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Montorsi L, Pitcher MJ, Zhao Y, Dionisi C, Demonti A, Tull TJ, Dhami P, Ellis RJ, Bishop C, Sanderson JD, Jain S, D'Cruz D, Gibbons DL, Winkler TH, Bemark M, Ciccarelli FD, Spencer J. Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue. Nat Commun 2024; 15:4051. [PMID: 38744839 PMCID: PMC11094119 DOI: 10.1038/s41467-024-48267-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Intestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is incompletely understood. By iterative application of spatial transcriptomics and multiplexed single-cell technologies, we identify that the double negative 2 subset of B cells, previously associated with autoimmune diseases, is present in the subepithelial dome in health. We show that in this location double negative 2 B cells interact with dendritic cells co-expressing the lupus autoantigens DNASE1L3 and C1q and microbicides. We observe that in humans, but not in mice, dendritic cells expressing DNASE1L3 are associated with sampled bacteria but not DNA derived from apoptotic cells. We propose that fundamental features of autoimmune diseases are microbiota-associated, interacting components of normal intestinal immunity.
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Affiliation(s)
- Lucia Montorsi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Michael J Pitcher
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Yuan Zhao
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Chiara Dionisi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Alicia Demonti
- School of Immunology and Microbial Sciences, King's College London, London, UK
- École Normale Supérieure de Lyon, Claude Bernard Lyon 1 University, Lyon, France
| | - Thomas J Tull
- St. John's Institute of Dermatology, King's College London, London, UK
| | - Pawan Dhami
- Genomics Research Platform and Single Cell Laboratory at Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Richard J Ellis
- Advanced Cytometry Platform (Flow Core), Research and Development Department at Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Cynthia Bishop
- Advanced Cytometry Platform (Flow Core), Research and Development Department at Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jeremy D Sanderson
- School of Immunology and Microbial Sciences, King's College London, London, UK
- Department of Gastroenterology, Guy's and St Thomas' Foundation Trust, London, UK
| | - Sahil Jain
- Louise Coote Lupus Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - David D'Cruz
- School of Immunology and Microbial Sciences, King's College London, London, UK
- Louise Coote Lupus Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Deena L Gibbons
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Thomas H Winkler
- Division of Genetics, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Mats Bemark
- Department of Translational Medicine - Human Immunology, Lund University, Malmö, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Jo Spencer
- School of Immunology and Microbial Sciences, King's College London, London, UK.
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2
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Peters CJ, Ang Y, Ciccarelli FD, Coles H, Coleman HG, Contino G, Crosby T, Devonshire G, Eldridge M, Freeman A, Grehan N, McCord M, Nutzinger B, Zamani S, Parsons SL, Petty R, Sharrocks AD, Skipworth RJE, Smyth EC, Soomro I, Underwood TJ, Fitzgerald RC. A decade of the Oesophageal Cancer Clinical and Molecular Stratification Consortium. Nat Med 2024; 30:14-16. [PMID: 38114667 DOI: 10.1038/s41591-023-02676-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Affiliation(s)
- C J Peters
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Y Ang
- Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester, UK
| | - F D Ciccarelli
- Cancer Systems Biology, The Francis Crick Institute, London, UK
| | - H Coles
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - H G Coleman
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - G Contino
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - T Crosby
- Velindre University NHS Trust, Cardiff, UK
| | - G Devonshire
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - M Eldridge
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - A Freeman
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - N Grehan
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - M McCord
- Heartburn Cancer UK, Basingstoke, UK
| | - B Nutzinger
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - S Zamani
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - S L Parsons
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - R Petty
- School of Medicine, University of Dundee, Dundee, UK
| | - A D Sharrocks
- Division of Molecular and Cellular Function, University of Manchester, Manchester, UK
| | | | - E C Smyth
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - I Soomro
- Nottingham University Hospital, Nottingham, UK
| | - T J Underwood
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - R C Fitzgerald
- Early Cancer Institute, University of Cambridge, Cambridge, UK.
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Cheung TS, Giacomini C, Cereda M, Avivar-Valderas A, Capece D, Bertolino GM, delaRosa O, Hicks R, Ciccocioppo R, Franzoso G, Galleu A, Ciccarelli FD, Dazzi F. Apoptosis in mesenchymal stromal cells activates an immunosuppressive secretome predicting clinical response in Crohn's disease. Mol Ther 2023; 31:3531-3544. [PMID: 37805713 PMCID: PMC10727969 DOI: 10.1016/j.ymthe.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/30/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023] Open
Abstract
In vivo apoptosis of human mesenchymal stromal cells (MSCs) plays a critical role in delivering immunomodulation. Yet, caspase activity not only mediates the dying process but also death-independent functions that may shape the immunogenicity of apoptotic cells. Therefore, a better characterization of the immunological profile of apoptotic MSCs (ApoMSCs) could shed light on their mechanistic action and therapeutic applications. We analyzed the transcriptomes of MSCs undergoing apoptosis and identified several immunomodulatory factors and chemokines dependent on caspase activation following Fas stimulation. The ApoMSC secretome inhibited human T cell proliferation and activation, and chemoattracted monocytes in vitro. Both immunomodulatory activities were dependent on the cyclooxygenase2 (COX2)/prostaglandin E2 (PGE2) axis. To assess the clinical relevance of ApoMSC signature, we used the peripheral blood mononuclear cells (PBMCs) from a cohort of fistulizing Crohn's disease (CD) patients who had undergone MSC treatment (ADMIRE-CD). Compared with healthy donors, MSCs exposed to patients' PBMCs underwent apoptosis and released PGE2 in a caspase-dependent manner. Both PGE2 and apoptosis were significantly associated with clinical responses to MSCs. Our findings identify a new mechanism whereby caspase activation delivers ApoMSC immunosuppression. Remarkably, such molecular signatures could implicate translational tools for predicting patients' clinical responses to MSC therapy in CD.
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Affiliation(s)
- Tik Shing Cheung
- School of Cancer and Pharmacological Sciences, King's College London, London, UK
| | - Chiara Giacomini
- School of Cancer and Pharmacological Sciences, King's College London, London, UK; School of Cardiovascular and Metabolic Medicine and Sciences, King's College London, London, UK
| | - Matteo Cereda
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy; Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, TO, Italy
| | | | - Daria Capece
- Centre for Molecular Immunology and Inflammation, Department of Immunology and Inflammation, Imperial College London, London, UK
| | | | - Olga delaRosa
- Takeda Madrid, Cell Therapy Technology Center, Tres Cantos, Spain
| | - Ryan Hicks
- School of Cardiovascular and Metabolic Medicine and Sciences, King's College London, London, UK; BioPharmaceuticals R&D Cell Therapy, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Rachele Ciccocioppo
- Gastroenterology Unit, Department of Medicine, A.O.U.I. Policlinico G.B. Rossi & University of Verona, Verona, Italy
| | - Guido Franzoso
- Centre for Molecular Immunology and Inflammation, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Antonio Galleu
- School of Cancer and Pharmacological Sciences, King's College London, London, UK
| | - Francesca D Ciccarelli
- School of Cancer and Pharmacological Sciences, King's College London, London, UK; Cancer Systems Biology Laboratory, The Francis Crick Institute, London, UK
| | - Francesco Dazzi
- School of Cancer and Pharmacological Sciences, King's College London, London, UK; School of Cardiovascular and Metabolic Medicine and Sciences, King's College London, London, UK; BioPharmaceuticals R&D Cell therapy, AstraZeneca, Cambridge, UK.
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4
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Kazachenka A, Loong JH, Attig J, Young GR, Ganguli P, Devonshire G, Grehan N, Ciccarelli FD, Fitzgerald RC, Kassiotis G. The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes. NAR Cancer 2023; 5:zcad040. [PMID: 37502711 PMCID: PMC10370457 DOI: 10.1093/narcan/zcad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/01/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Most cancer types exhibit aberrant transcriptional activity, including derepression of retrotransposable elements (RTEs). However, the degree, specificity and potential consequences of RTE transcriptional activation may differ substantially among cancer types and subtypes. Representing one extreme of the spectrum, we characterize the transcriptional activity of RTEs in cohorts of esophageal adenocarcinoma (EAC) and its precursor Barrett's esophagus (BE) from the OCCAMS (Oesophageal Cancer Clinical and Molecular Stratification) consortium, and from TCGA (The Cancer Genome Atlas). We found exceptionally high RTE inclusion in the EAC transcriptome, driven primarily by transcription of genes incorporating intronic or adjacent RTEs, rather than by autonomous RTE transcription. Nevertheless, numerous chimeric transcripts straddling RTEs and genes, and transcripts from stand-alone RTEs, particularly KLF5- and SOX9-controlled HERVH proviruses, were overexpressed specifically in EAC. Notably, incomplete mRNA splicing and EAC-characteristic intronic RTE inclusion was mirrored by relative loss of the respective fully-spliced, functional mRNA isoforms, consistent with compromised cellular fitness. Defective RNA splicing was linked with strong transcriptional activation of a HERVH provirus on Chr Xp22.32 and defined EAC subtypes with distinct molecular features and prognosis. Our study defines distinguishable RTE transcriptional profiles of EAC, reflecting distinct underlying processes and prognosis, thus providing a framework for targeted studies.
