsha 410022, China
- Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha 410022, China
| | - Xiaowen Xiang
- College of Computer Science and Engineering, Changsha University, Changsha 410022, China
| | - Bihai Zhao
- College of Computer Science and Engineering, Changsha University, Changsha 410022, China
- Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha 410022, China
| | - Jianlin Huang
- College of Computer Science and Engineering, Changsha University, Changsha 410022, China
| | - Lan Yang
- College of Computer Science and Engineering, Changsha University, Changsha 410022, China
| | - Yifu Zeng
- College of Computer Science and Engineering, Changsha University, Changsha 410022, China
- Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha 410022, China
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148
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Embaby A, Kutzera J, Geenen JJ, Pluim D, Hofland I, Sanders J, Lopez-Yurda M, Beijnen JH, Huitema ADR, Witteveen PO, Steeghs N, van Haaften G, van Vugt MATM, de Ridder J, Opdam FL. WEE1 inhibitor adavosertib in combination with carboplatin in advanced TP53 mutated ovarian cancer: A biomarker-enriched phase II study. Gynecol Oncol 2023; 174:239-246. [PMID: 37236033 DOI: 10.1016/j.ygyno.2023.05.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
OBJECTIVE In the first part of this phase II study (NCT01164995), the combination of carboplatin and adavosertib (AZD1775) was shown to be safe and effective in patients with TP53 mutated platinum-resistant ovarian cancer (PROC). Here, we present the results of an additional safety and efficacy cohort and explore predictive biomarkers for resistance and response to this combination treatment. METHODS This is a phase II, open-label, non-randomized study. Patients with TP53 mutated PROC received carboplatin AUC 5 mg/ ml·min intravenously and adavosertib 225 mg BID orally for 2.5 days in a 21-day cycle. The primary objective is to determine the efficacy and safety of carboplatin and adavosertib. Secondary objectives include progression-free survival (PFS), changes in circulating tumor cells (CTC) and exploration of genomic alterations. RESULTS Thirty-two patients with a median age of 63 years (39-77 years) were enrolled and received treatment. Twenty-nine patients were evaluable for efficacy. Bone marrow toxicity, nausea and vomiting were the most common adverse events. Twelve patients showed partial response (PR) as best response, resulting in an objective ORR of 41% in the evaluable patients (95% CI: 23%-61%). The median PFS was 5.6 months (95% CI: 3.8-10.3). In patients with tumors harboring CCNE1 amplification, treatment efficacy was slightly but not significantly better. CONCLUSIONS Adavosertib 225 mg BID for 2.5 days and carboplatin AUC 5 could be safely combined and showed anti-tumor efficacy in patients with PROC. However, bone marrow toxicity remains a point of concern, since this is the most common reason for dose reductions and dose delays.
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Affiliation(s)
- Alaa Embaby
- Department of Clinical Pharmacology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.
| | - Joachim Kutzera
- Department of Genetics, Utrecht University, Utrecht, the Netherlands
| | - Jill J Geenen
- Department of Clinical Pharmacology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Dick Pluim
- Department of Clinical Pharmacology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Ingrid Hofland
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Marta Lopez-Yurda
- Biometrics Department, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Jos H Beijnen
- Department of Clinical Pharmacology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands; Department of Pharmacy, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Alwin D R Huitema
- Department of Clinical Pharmacology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands; Department of Pharmacy, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Pharmacology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Petronella O Witteveen
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Neeltje Steeghs
- Department of Medical Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Gijs van Haaften
- Department of Genetics, Utrecht University, Utrecht, the Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Frans L Opdam
- Department of Medical Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
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149
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Amodeo V, Davies T, Martinez-Segura A, Clements MP, Ragdale HS, Bailey A, Dos Santos MS, MacRae JI, Mokochinski J, Kramer H, Garcia-Diaz C, Gould AP, Marguerat S, Parrinello S. Diet suppresses glioblastoma initiation in mice by maintaining quiescence of mutation-bearing neural stem cells. Dev Cell 2023; 58:836-846.e6. [PMID: 37084728 PMCID: PMC10618406 DOI: 10.1016/j.devcel.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 12/09/2021] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
Abstract
Glioblastoma is thought to originate from neural stem cells (NSCs) of the subventricular zone that acquire genetic alterations. In the adult brain, NSCs are largely quiescent, suggesting that deregulation of quiescence maintenance may be a prerequisite for tumor initiation. Although inactivation of the tumor suppressor p53 is a frequent event in gliomagenesis, whether or how it affects quiescent NSCs (qNSCs) remains unclear. Here, we show that p53 maintains quiescence by inducing fatty-acid oxidation (FAO) and that acute p53 deletion in qNSCs results in their premature activation to a proliferative state. Mechanistically, this occurs through direct transcriptional induction of PPARGC1a, which in turn activates PPARα to upregulate FAO genes. Dietary supplementation with fish oil containing omega-3 fatty acids, natural PPARα ligands, fully restores quiescence of p53-deficient NSCs and delays tumor initiation in a glioblastoma mouse model. Thus, diet can silence glioblastoma driver mutations, with important implications for cancer prevention.