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Affiliation(s)
| | - Jane Hc Loong
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Jan Attig
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - George R Young
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, UK
| | - Piyali Ganguli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Nicola Grehan
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Rebecca C Fitzgerald
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
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5
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Misetic H, Keddar MR, Jeannon JP, Ciccarelli FD. Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment. Genome Med 2023; 15:40. [PMID: 37277866 DOI: 10.1186/s13073-023-01197-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND The crosstalk between cancer and the tumour immune microenvironment (TIME) has attracted significant interest in the latest years because of its impact on cancer evolution and response to treatment. Despite this, cancer-specific tumour-TIME interactions and their mechanistic insights are still poorly understood. METHODS Here, we compute the significant interactions occurring between cancer-specific genetic drivers and five anti- and pro-tumour TIME features in 32 cancer types using Lasso regularised ordinal regression. Focusing on head and neck squamous cancer (HNSC), we rebuild the functional networks linking specific TIME driver alterations to the TIME state they associate with. RESULTS The 477 TIME drivers that we identify are multifunctional genes whose alterations are selected early in cancer evolution and recur across and within cancer types. Tumour suppressors and oncogenes have an opposite effect on the TIME and the overall anti-tumour TIME driver burden is predictive of response to immunotherapy. TIME driver alterations predict the immune profiles of HNSC molecular subtypes, and perturbations in keratinization, apoptosis and interferon signalling underpin specific driver-TIME interactions. CONCLUSIONS Overall, our study delivers a comprehensive resource of TIME drivers, gives mechanistic insights into their immune-regulatory role, and provides an additional framework for patient prioritisation to immunotherapy. The full list of TIME drivers and associated properties are available at http://www.network-cancer-genes.org .
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Affiliation(s)
- Hrvoje Misetic
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Mohamed Reda Keddar
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Jean-Pierre Jeannon
- Department of Head & Neck Surgery, Great Maze Pond, Guy's Hospital, London, SE1 9RT, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK.
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6
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Rodrigues FS, Ciccarelli FD, Malanchi I. Reflected stemness as a potential driver of the tumour microenvironment. Trends Cell Biol 2022; 32:979-987. [PMID: 35589467 DOI: 10.1016/j.tcb.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 01/21/2023]
Abstract
A fundamental requirement for cancer initiation is the activation of developmental programmes by mutant cells. Oncogenic signals often confer an undifferentiated, stem cell-like phenotype that supports the long-term proliferative potential of cancer cells. Although cancer is a genetically driven disease, mutations in cancer-driver genes alone are insufficient for tumour formation, and the proliferation of cells harbouring oncogenic mutations depends on their microenvironment. In this Opinion article we discuss how the reprogrammed status of cancer cells not only represents the essence of their tumorigenicity but triggers 'reflected stemness' in their surrounding normal counterparts. We propose that this reciprocal interaction underpins the establishment of the tumour microenvironment (TME).
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Affiliation(s)
- Felipe S Rodrigues
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Ilaria Malanchi
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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7
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Gunady EF, Ware KE, Hoskinson Plumlee S, Devos N, Corcoran D, Prinz J, Misetic H, Ciccarelli FD, Harrison TM, Thorne JL, Schopler R, Everitt JI, Eward WC, Somarelli JA. Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study. Evol Med Public Health 2022; 10:221-230. [PMID: 35557512 PMCID: PMC9086584 DOI: 10.1093/emph/eoac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/17/2022] [Indexed: 11/24/2022] Open
Abstract
Background and objectives Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers in this group is unknown. Characterizing the genetic changes associated with hepatocellular carcinoma in prosimians may point to possible causes, treatments and methods of prevention, aiding conservation efforts that are particularly crucial to the survival of endangered lemurs. Although genomic studies of cancer in non-human primates have been hampered by a lack of tools, recent studies have demonstrated the efficacy of using human exome capture reagents across primates. Methodology In this proof-of-principle study, we applied human exome capture reagents to tumor-normal pairs from five lemurs with hepatocellular carcinoma to characterize the mutational landscape of this disease in lemurs. Results Several genes implicated in human hepatocellular carcinoma, including ARID1A, TP53 and CTNNB1, were mutated in multiple lemurs, and analysis of cancer driver genes mutated in these samples identified enrichment of genes involved with TP53 degradation and regulation. In addition to these similarities with human hepatocellular carcinoma, we also noted unique features, including six genes that contain mutations in all five lemurs. Interestingly, these genes are infrequently mutated in human hepatocellular carcinoma, suggesting potential differences in the etiology and/or progression of this cancer in lemurs and humans. Conclusions and implications Collectively, this pilot study suggests that human exome capture reagents are a promising tool for genomic studies of cancer in lemurs and other non-human primates. Lay Summary Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers is unknown. In this proof-of-principle study, we applied human DNA sequencing tools to tumor-normal pairs from five lemurs with hepatocellular carcinoma and compared the lemur mutation profiles to those of human hepatocellular carcinomas.
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Affiliation(s)
- Ella F Gunady
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Kathryn E Ware
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Nicolas Devos
- Duke Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - David Corcoran
- Duke Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joseph Prinz
- Duke Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hrvoje Misetic
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London SE1 1UL, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London SE1 1UL, UK
| | - Tara M Harrison
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
- Exotic Species Cancer Research Alliance, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey L Thorne
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | | | - Jeffrey I Everitt
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Durham, NC 27710, USA
| | - William C Eward
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Durham, NC 27710, USA
| | - Jason A Somarelli
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Durham, NC 27710, USA
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Dressler L, Bortolomeazzi M, Keddar MR, Misetic H, Sartini G, Acha-Sagredo A, Montorsi L, Wijewardhane N, Repana D, Nulsen J, Goldman J, Pollitt M, Davis P, Strange A, Ambrose K, Ciccarelli FD. Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. Genome Biol 2022; 23:35. [PMID: 35078504 PMCID: PMC8790917 DOI: 10.1186/s13059-022-02607-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/10/2022] [Indexed: 12/30/2022] Open
Abstract
Background Genetic alterations of somatic cells can drive non-malignant clone formation and promote cancer initiation. However, the link between these processes remains unclear and hampers our understanding of tissue homeostasis and cancer development. Results Here, we collect a literature-based repertoire of 3355 well-known or predicted drivers of cancer and non-cancer somatic evolution in 122 cancer types and 12 non-cancer tissues. Mapping the alterations of these genes in 7953 pan-cancer samples reveals that, despite the large size, the known compendium of drivers is still incomplete and biased towards frequently occurring coding mutations. High overlap exists between drivers of cancer and non-cancer somatic evolution, although significant differences emerge in their recurrence. We confirm and expand the unique properties of drivers and identify a core of evolutionarily conserved and essential genes whose germline variation is strongly counter-selected. Somatic alteration in even one of these genes is sufficient to drive clonal expansion but not malignant transformation. Conclusions Our study offers a comprehensive overview of our current understanding of the genetic events initiating clone expansion and cancer revealing significant gaps and biases that still need to be addressed. The compendium of cancer and non-cancer somatic drivers, their literature support, and properties are accessible in the Network of Cancer Genes and Healthy Drivers resource at http://www.network-cancer-genes.org/. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02607-z.
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Acha-Sagredo A, Malanchi I, Ciccarelli FD. Clone competition as a mechanism to reduce tumor formation. Dev Cell 2021; 56:3307-3308. [PMID: 34932947 DOI: 10.1016/j.devcel.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
With age, clones carrying somatic mutations in well-known cancer driver genes progressively populate adult tissues, yet cancer transformation is rare. In a recent issue of Nature, Colom et al. showed that competition between mutated clones with different fitness could act as a tumor-protective mechanism.
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Affiliation(s)
- Amelia Acha-Sagredo
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Ilaria Malanchi
- Tumor Host Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK.
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10
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Bortolomeazzi M, Keddar MR, Montorsi L, Acha-Sagredo A, Benedetti L, Temelkovski D, Choi S, Petrov N, Todd K, Wai P, Kohl J, Denner T, Nye E, Goldstone R, Ward S, Wilson GA, Al Bakir M, Swanton C, John S, Miles J, Larijani B, Kunene V, Fontana E, Arkenau HT, Parker PJ, Rodriguez-Justo M, Shiu KK, Spencer J, Ciccarelli FD. Immunogenomics of Colorectal Cancer Response to Checkpoint Blockade: Analysis of the KEYNOTE 177 Trial and Validation Cohorts. Gastroenterology 2021; 161:1179-1193. [PMID: 34197832 PMCID: PMC8527923 DOI: 10.1053/j.gastro.2021.06.064] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/18/2021] [Accepted: 06/22/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer (CRC) shows variable response to immune checkpoint blockade, which can only partially be explained by high tumor mutational burden (TMB). We conducted an integrated study of the cancer tissue and associated tumor microenvironment (TME) from patients treated with pembrolizumab (KEYNOTE 177 clinical trial) or nivolumab to dissect the cellular and molecular determinants of response to anti- programmed cell death 1 (PD1) immunotherapy. METHODS We selected multiple regions per tumor showing variable T-cell infiltration for a total of 738 regions from 29 patients, divided into discovery and validation cohorts. We performed multiregional whole-exome and RNA sequencing of the tumor cells and integrated these with T-cell receptor sequencing, high-dimensional imaging mass cytometry, detection of programmed death-ligand 1 (PDL1) interaction in situ, multiplexed immunofluorescence, and computational spatial analysis of the TME. RESULTS In hypermutated CRCs, response to anti-PD1 immunotherapy was not associated with TMB but with high clonality of immunogenic mutations, clonally expanded T cells, low activation of Wnt signaling, deregulation of the interferon gamma pathway, and active immune escape mechanisms. Responsive hypermutated CRCs were also rich in cytotoxic and proliferating PD1+CD8 T cells interacting with PDL1+ antigen-presenting macrophages. CONCLUSIONS Our study clarified the limits of TMB as a predictor of response of CRC to anti-PD1 immunotherapy. It identified a population of antigen-presenting macrophages interacting with CD8 T cells that consistently segregate with response. We therefore concluded that anti-PD1 agents release the PD1-PDL1 interaction between CD8 T cells and macrophages to promote cytotoxic antitumor activity.
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Affiliation(s)
- Michele Bortolomeazzi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Mohamed Reda Keddar
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Lucia Montorsi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Amelia Acha-Sagredo
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Damjan Temelkovski
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Subin Choi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Nedyalko Petrov
- Biomedical Research Centre, Guy's and St. Thomas' National Health Service Trust, London, United Kingdom
| | - Katrina Todd
- Biomedical Research Centre, Guy's and St. Thomas' National Health Service Trust, London, United Kingdom
| | - Patty Wai
- State-Dependent Neural Processing Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Johannes Kohl
- State-Dependent Neural Processing Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Tamara Denner
- Experimental Histopathology, The Francis Crick Institute, London, United Kingdom
| | - Emma Nye
- Experimental Histopathology, The Francis Crick Institute, London, United Kingdom
| | - Robert Goldstone
- Advanced Sequencing Facility, The Francis Crick Institute, London, United Kingdom
| | - Sophia Ward
- Advanced Sequencing Facility, The Francis Crick Institute, London, United Kingdom
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Susan John
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | | | - Banafshe Larijani
- FASTBASE Solutions S.L, Derio, Spain; Cell Biophysics Laboratory, Ikerbasque, Basque Foundation for Science, Research Centre for Experimental Marine Biology and Biotechnology & Biophysics Institute, University of the Basque Country, Leioa, Bizkaia, Spain; Centre for Therapeutic Innovation, Cell Biophysics Laboratory, Department of Pharmacy and Pharmacology & Department of Physics, University of Bath, Bath, United Kingdom
| | - Victoria Kunene
- Medical Oncology, University Hospitals Birmingham National Health Service Foundation Trust, Birmingham, United Kingdom
| | - Elisa Fontana
- Drug Development Unit, Sarah Cannon Research Institute UK, London, United Kingdom
| | - Hendrik-Tobias Arkenau
- Drug Development Unit, Sarah Cannon Research Institute UK, London, United Kingdom; Department of Oncology, University College Hospital, London, United Kingdom
| | - Peter J Parker
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom; Protein Phosphorylation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Manuel Rodriguez-Justo
- Department of Histopathology, University College London Cancer Institute, London, United Kingdom
| | - Kai-Keen Shiu
- Department of Gastrointestinal Oncology, University College London Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Jo Spencer
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom.
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom.
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11
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Tajadura-Ortega V, Gambardella G, Skinner A, Halim A, Van Coillie J, Schjoldager KTBG, Beatson R, Graham R, Achkova D, Taylor-Papadimitriou J, Ciccarelli FD, Burchell JM. O-linked mucin-type glycosylation regulates the transcriptional programme downstream of EGFR. Glycobiology 2021; 31:200-210. [PMID: 32776095 DOI: 10.1093/glycob/cwaa075] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/23/2020] [Accepted: 07/29/2020] [Indexed: 12/25/2022] Open
Abstract
Aberrant mucin-type O-linked glycosylation is a common occurrence in cancer where the upregulation of sialyltransferases is often seen leading to the early termination of O-glycan chains. Mucin-type O-linked glycosylation is not limited to mucins and occurs on many cell surface glycoproteins including EGFR, where the number of sites can be limited. Upon EGF ligation, EGFR induces a signaling cascade and may also translocate to the nucleus where it directly regulates gene transcription, a process modulated by Galectin-3 and MUC1 in some cancers. Here, we show that upon EGF binding, breast cancer cells carrying different O-glycans respond by transcribing different gene expression signatures. MMP10, the principal gene upregulated when cells carrying sialylated core 1 glycans were stimulated with EGF, is also upregulated in ER-positive breast carcinoma reported to express high levels of ST3Gal1 and hence mainly core 1 sialylated O-glycans. In contrast, isogenic cells engineered to carry core 2 glycans upregulate CX3CL1 and FGFBP1 and these genes are upregulated in ER-negative breast carcinomas, also known to express longer core 2 O-glycans. Changes in O-glycosylation did not significantly alter signal transduction downstream of EGFR in core 1 or core 2 O-glycan expressing cells. However, striking changes were observed in the formation of an EGFR/galectin-3/MUC1/β-catenin complex at the cell surface that is present in cells carrying short core 1-based O-glycans but absent in core 2 carrying cells.
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Affiliation(s)
- Virginia Tajadura-Ortega
- Breast Cancer Biology Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London SE1 9RT, UK
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Burlington Danes Building, Du Cane Road, London W12 0NN, UK
| | - Gennaro Gambardella
- Department of Chemical Materials and Industrial Engineering, University of Naples Federico II, 1-80125 Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Alexandra Skinner
- Breast Cancer Biology Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London SE1 9RT, UK
| | - Adnan Halim
- Functional and Cellular Glycobiology, Glycomics Programme, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julie Van Coillie
- Functional and Cellular Glycobiology, Glycomics Programme, University of Copenhagen, Copenhagen DK-2200, Denmark
| | | | - Richard Beatson
- Breast Cancer Biology Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London SE1 9RT, UK
| | - Rosalind Graham
- Breast Cancer Biology Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London SE1 9RT, UK
| | - Daniela Achkova
- CAR Mechanics Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London SE1 9RT, UK
- Autolus Ltd. Forest House, 58 Wood Ln, White City, London W12 7RZ, UK
| | - Joyce Taylor-Papadimitriou
- Breast Cancer Biology Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London SE1 9RT, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, Francis Crick Institute, London NW1 1AT, UK
- CRUK King's Health Partner Centre, King's College London, London SE1 9RT, UK
| | - Joy M Burchell
- Breast Cancer Biology Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London SE1 9RT, UK
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12
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Abstract
Gene alterations play a prominent role in driving cancer initiation and progression. However, the genetic events that occur in normal cells prior to tumorigenesis are still unknown. Recent studies have started to map somatic mutations in normal human tissues, and here we discuss their implications for our understanding of tumorigenesis.
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Affiliation(s)
- Neshika Wijewardhane
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Lisa Dressler
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK; Department of Medical and Molecular Genetics, King's College London, London WC2R 2LS, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK.
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13
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Abstract
BACKGROUND Identifying the complete repertoire of genes that drive cancer in individual patients is crucial for precision oncology. Most established methods identify driver genes that are recurrently altered across patient cohorts. However, mapping these genes back to patients leaves a sizeable fraction with few or no drivers, hindering our understanding of cancer mechanisms and limiting the choice of therapeutic interventions. RESULTS We present sysSVM2, a machine learning software that integrates cancer genetic alterations with gene systems-level properties to predict drivers in individual patients. Using simulated pan-cancer data, we optimise sysSVM2 for application to any cancer type. We benchmark its performance on real cancer data and validate its applicability to a rare cancer type with few known driver genes. We show that drivers predicted by sysSVM2 have a low false-positive rate, are stable and disrupt well-known cancer-related pathways. CONCLUSIONS sysSVM2 can be used to identify driver alterations in patients lacking sufficient canonical drivers or belonging to rare cancer types for which assembling a large enough cohort is challenging, furthering the goals of precision oncology. As resources for the community, we provide the code to implement sysSVM2 and the pre-trained models in all TCGA cancer types ( https://github.com/ciccalab/sysSVM2 ).
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Affiliation(s)
- Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 1UL, UK
| | - Hrvoje Misetic
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 1UL, UK
| | - Christopher Yau
- School of Health Sciences, University of Manchester, Manchester, M13 9PL, UK
- The Alan Turing Institute, London, NW1 2DB, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 1UL, UK.
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14
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Abstract
Dr Francesca Ciccarelli (The Francis Crick Institute, UK) and Dr James De Gregori (University of Colorado, USA) interview 3 top scientists in clinical (Dr Charles Swanton, The Francis Crick Institute, UK), molecular (Dr Kornelia Polyak, Dana-Farber Cancer Institute, USA), and evolutionary cancer research (Dr Carlo Maley, Arizona State University, USA) to discuss the current status of knowledge, the challenges, and the opportunities to move the field forward.