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Affiliation(s)
- Valeria Amodeo
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Timothy Davies
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Amalia Martinez-Segura
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Melanie P Clements
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | | | - Andrew Bailey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AA, UK
| | | | - James I MacRae
- The Francis Crick Institute, 1 Midland Road, London NW1 1AA, UK
| | - Joao Mokochinski
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Claudia Garcia-Diaz
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Alex P Gould
- The Francis Crick Institute, 1 Midland Road, London NW1 1AA, UK
| | - Samuel Marguerat
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK.
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Wu X, Chen H, You C, Peng Z. A potential immunotherapeutic and prognostic biomarker for multiple tumors including glioma: SHOX2. Hereditas 2023; 160:21. [PMID: 37170390 PMCID: PMC10173633 DOI: 10.1186/s41065-023-00279-8] [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: 02/13/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Short stature homeobox 2 (SHOX2) is significant gene in the development and progression of multiple types of tumors. Nonetheless, the biological role of SHOX2 within pan-cancer datasets has not been investigated. Thus, comprehensive bioinformatics analyses of pan-cancer datasets were conducted to explore how SHOX2 regulates tumorigenesis. METHODS A variety of tumor datasets and online analytical tools, including SangerBox, TIMER2, LinkedOmic, GEPIA2 and cBioPortal, were applied to explore SHOX2 expression in various tumors. To ascertain the connections between SHOX2 expression and genetic alterations, SHOX2-related genes and tumor immunity, the pan-cancer datasets were examined. In vitro assays were applied to verify the biological functions of SHOX2 in glioma cells via CCK-8, wound healing, Transwell and colony formation assays. RESULTS Analyses found that SHOX2 was overexpressed in multiple cancer types. SHOX2 expression level was significantly correlated with isocitrate dehydrogenase (IDH), 1p/19q, O6-methylguanine DNA methyltransferase (MGMT) status and new types of glioma patients. High mRNA expression levels of SHOX2 were associated with a poor prognosis in multiple tumor patients. KEGG enrichment analysis showed that SHOX2-related genes were associated with cell cycle and DNA damage repair. Genetic alterations of SHOX2 were identified in multiple types of cancers, including duplications and deep mutations. Immune analysis showed that SHOX2 was closely correlated with the tumor mutation burden (TMB), microsatellite instability (MSI), neoantigen and neoantigens and immune checkpoint (ICP) in a variety of tumors and could influence the immunotherapy sensitivity of cancers. CCK-8, wound healing, Transwell and colony formation experiments showed that SHOX2 knockdown inhibited glioma cell proliferation, migration, invasion and colony formation abilities. CONCLUSION SHOX2 was overexpressed in multiple cancer types in TCGA cohort. SHOX2 knockdown inhibited glioma cell proliferation, migration and colony formation ability. Our study showed that SHOX2 may be an immunotherapeutic and promising prognostic biomarker in certain types of tumors.
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Affiliation(s)
- Xiaocong Wu
- Department of Neurosurgery, Sichuan Friendship Hospital, 96 Shangshahepu Street, Jinjiang District, Chengdu, Sichuan, 610066, China
| | - Hui Chen
- Department of Neurosurgery, Sichuan Friendship Hospital, 96 Shangshahepu Street, Jinjiang District, Chengdu, Sichuan, 610066, China
| | - Chao You
- Department of Neurosurgery, West China Hospital, Sichuan University, 37 Guoxue Lane, Wuhou District, Chengdu, Sichuan, 610041, China.
| | - Zongjun Peng
- Department of Neurosurgery, Sichuan Friendship Hospital, 96 Shangshahepu Street, Jinjiang District, Chengdu, Sichuan, 610066, China.
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