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Affiliation(s)
- Francesca D. Ciccarelli
- Cancer Systems Biology Laboratory, the Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, U S A
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15
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Bortolomeazzi M, Keddar MR, Ciccarelli FD, Benedetti L. Identification of non-cancer cells from cancer transcriptomic data. Biochim Biophys Acta Gene Regul Mech 2020; 1863:194445. [PMID: 31654804 PMCID: PMC7346884 DOI: 10.1016/j.bbagrm.2019.194445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Interactions between cancer cells and non-cancer cells composing the tumour microenvironment play a primary role in determining cancer progression and shaping the response to therapy. The qualitative and quantitative characterisation of the different cell populations in the tumour microenvironment is therefore crucial to understand its role in cancer. In recent years, many experimental and computational approaches have been developed to identify the cell populations composing heterogeneous tissue samples, such as cancer. In this review, we describe the state-of-the-art approaches for the quantification of non-cancer cells from bulk and single-cell cancer transcriptomic data, with a focus on immune cells. We illustrate the main features of these approaches and highlight their applications for the analysis of the tumour microenvironment in solid cancers. We also discuss techniques that are complementary and alternative to RNA sequencing, particularly focusing on approaches that can provide spatial information on the distribution of the cells within the tumour in addition to their qualitative and quantitative measurements. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Michele Bortolomeazzi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK
| | - Mohamed Reda Keddar
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK.
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK.
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16
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Owusu M, Bannauer P, Ferreira da Silva J, Mourikis TP, Jones A, Májek P, Caldera M, Wiedner M, Lardeau CH, Mueller AC, Menche J, Kubicek S, Ciccarelli FD, Loizou JI. Mapping the Human Kinome in Response to DNA Damage. Cell Rep 2020; 26:555-563.e6. [PMID: 30650350 DOI: 10.1016/j.celrep.2018.12.087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/31/2018] [Accepted: 12/18/2018] [Indexed: 01/02/2023] Open
Abstract
We provide a catalog for the effects of the human kinome on cell survival in response to DNA-damaging agents, covering all major DNA repair pathways. By treating 313 kinase-deficient cell lines with ten diverse DNA-damaging agents, including seven commonly used chemotherapeutics, we identified examples of vulnerability and resistance that are kinase specific. To investigate synthetic lethal interactions, we tested the response to carmustine for 25 cell lines by establishing a phenotypic fluorescence-activated cell sorting (FACS) assay designed to validate gene-drug interactions. We show apoptosis, cell cycle changes, and DNA damage and proliferation after alkylation- or crosslink-induced damage. In addition, we reconstitute the cellular sensitivity of DYRK4, EPHB6, MARK3, and PNCK as a proof of principle for our study. Furthermore, using global phosphoproteomics on cells lacking MARK3, we provide evidence for its role in the DNA damage response. Our data suggest that cancers with inactivating mutations in kinases, including MARK3, are particularly vulnerable to alkylating chemotherapeutic agents.
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Affiliation(s)
- Michel Owusu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Peter Bannauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Joana Ferreira da Silva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Thanos P Mourikis
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Alistair Jones
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Michael Caldera
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Marc Wiedner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Charles-Hugues Lardeau
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - André C Mueller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
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17
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Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk JN, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular Biology and Evolution of Cancer: From Discovery to Action. Mol Biol Evol 2020; 37:320-326. [PMID: 31642480 PMCID: PMC6993850 DOI: 10.1093/molbev/msz242] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understanding of the underlying molecular evolutionary processes. Herein we discuss a suite of concepts and tools from evolutionary and ecological theory that can inform cancer biology in new and meaningful ways. We also highlight current challenges to applying these concepts, and propose ways in which incorporating these concepts could identify new therapeutic modes and vulnerabilities in cancer.
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Affiliation(s)
- Jason A Somarelli
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Heather Gardner
- Sackler School of Graduate Biomedical Sciences, Tufts University, Medford, MA
| | | | - Ella F Gunady
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Amy M Boddy
- Department of Anthropology, University of California, Santa Barbara, CA
| | | | | | - Stephen G Gaffney
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
| | | | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom
- King’s College London, London, United Kingdom
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, Kingston, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Kate Megquier
- Broad Institute, Massachusettes Institute of Technology and Harvard University
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, and Department of Biology, Temple University, Philadelphia, PA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
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18
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Catapano M, Vergnano M, Romano M, Mahil SK, Choon SE, Burden AD, Young HS, Carr IM, Lachmann HJ, Lombardi G, Smith CH, Ciccarelli FD, Barker JN, Capon F. IL-36 Promotes Systemic IFN-I Responses in Severe Forms of Psoriasis. J Invest Dermatol 2019; 140:816-826.e3. [PMID: 31539532 PMCID: PMC7097848 DOI: 10.1016/j.jid.2019.08.444] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/24/2019] [Accepted: 08/06/2019] [Indexed: 12/16/2022]
Abstract
Psoriasis is an immune-mediated skin disorder associated with severe systemic comorbidities. Whereas IL-36 is a key disease driver, the pathogenic role of this cytokine has mainly been investigated in skin. Thus, its effects on systemic immunity and extracutaneous disease manifestations remain poorly understood. To address this issue, we investigated the consequences of excessive IL-36 activity in circulating immune cells. We initially focused our attention on generalized pustular psoriasis (GPP), a clinical variant associated with pervasive upregulation of IL-36 signaling. By undertaking blood and neutrophil RNA sequencing, we demonstrated that affected individuals display a prominent IFN-I signature, which correlates with abnormal IL-36 activity. We then validated the association between IL-36 deregulation and IFN-I over-expression in patients with severe psoriasis vulgaris (PV). We also found that the activation of IFN-I genes was associated with extracutaneous morbidity, in both GPP and PV. Finally, we undertook mechanistic experiments, demonstrating that IL-36 acts directly on plasmacytoid dendritic cells, where it potentiates toll-like receptor (TLR)-9 activation and IFN-α production. This effect was mediated by the upregulation of PLSCR1, a phospholipid scramblase mediating endosomal TLR-9 translocation. These findings identify an IL-36/ IFN-I axis contributing to extracutaneous inflammation in psoriasis.
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Affiliation(s)
- Marika Catapano
- Department of Medical and Molecular Genetics, School of Basic & Medical Biosciences, King's College London, London, United Kingdom
| | - Marta Vergnano
- Department of Medical and Molecular Genetics, School of Basic & Medical Biosciences, King's College London, London, United Kingdom
| | - Marco Romano
- Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Satveer K Mahil
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, London, United Kingdom
| | - Siew-Eng Choon
- Department of Dermatology, Sultanah Aminah Hospital, Johor Bahru, Malaysia
| | - A David Burden
- Department of Dermatology, University of Glasgow, Glasgow, United Kingdom
| | - Helen S Young
- Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, United Kingdom
| | - Ian M Carr
- School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Helen J Lachmann
- National Amyloidosis Centre and Centre for Acute Phase Proteins, Division of Medicine, University College London, London, United Kingdom
| | - Giovanna Lombardi
- Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Catherine H Smith
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, London, United Kingdom
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom; School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Jonathan N Barker
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, London, United Kingdom
| | - Francesca Capon
- Department of Medical and Molecular Genetics, School of Basic & Medical Biosciences, King's College London, London, United Kingdom.
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19
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Mourikis TP, Benedetti L, Foxall E, Temelkovski D, Nulsen J, Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald RC, Scaffidi P, Ciccarelli FD. Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. Nat Commun 2019; 10:3101. [PMID: 31308377 PMCID: PMC6629660 DOI: 10.1038/s41467-019-10898-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/04/2019] [Indexed: 12/25/2022] Open
Abstract
The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy.
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Affiliation(s)
- Thanos P Mourikis
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Elizabeth Foxall
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Damjan Temelkovski
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Juliane Perner
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Matteo Cereda
- Italian Institute for Genomic Medicine (IIGM), Turin, 10126, Italy
| | - Jesper Lagergren
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK.
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20
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Repana D, Nulsen J, Dressler L, Bortolomeazzi M, Venkata SK, Tourna A, Yakovleva A, Palmieri T, Ciccarelli FD. The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. Genome Biol 2019; 20:1. [PMID: 30606230 PMCID: PMC6317252 DOI: 10.1186/s13059-018-1612-0] [Citation(s) in RCA: 336] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34,905 cancer donors and multiple primary sites. This represents a more than 1.5-fold content increase compared to the previous version. NCG also annotates properties of cancer genes, such as duplicability, evolutionary origin, RNA and protein expression, miRNA and protein interactions, and protein function and essentiality. NCG is accessible at http://ncg.kcl.ac.uk/ .
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Affiliation(s)
- Dimitra Repana
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Lisa Dressler
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Michele Bortolomeazzi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Santhilata Kuppili Venkata
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Aikaterini Tourna
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Anna Yakovleva
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Tommaso Palmieri
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Francesca D. Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
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21
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22
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Mahil SK, Catapano M, Di Meglio P, Dand N, Ahlfors H, Carr IM, Smith CH, Trembath RC, Peakman M, Wright J, Ciccarelli FD, Barker JN, Capon F. An analysis of IL-36 signature genes and individuals with IL1RL2 knockout mutations validates IL-36 as a psoriasis therapeutic target. Sci Transl Med 2018; 9:9/411/eaan2514. [PMID: 29021166 DOI: 10.1126/scitranslmed.aan2514] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/16/2017] [Accepted: 08/21/2017] [Indexed: 12/13/2022]
Abstract
Interleukin (IL)-36α, IL-36β, and IL-36γ are innate mediators of acute epithelial inflammation. We sought to demonstrate that these cytokines are also required for the pathogenesis of plaque psoriasis, a common and chronic skin disorder, caused by abnormal T helper 17 (TH17) cell activation. To investigate this possibility, we first defined the genes that are induced by IL-36 cytokines in primary human keratinocytes. This enabled us to demonstrate a significant IL-36 signature among the transcripts that are up-regulated in plaque psoriasis and the susceptibility loci associated with the disease in genome-wide studies. Next, we investigated the impact of in vivo and ex vivo IL-36 receptor blockade using a neutralizing antibody or a recombinant antagonist. Both inhibitors had marked anti-inflammatory effects on psoriatic skin, demonstrated by statistically significant reductions in IL-17 expression, keratinocyte activation, and leukocyte infiltration. Finally, we explored the potential safety profile associated with IL-36 blockade by phenotyping 12 individuals carrying knockout mutations of the IL-36 receptor gene. We found that normal immune function was broadly preserved in these individuals, suggesting that IL-36 signaling inhibition would not substantially compromise host defenses. These observations, which integrate the results of transcriptomics and model system analysis, pave the way for early-stage clinical trials of IL-36 antagonists.
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Affiliation(s)
- Satveer K Mahil
- Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK
| | - Marika Catapano
- Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK.,Cancer Systems Biology Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Paola Di Meglio
- Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK.,AhRimmunity Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Nick Dand
- Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK
| | - Helena Ahlfors
- UCL Institute of Child Health, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Ian M Carr
- School of Medicine, University of Leeds, Leeds, LS9 7TF, UK
| | - Catherine H Smith
- Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK
| | - Mark Peakman
- Department of Immunobiology, King's College London, London SE1 9RT, UK
| | - John Wright
- Bradford Royal Infirmary, Bradford Institute for Health Research, Bradford BD9 6RJ, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, Francis Crick Institute, London NW1 1AT, UK.,Division of Cancer Studies, King's College London, London SE1 1UL, UK
| | - Jonathan N Barker
- Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK.
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Benedetti L, Cereda M, Monteverde L, Desai N, Ciccarelli FD. Synthetic lethal interaction between the tumour suppressor STAG2 and its paralog STAG1. Oncotarget 2017; 8:37619-37632. [PMID: 28430577 PMCID: PMC5514935 DOI: 10.18632/oncotarget.16838] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/08/2017] [Indexed: 12/17/2022] Open
Abstract
Cohesin is a multi-protein complex that tethers sister chromatids during mitosis and mediates DNA repair, genome compartmentalisation and regulation of gene expression. Cohesin subunits frequently acquire cancer loss-of-function alterations and act as tumour suppressors in several tumour types. This has led to increased interest in cohesin as potential target in anti-cancer therapy. Here we show that the loss-of-function of STAG2, a core component of cohesin and an emerging tumour suppressor, leads to synthetic dependency of mutated cancer cells on its paralog STAG1. STAG1 and STAG2 share high sequence identity, encode mutually exclusive cohesin subunits and retain partially overlapping functions. We inhibited STAG1 and STAG2 in several cancer cell lines where the two genes have variable mutation and copy number status. In all cases, we observed that the simultaneous blocking of STAG1 and STAG2 significantly reduces cell proliferation. We further confirmed the synthetic lethal interaction developing a vector-free CRISPR system to induce STAG1/STAG2 double gene knockout. We provide strong evidence that STAG1 is a promising therapeutic target in cancers with inactivating alterations of STAG2.
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Affiliation(s)
- Lorena Benedetti
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Matteo Cereda
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - LeeAnn Monteverde
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikita Desai
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Francesca D. Ciccarelli
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
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24
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Gambardella G, Cereda M, Benedetti L, Ciccarelli FD. MEGA-V: detection of variant gene sets in patient cohorts. Bioinformatics 2017; 33:1248-1249. [PMID: 28003259 PMCID: PMC5408849 DOI: 10.1093/bioinformatics/btw809] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/19/2016] [Indexed: 11/25/2022] Open
Abstract
Summary Detecting significant associations between genetic variants and disease may prove particularly challenging when the variants are rare in the population and/or act together with other variants to cause the disease. We have developed a statistical framework named Mutation Enrichment Gene set Analysis of Variants (MEGA-V) that specifically detects the enrichments of genetic alterations within a process in a cohort of interest. By focusing on the mutations of several genes contributing to the same function rather than on those affecting a single gene, MEGA-V increases the power to detect statistically significant associations. Availability and Implementation MEGA-V is available at https://github.com/ciccalab/MEGA Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Matteo Cereda
- Division of Cancer Studies, King’s College London, London, UK
| | | | - Francesca D Ciccarelli
- Division of Cancer Studies, King’s College London, London, UK
- To whom correspondence should be addressed.
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25
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Cereda M, Mourikis TP, Ciccarelli FD. Genetic Redundancy, Functional Compensation, and Cancer Vulnerability. Trends Cancer 2016; 2:160-162. [PMID: 28741568 DOI: 10.1016/j.trecan.2016.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 01/28/2023]
Abstract
Cancer genomes acquire somatic alterations that largely differ between and within cancer types. Several of these alterations inactivate genes that are normally functional with no deleterious consequences on cancer cells due to genetic redundancy. Here we discuss how this leads to cancer synthetic dependencies that can be exploited in therapy.
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Affiliation(s)
- Matteo Cereda
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
| | - Thanos P Mourikis
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
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26
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An O, Dall'Olio GM, Mourikis TP, Ciccarelli FD. NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. Nucleic Acids Res 2015; 44:D992-9. [PMID: 26516186 PMCID: PMC4702816 DOI: 10.1093/nar/gkv1123] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/14/2015] [Indexed: 12/21/2022] Open
Abstract
The Network of Cancer Genes (NCG, http://ncg.kcl.ac.uk/) is a manually curated repository of cancer genes derived from the scientific literature. Due to the increasing amount of cancer genomic data, we have introduced a more robust procedure to extract cancer genes from published cancer mutational screenings and two curators independently reviewed each publication. NCG release 5.0 (August 2015) collects 1571 cancer genes from 175 published studies that describe 188 mutational screenings of 13 315 cancer samples from 49 cancer types and 24 primary sites. In addition to collecting cancer genes, NCG also provides information on the experimental validation that supports the role of these genes in cancer and annotates their properties (duplicability, evolutionary origin, expression profile, function and interactions with proteins and miRNAs).
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Affiliation(s)
- Omer An
- Division of Cancer Studies, King's College London, London SE11UL, UK
| | | | - Thanos P Mourikis
- Division of Cancer Studies, King's College London, London SE11UL, UK
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27
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Iannelli F, Collino A, Sinha S, Radaelli E, Nicoli P, D’Antiga L, Sonzogni A, Faivre J, Buendia MA, Sturm E, Thompson RJ, Knisely AS, Natoli G, Ghisletti S, Ciccarelli FD. Erratum: Corrigendum: Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency. Nat Commun 2015; 6:7456. [DOI: 10.1038/ncomms8456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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28
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De Grassi A, Iannelli F, Cereda M, Volorio S, Melocchi V, Viel A, Basso G, Laghi L, Caselle M, Ciccarelli FD. Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas. Genome Biol 2014; 15:437. [PMID: 25175524 PMCID: PMC4181412 DOI: 10.1186/s13059-014-0437-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/06/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Mismatch repair deficient colorectal adenomas are composed of transformed cells that descend from a common founder and progressively accumulate genomic alterations. The proliferation history of these tumors is still largely unknown. Here we present a novel approach to rebuild the proliferation trees that recapitulate the history of individual colorectal adenomas by mapping the progressive acquisition of somatic point mutations during tumor growth. RESULTS Using our approach, we called high and low frequency mutations acquired in the X chromosome of four mismatch repair deficient colorectal adenomas deriving from male individuals. We clustered these mutations according to their frequencies and rebuilt the proliferation trees directly from the mutation clusters using a recursive algorithm. The trees of all four lesions were formed of a dominant subclone that co-existed with other genetically heterogeneous subpopulations of cells. However, despite this similar hierarchical organization, the growth dynamics varied among and within tumors, likely depending on a combination of tumor-specific genetic and environmental factors. CONCLUSIONS Our study provides insights into the biological properties of individual mismatch repair deficient colorectal adenomas that may influence their growth and also the response to therapy. Extended to other solid tumors, our novel approach could inform on the mechanisms of cancer progression and on the best treatment choice.
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Affiliation(s)
- Anna De Grassi
- />Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, 20139 Italy
- />Present address: Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70125 Italy
| | - Fabio Iannelli
- />Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, 20139 Italy
| | - Matteo Cereda
- />Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, 20139 Italy
- />Division of Cancer Studies, King’s College London, London, SE1 1UL UK
| | - Sara Volorio
- />Cogentech-IFOM Istituto FIRC di Oncologia Molecolare, Milan, 20139 Italy
| | - Valentina Melocchi
- />Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, 20139 Italy
| | - Alessandra Viel
- />CRO Aviano National Cancer Institute, Aviano, (PN) 33081 Italy
| | - Gianluca Basso
- />Laboratory of Molecular Gastroenterology, Department of Gastroenterology, Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI), 20089 Italy
| | - Luigi Laghi
- />Laboratory of Molecular Gastroenterology, Department of Gastroenterology, Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI), 20089 Italy
| | - Michele Caselle
- />Department of Theoretical Physics and INFN University of Turin, Turin, 10125 Italy
| | - Francesca D Ciccarelli
- />Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, 20139 Italy
- />Division of Cancer Studies, King’s College London, London, SE1 1UL UK
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Iannelli F, Collino A, Sinha S, Radaelli E, Nicoli P, D'Antiga L, Sonzogni A, Faivre J, Buendia MA, Sturm E, Thompson RJ, Knisely AS, Natoli G, Ghisletti S, Ciccarelli FD. Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency. Nat Commun 2014; 5:3850. [PMID: 24819516 DOI: 10.1038/ncomms4850] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/10/2014] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse HCCs induced by defects in hepatocyte biliary transporters, which expose hepatocytes to bile salts and cause chronic inflammation that develops into cancer. In both human and mouse cancer genomes, we find few somatic point mutations with no impairment of cancer genes, but massive gene amplification and rearrangements. This genomic landscape differs from that of virus- and alcohol-associated liver cancer. Copy-number gains preferentially occur at late stages of cancer development and frequently target the MAPK signalling pathway, and in particular direct regulators of JNK. The pharmacological inhibition of JNK retards cancer progression in the mouse. Our study demonstrates that intrahepatic cholestasis leading to hepatocyte exposure to bile acids and inflammation promotes cancer through genomic modifications that can be distinguished from those determined by other aetiological factors.
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Affiliation(s)
- Fabio Iannelli
- 1] European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy [2]
| | - Agnese Collino
- 1] European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy [2]
| | - Shruti Sinha
- 1] European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy [2] Division of Cancer Studies, King's College London, London SE1 1UL, UK [3]
| | - Enrico Radaelli
- VIB Center for the Biology of Disease, KU Leuven Center for Human Genetics, O&N4 Herestraat 49 box 602, B-3000 Leuven, Belgium
| | - Paola Nicoli
- European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Lorenzo D'Antiga
- Paediatric Hepatology, Gastroenterology and Transplantation, Ospedale Papa Giovanni XXIII, Piazza OMS - Organizzazione Mondiale della Sanità 1, 24128 Bergamo, Italy
| | - Aurelio Sonzogni
- Department of Pathology, Ospedale Papa Giovanni XXIII, Piazza OMS - Organizzazione Mondiale della Sanità 1, 24128 Bergamo, Italy
| | - Jamila Faivre
- Institut National de la Santé et de la Recherche Médicale (INSERM) U785, University Paris-Sud, France, Centre Hépatobiliaire, Hôpital Paul Brousse, Villejuif F94800, France
| | - Marie Annick Buendia
- Institut National de la Santé et de la Recherche Médicale (INSERM) U785, University Paris-Sud, France, Centre Hépatobiliaire, Hôpital Paul Brousse, Villejuif F94800, France
| | - Ekkehard Sturm
- University Hospital for Children and Adolescents, University of Tuebingen, 72076 Tuebingen, Germany
| | | | - A S Knisely
- Institute of Liver Studies, King's College Hospital, London SE5 9RS, UK
| | - Gioacchino Natoli
- European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Serena Ghisletti
- European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Francesca D Ciccarelli
- 1] European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy [2] Division of Cancer Studies, King's College London, London SE1 1UL, UK
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30
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An O, Pendino V, D'Antonio M, Ratti E, Gentilini M, Ciccarelli FD. NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. Database (Oxford) 2014; 2014:bau015. [PMID: 24608173 PMCID: PMC3948431 DOI: 10.1093/database/bau015] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
NCG 4.0 is the latest update of the Network of Cancer Genes, a web-based repository of systems-level properties of cancer genes. In its current version, the database collects information on 537 known (i.e. experimentally supported) and 1463 candidate (i.e. inferred using statistical methods) cancer genes. Candidate cancer genes derive from the manual revision of 67 original publications describing the mutational screening of 3460 human exomes and genomes in 23 different cancer types. For all 2000 cancer genes, duplicability, evolutionary origin, expression, functional annotation, interaction network with other human proteins and with microRNAs are reported. In addition to providing a substantial update of cancer-related information, NCG 4.0 also introduces two new features. The first is the annotation of possible false-positive cancer drivers, defined as candidate cancer genes inferred from large-scale screenings whose association with cancer is likely to be spurious. The second is the description of the systems-level properties of 64 human microRNAs that are causally involved in cancer progression (oncomiRs). Owing to the manual revision of all information, NCG 4.0 constitutes a complete and reliable resource on human coding and non-coding genes whose deregulation drives cancer onset and/or progression. NCG 4.0 can also be downloaded as a free application for Android smart phones. Database URL: http://bio.ieo.eu/ncg/.
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Affiliation(s)
- Omer An
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy and Division of Cancer Studies, King's College London, London SE1 1UL, UK
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D'Antonio M, Guerra RF, Cereda M, Marchesi S, Montani F, Nicassio F, Di Fiore PP, Ciccarelli FD. Recessive cancer genes engage in negative genetic interactions with their functional paralogs. Cell Rep 2013; 5:1519-26. [PMID: 24360954 DOI: 10.1016/j.celrep.2013.11.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/25/2013] [Accepted: 11/18/2013] [Indexed: 01/01/2023] Open
Abstract
Cancer genetic heterogeneity offers a wide repertoire of molecular determinants to be screened as therapeutic targets. Here, we identify potential anticancer targets by exploiting negative genetic interactions between genes with driver loss-of-function mutations (recessive cancer genes) and their functionally redundant paralogs. We identify recessive genes with additional copies and experimentally test our predictions on three paralogous pairs. We confirm digenic negative interactions between two cancer genes (SMARCA4 and CDH1) and their corresponding paralogs (SMARCA2 and CDH3). Furthermore, we identify a trigenic negative interaction between the cancer gene DNMT3A, its functional paralog DNMT3B, and a third gene, DNMT1, which encodes the only other human DNA-methylase domain. Although our study does not exclude other causes of synthetic lethality, it suggests that functionally redundant paralogs of cancer genes could be targets in anticancer therapy.
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Affiliation(s)
- Matteo D'Antonio
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Rosalinda F Guerra
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Matteo Cereda
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Stefano Marchesi
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Francesca Montani
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Francesco Nicassio
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy; Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Pier Paolo Di Fiore
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy; IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Dipartimento di Scienze della Salute, Università degli Studi di Milano, Via di Rudinì 8, 20122 Milan, Italy
| | - Francesca D Ciccarelli
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy; Division of Cancer Studies, King's College London, London SE1 1UL, UK.
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D'Antonio M, Ciccarelli FD. Integrated analysis of recurrent properties of cancer genes to identify novel drivers. Genome Biol 2013; 14:R52. [PMID: 23718799 PMCID: PMC4054099 DOI: 10.1186/gb-2013-14-5-r52] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 05/29/2013] [Indexed: 11/10/2022] Open
Abstract
The heterogeneity of cancer genomes in terms of acquired mutations complicates the identification of genes whose modification may exert a driver role in tumorigenesis. In this study, we present a novel method that integrates expression profiles, mutation effects, and systemic properties of mutated genes to identify novel cancer drivers. We applied our method to ovarian cancer samples and were able to identify putative drivers in the majority of carcinomas without mutations in known cancer genes, thus suggesting that it can be used as a complementary approach to find rare driver mutations that cannot be detected using frequency-based approaches.
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33
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D'Antonio M, Pendino V, Sinha S, Ciccarelli FD. Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes. Nucleic Acids Res 2012; 40:D978-83. [PMID: 22080562 PMCID: PMC3245144 DOI: 10.1093/nar/gkr952] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 10/12/2011] [Indexed: 12/22/2022] Open
Abstract
The identification of a constantly increasing number of genes whose mutations are causally implicated in tumor initiation and progression (cancer genes) requires the development of tools to store and analyze them. The Network of Cancer Genes (NCG 3.0) collects information on 1494 cancer genes that have been found mutated in 16 different cancer types. These genes were collected from the Cancer Gene Census as well as from 18 whole exome and 11 whole-genome screenings of cancer samples. For each cancer gene, NCG 3.0 provides a summary of the gene features and the cross-reference to other databases. In addition, it describes duplicability, evolutionary origin, orthology, network properties, interaction partners, microRNA regulation and functional roles of cancer genes and of all genes that are related to them. This integrated network of information can be used to better characterize cancer genes in the context of the system in which they act. The data can also be used to identify novel candidates that share the same properties of known cancer genes and may therefore play a similar role in cancer. NCG 3.0 is freely available at http://bio.ifom-ieo-campus.it/ncg.
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Affiliation(s)
| | | | | | - Francesca D. Ciccarelli
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
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34
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D'Antonio M, Ciccarelli FD. Modification of gene duplicability during the evolution of protein interaction network. PLoS Comput Biol 2011; 7:e1002029. [PMID: 21490719 PMCID: PMC3072358 DOI: 10.1371/journal.pcbi.1002029] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 02/24/2011] [Indexed: 11/21/2022] Open
Abstract
Duplications of genes encoding highly connected and essential proteins are selected against in several species but not in human, where duplicated genes encode highly connected proteins. To understand when and how gene duplicability changed in evolution, we compare gene and network properties in four species (Escherichia coli, yeast, fly, and human) that are representative of the increase in evolutionary complexity, defined as progressive growth in the number of genes, cells, and cell types. We find that the origin and conservation of a gene significantly correlates with the properties of the encoded protein in the protein-protein interaction network. All four species preserve a core of singleton and central hubs that originated early in evolution, are highly conserved, and accomplish basic biological functions. Another group of hubs appeared in metazoans and duplicated in vertebrates, mostly through vertebrate-specific whole genome duplication. Such recent and duplicated hubs are frequently targets of microRNAs and show tissue-selective expression, suggesting that these are alternative mechanisms to control their dosage. Our study shows how networks modified during evolution and contributes to explaining the occurrence of somatic genetic diseases, such as cancer, in terms of network perturbations.
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Affiliation(s)
- Matteo D'Antonio
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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Miklos I, Ciccarelli FD. Preface. The seventh RECOMB-CG Workshop, September 27–29, 2009, Alfréd Rényi Institute of Mathematics, Budapest, Hungary. J Comput Biol 2010; 17:1095-6. [PMID: 20874397 DOI: 10.1089/cmb.2010.004p] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Istvan Miklos
- Rényi Institute, Realtanoda u. 13-15, Budapest, Hungary.
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Civril F, Wehenkel A, Giorgi FM, Santaguida S, Di Fonzo A, Grigorean G, Ciccarelli FD, Musacchio A. Structural analysis of the RZZ complex reveals common ancestry with multisubunit vesicle tethering machinery. Structure 2010; 18:616-26. [PMID: 20462495 DOI: 10.1016/j.str.2010.02.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 01/22/2010] [Accepted: 02/19/2010] [Indexed: 01/31/2023]
Abstract
The RZZ complex recruits dynein to kinetochores. We investigated structure, topology, and interactions of the RZZ subunits (ROD, ZWILCH, and ZW10) in vitro, in vivo, and in silico. We identify neuroblastoma-amplified gene (NAG), a ZW10 binder, as a ROD homolog. ROD and NAG contain an N-terminal beta propeller followed by an alpha solenoid, which is the architecture of certain nucleoporins and vesicle coat subunits, suggesting a distant evolutionary relationship. ZW10 binding to ROD and NAG is mutually exclusive. The resulting ZW10 complexes (RZZ and NRZ) respectively contain ZWILCH and RINT1 as additional subunits. The X-ray structure of ZWILCH, the first for an RZZ subunit, reveals a novel fold distinct from RINT1's. The evolutionarily conserved NRZ likely acts as a tethering complex for retrograde trafficking of COPI vesicles from the Golgi to the endoplasmic reticulum. The RZZ, limited to metazoans, probably evolved from the NRZ, exploiting the dynein-binding capacity of ZW10 to direct dynein to kinetochores.
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Affiliation(s)
- Filiz Civril
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, I-20139 Milan, Italy
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Abstract
The identification of an increasing number of cancer genes is opening up unexpected scenarios in cancer genetics. When analyzed for their systemic properties, these genes show a general fragility towards perturbation. A recent paper published in BMC Biology shows how the founder domains of known cancer genes emerged at two macroevolutionary transitions - the advent of the first cell and the transition to metazoan multicellularity. See research article http://www.biomedcentral.com/1741-7007/8/66
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Affiliation(s)
- Francesca D Ciccarelli
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, 20139 Milan, Italy.
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De Grassi A, Segala C, Iannelli F, Volorio S, Bertario L, Radice P, Bernard L, Ciccarelli FD. Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability. PLoS Biol 2010; 8:e1000275. [PMID: 20052272 PMCID: PMC2794366 DOI: 10.1371/journal.pbio.1000275] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 11/24/2009] [Indexed: 12/27/2022] Open
Abstract
Ultradeep sequencing of genomes permits the detection of very low-level genomic instability in non-neoplastic tissues of patients with the most common form of inherited colorectal cancer. Early detection of cancer-associated genomic instability is crucial, particularly in tumour types in which this instability represents the essential underlying mechanism of tumourigenesis. Currently used methods require the presence of already established neoplastic cells because they only detect clonal mutations. In principle, parallel sequencing of single DNA filaments could reveal the early phases of tumour initiation by detecting low-frequency mutations, provided an adequate depth of coverage and an effective control of the experimental error. We applied ultradeep sequencing to estimate the genomic instability of individuals with hereditary non-polyposis colorectal cancer (HNPCC). To overcome the experimental error, we used an ultraconserved region (UCR) of the human genome as an internal control. By comparing the mutability outside and inside the UCR, we observed a tendency of the ultraconserved element to accumulate significantly fewer mutations than the flanking segments in both neoplastic and nonneoplastic HNPCC samples. No difference between the two regions was detectable in cells from healthy donors, indicating that all three HNPCC samples have mutation rates higher than the healthy genome. This is the first, to our knowledge, direct evidence of an intrinsic genomic instability of individuals with heterozygous mutations in mismatch repair genes, and constitutes the proof of principle for the development of a more sensitive molecular assay of genomic instability. In hereditary non-polyposis colorectal cancer (HNPCC), a germline mutation in one allele of a gene responsible for repairing DNA damage predisposes the host to cancer, because subsequent somatic inactivation of the one wild-type allele leads to genomic instability that favours tumourigenesis. Nonneoplastic tissues of HNPCC individuals are believed to repair DNA normally, as they are heterozygous and thus are thought to be genomically stable. However, methods used to date are known to be incapable of detecting very low levels of genome instability. Here, we present a more sensitive procedure based on the resequencing of a HNPCC genomic region using next-generation sequencing technology. With this approach, we show that genomic instability is in fact detectable in nonneoplastic tissues of HNPCC patients compared with healthy donors. This constitutional instability may predispose them to acquiring the second somatic mutation event needed for cancer development.
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Affiliation(s)
- Anna De Grassi
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Cinzia Segala
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Fabio Iannelli
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Sara Volorio
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, IFOM-IEO Campus, Milan, Italy
| | - Lucio Bertario
- Hereditary Colorectal Tumor Registry; Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Radice
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, IFOM-IEO Campus, Milan, Italy
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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Syed AS, D’Antonio M, Ciccarelli FD. Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. Nucleic Acids Res 2010; 38:D670-5. [PMID: 19906700 PMCID: PMC2808873 DOI: 10.1093/nar/gkp957] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 10/02/2009] [Accepted: 10/13/2009] [Indexed: 01/19/2023] Open
Abstract
The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network. NCG also stores information on all primary interactors of cancer proteins, thus providing a complete overview of 5357 proteins that constitute direct and indirect determinants of human cancer. With the constant delivery of results from the mutational screenings of cancer genomes, NCG represents a versatile resource for retrieving detailed information on particular cancer genes, as well as for identifying common properties of precompiled lists of cancer genes. NCG is freely available at: http://bio.ifom-ieo-campus.it/ncg.
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Affiliation(s)
| | | | - Francesca D. Ciccarelli
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
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Anelli V, Santoriello C, Distel M, Köster RW, Ciccarelli FD, Mione M. Global Repression of Cancer Gene Expression in a Zebrafish Model of Melanoma Is Linked to Epigenetic Regulation. Zebrafish 2009; 6:417-24. [DOI: 10.1089/zeb.2009.0612] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Viviana Anelli
- IFOM Foundation—FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Cristina Santoriello
- IFOM Foundation—FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Martin Distel
- Institute of Developmental Genetics, Helmholtz Center Munich, Munich, Germany
| | - Reinhard W. Köster
- Institute of Developmental Genetics, Helmholtz Center Munich, Munich, Germany
| | | | - Marina Mione
- IFOM Foundation—FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
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Rambaldi D, Ciccarelli FD. FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci. Bioinformatics 2009; 25:2281-2. [PMID: 19542150 PMCID: PMC2734320 DOI: 10.1093/bioinformatics/btp381] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 06/09/2009] [Accepted: 06/16/2009] [Indexed: 11/13/2022] Open
Abstract
SUMMARY FancyGene is a fast and user-friendly web-based tool for producing images of one or more genes directly on the corresponding genomic locus. Starting from a variety of input formats, FancyGene rebuilds the basic components of a gene (UTRs, intron, exons). Once the initial representation is obtained, the user can superimpose additional features-such as protein domains and/or a variety of biological markers-in specific positions. FancyGene is extremely flexible allowing the user to change the resulting image dynamically, modifying colors and shapes and adding and/or removing objects. The output images are generated either in portable network graphics (PNG) or portable document format (PDF) formats and can be used for scientific presentations as well as for publications. The PDF format preserves editing capabilities, allowing picture modification using any vector graphics editor.
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Affiliation(s)
- Davide Rambaldi
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
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Ciccarelli FD, Miklós I. Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples. Comparative Genomics 2009. [PMCID: PMC7120581 DOI: 10.1007/978-3-642-04744-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The inference of ancestral genomes is a fundamental problem in molecular evolution. Due to the statistical nature of this problem, the most likely or the most parsimonious ancestral genomes usually include considerable error rates. In general, these errors cannot be abolished by utilizing more exhaustive computational approaches, by using longer genomic sequences, or by analyzing more taxa. In recent studies we showed that co-evolution is an important force that can be used for significantly improving the inference of ancestral genome content. In this work we formally define a computational problem for the inference of ancestral genome content by co-evolution. We show that this problem is NP-hard and present both a Fixed Parameter Tractable (FPT) algorithm, and heuristic approximation algorithms for solving it. The running time of these algorithms on simulated inputs with hundreds of protein families and hundreds of co-evolutionary relations was fast (up to four minutes) and it achieved an approximation ratio < 1.3. We use our approach to study the ancestral genome content of the Fungi. To this end, we implement our approach on a dataset of 33,931 protein families and 20,317 co-evolutionary relations. Our algorithm added and removed hundreds of proteins from the ancestral genomes inferred by maximum likelihood (ML) or maximum parsimony (MP) while slightly affecting the likelihood/parsimony score of the results. A biological analysis revealed various pieces of evidence that support the biological plausibility of the new solutions.
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Affiliation(s)
| | - István Miklós
- Rényi Institute, Hungarian Academy of Sciences, Reáltanoda utca 13-15, 1053 Budapest, Hungary
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Rambaldi D, Giorgi FM, Capuani F, Ciliberto A, Ciccarelli FD. Low duplicability and network fragility of cancer genes. Trends Genet 2008; 24:427-30. [PMID: 18675489 DOI: 10.1016/j.tig.2008.06.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 06/19/2008] [Accepted: 06/24/2008] [Indexed: 11/24/2022]
Abstract
We identified genomic and network properties of approximately 600 genes mutated in different cancer types. These genes tend not to duplicate but, unlike most human singletons, they encode central hubs of highly interconnected modules within the protein-protein interaction network (PIN). We find that cancer genes are fragile components of the human gene repertoire, sensitive to dosage modification. Furthermore, other nodes of the human PIN with similar properties are rare and probably enriched in candidate cancer genes.
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Affiliation(s)
- Davide Rambaldi
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD. Non-random retention of protein-coding overlapping genes in Metazoa. BMC Genomics 2008; 9:174. [PMID: 18416813 PMCID: PMC2330155 DOI: 10.1186/1471-2164-9-174] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 04/16/2008] [Indexed: 11/26/2022] Open
Abstract
Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm). Results For all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression. Conclusion Our data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.
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Affiliation(s)
- Giulia Soldà
- 1Department of Biology and Genetics for Medical Sciences, University of Milan, 20133 Milan, Italy.
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Fumasoni I, Meani N, Rambaldi D, Scafetta G, Alcalay M, Ciccarelli FD. Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. BMC Evol Biol 2007; 7:187. [PMID: 17916234 PMCID: PMC2082429 DOI: 10.1186/1471-2148-7-187] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 10/04/2007] [Indexed: 12/11/2022] Open
Abstract
Background Progressive diversification of paralogs after gene expansion is essential to increase their functional specialization. However, mode and tempo of this divergence remain mostly unclear. Here we report the comparative analysis of PRDM genes, a family of putative transcriptional regulators involved in human tumorigenesis. Results Our analysis assessed that the PRDM genes originated in metazoans, expanded in vertebrates and further duplicated in primates. We experimentally showed that fast-evolving paralogs are poorly expressed, and that the most recent duplicates, such as primate-specific PRDM7, acquire tissue-specificity. PRDM7 underwent major structural rearrangements that decreased the number of encoded Zn-Fingers and modified gene splicing. Through internal duplication and activation of a non-canonical splice site (GC-AG), PRDM7 can acquire a novel intron. We also detected an alternative isoform that can retain the intron in the mature transcript and that is predominantly expressed in human melanocytes. Conclusion Our findings show that (a) molecular evolution of paralogs correlates with their expression pattern; (b) gene diversification is obtained through massive genomic rearrangements; and (c) splicing modification contributes to the functional specialization of novel genes.
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Affiliation(s)
- Irene Fumasoni
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy.
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Abstract
We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.
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Mees A, Rock R, Ciccarelli FD, Leberfinger CB, Borawski JM, Bork P, Wiese S, Gessler M, Kerkhoff E. Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases. Gene Expr Patterns 2005; 6:79-85. [PMID: 16099729 DOI: 10.1016/j.modgep.2005.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 02/28/2005] [Accepted: 04/25/2005] [Indexed: 11/18/2022]
Abstract
The kinase non-catalytic c-lobe domain (KIND) evolved from the catalytic protein kinase fold into a potential protein interaction module for signalling proteins. Spir family actin organizers and the non-receptor phosphatase type 13 (PTP type 13) encode a KIND domain in the very N-terminal parts of the proteins. Here we report the characterization and cloning of a third member of the KIND protein family, which we have named very-KIND (VKIND) because of its two KIND domains. Like the other members of the protein family, VKIND has a KIND domain at the N-terminus. A second KIND domain is located in the central part of the protein. The C-terminal half encodes a guanine nucleotide exchange factor motif for Ras-like GTPases (RasGEF) and a RasGEF N-terminal module (RasGEFN). There is only one VKIND gene in the mammalian genomes and up to now we have found the gene only in vertebrates. During mouse embryogenesis the VKIND gene was specifically expressed in the developing nervous system. In adult mice Northern hybridizations revealed high expression only in brain. Low expression could be detected in ovary. In situ hybridizations showed a specific expression of VKIND in neuronal cells of the granular and Purkinje cell layers of the cerebellum.
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Affiliation(s)
- Anaid Mees
- Institut für Medizinische Strahlenkunde und Zellforschung (MSZ), Universität Würzburg, Versbacher Str. 5, 97078 Würzburg, Germany
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Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 2005; 434:724-31. [PMID: 15815621 DOI: 10.1038/nature03466] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Accepted: 02/11/2005] [Indexed: 12/27/2022]
Abstract
Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.
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MESH Headings
- Animals
- Base Composition
- Base Sequence
- Centromere/genetics
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 4/genetics
- Conserved Sequence/genetics
- CpG Islands/genetics
- Euchromatin/genetics
- Expressed Sequence Tags
- Gene Duplication
- Genetic Variation/genetics
- Genomics
- Humans
- Molecular Sequence Data
- Physical Chromosome Mapping
- Polymorphism, Genetic/genetics
- Primates/genetics
- Proteins/genetics
- Pseudogenes/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Untranslated/analysis
- RNA, Untranslated/genetics
- Recombination, Genetic/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Ladeana W Hillier
- Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St. Louis, Missouri 63108, USA
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Abstract
Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive may have escaped the dosage control by rapid and sizable changes in their function. To test this hypothesis and to develop a strategy for the identification of novel gene functions, we have analyzed 22 primate-specific intrachromosomal duplications of genes with a single-copy ortholog in all other completely sequenced metazoans. When comparing this set to genes not exposed to the single-copy status constraint, we observed a higher tendency of the former to modify their gene structure, often through complex genomic rearrangements. The analysis of the most dramatic of these duplications, affecting approximately 10% of human Chromosome 2, enabled a detailed reconstruction of the events leading to the appearance of a novel gene family. The eight members of this family originated from the highly conserved nucleoporin RanBP2 by several genetic rearrangements such as segmental duplications, inversions, translocations, exon loss, and domain accretion. We have experimentally verified that at least one of the newly formed proteins has a cellular localization different from RanBP2's, and we show that positive selection did act on specific domains during evolution.
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Abstract
MOTIVATION The hypersensitive response (HR) is a process activated by plants after microbial infection. Its main phenotypic effects are both a programmed death of the plant cells near the infection site and a reduction of the microbial proliferation. Although many resistance genes (R genes) associated to HR have been identified, very little is known about the molecular mechanisms activated after their expression. RESULTS The analysis of the product of one of the R genes, the Hin1 protein, led to the identification of a novel domain, which we named WHy because it is detectable in proteins involved in Water stress and Hypersensitive response. The expression of this domain during both biotic infection and response to desiccation points to a molecular machinery common to these two stress conditions. Moreover, its presence in a restricted number of bacteria suggests a possible use for marking plant pathogenicity. CONTACT francesca.ciccarelli@embl.de SUPPLEMENTARY INFORMATION Supplementary data (Figures S1 and S2 and Table S1) and the alignment in clustal format are available at http://www.bork.embl.de/~ciccarel/WHy_add_data.html.
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