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Chicón‐Bosch M, Sánchez‐Serra S, Rosàs‐Lapeña M, Costa‐Fraga N, Besalú‐Velázquez J, Illa‐Bernadí J, Mateo‐Lozano S, Cidre‐Aranaz F, Grünewald TG, Díaz‐Lagares Á, Lopez‐Alemany R, Tirado ÒM. Multi-omics profiling reveals key factors involved in Ewing sarcoma metastasis. Mol Oncol 2025; 19:1002-1028. [PMID: 39757762 PMCID: PMC11977646 DOI: 10.1002/1878-0261.13788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 08/28/2024] [Accepted: 11/14/2024] [Indexed: 01/07/2025] Open
Abstract
Ewing sarcoma (EWS) is the second most common bone tumor affecting children and young adults, with dismal outcomes for patients with metastasis at diagnosis. Mechanisms leading to metastasis remain poorly understood. To deepen our knowledge on EWS progression, we have profiled tumors and metastases from a spontaneous metastasis mouse model using a multi-omics approach. Combining transcriptomics, proteomics, and methylomics analyses, we identified signaling cascades and candidate genes enriched in metastases that could be modulating aggressiveness in EWS. Phenotypical validation of two of these candidates, cyclic AMP-responsive element-binding protein 1 (CREB1) and lipoxygenase homology domain-containing protein 1 (LOXHD1), showed an association with migration and clonogenic abilities. Moreover, previously described CREB1 downstream targets were present amongst the metastatic-enriched results. Combining the different omics datasets, we identified FYVE, RhoGEF, and PH domain-containing protein 4 (FGD4) as a CREB1 target interconnecting the different EWS biological layers (RNA, protein and methylation status) and whose high expression is associated with worse clinical outcome. Further studies will provide insight into EWS metastasis mechanisms and ultimately improve survival rates for EWS patients.
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Affiliation(s)
- Mariona Chicón‐Bosch
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Sara Sánchez‐Serra
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
- Universitat de Barcelona (UB)BarcelonaSpain
| | - Marta Rosàs‐Lapeña
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Nicolás Costa‐Fraga
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology (ONCOMET), Health Research Institute of Santiago (IDIS)University Clinical Hospital of Santiago (CHUS/SERGAS)Santiago de CompostelaSpain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry SchoolUniversidade de Santiago de Compostela (USC)Spain
- Universidad de Santiago de Compostela (USC)Spain
- Department of Clinical AnalysisUniversity Hospital Complex of Santiago de Compostela (CHUS)Spain
| | - Judit Besalú‐Velázquez
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Janet Illa‐Bernadí
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Silvia Mateo‐Lozano
- Developmental Tumor Biology LaboratoryInstitut de Recerca Sant Joan de Déu, Hospital Sant Joan de DéuBarcelonaSpain
- Pediatric Cancer Center BarcelonaHospital Sant Joan de DéuBarcelonaSpain
| | - Florencia Cidre‐Aranaz
- Division of Translational Paediatric Sarcoma ResearchGerman Cancer Research Center (DKFZ), German Cancer Consortium (DKTK)HeidelbergGermany
- Hopp‐Children's Cancer Center (KiTZ)HeidelbergGermany
- National Center for Tumor Diseases (NCT)NCT Heidelberg, a partnership between DKFZ and Heidelberg University HospitalGermany
| | - Thomas G.P. Grünewald
- Division of Translational Paediatric Sarcoma ResearchGerman Cancer Research Center (DKFZ), German Cancer Consortium (DKTK)HeidelbergGermany
- Hopp‐Children's Cancer Center (KiTZ)HeidelbergGermany
- National Center for Tumor Diseases (NCT)NCT Heidelberg, a partnership between DKFZ and Heidelberg University HospitalGermany
- Institute of PathologyHeidelberg University HospitalHeidelbergGermany
| | - Ángel Díaz‐Lagares
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology (ONCOMET), Health Research Institute of Santiago (IDIS)University Clinical Hospital of Santiago (CHUS/SERGAS)Santiago de CompostelaSpain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry SchoolUniversidade de Santiago de Compostela (USC)Spain
- Universidad de Santiago de Compostela (USC)Spain
- Department of Clinical AnalysisUniversity Hospital Complex of Santiago de Compostela (CHUS)Spain
- CIBERONCCarlos III Institute of Health (ISCIII)MadridSpain
| | - Roser Lopez‐Alemany
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Òscar M. Tirado
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
- CIBERONCCarlos III Institute of Health (ISCIII)MadridSpain
- Institut Català d'Oncologia (ICO)L'Hospitalet de LlobregatBarcelonaSpain
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2
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Sánchez S, Juárez U, Domínguez J, Molina B, Barrientos R, Martínez-Hernández A, Carnevale A, Grether-González P, Mayen DG, Villarroel C, Lieberman E, Yokoyama E, Del Castillo V, Torres L, Frias S. Frequent copy number variants in a cohort of Mexican-Mestizo individuals. Mol Cytogenet 2023; 16:2. [PMID: 36631885 PMCID: PMC9835318 DOI: 10.1186/s13039-022-00631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The human genome presents variation at distinct levels, copy number variants (CNVs) are DNA segments of variable lengths that range from several base pairs to megabases and are present at a variable number of copies in human genomes. Common CNVs have no apparent influence on the phenotype; however, some rare CNVs have been associated with phenotypic traits, depending on their size and gene content. CNVs are detected by microarrays of different densities and are generally visualized, and their frequencies analysed using the HapMap as default reference population. Nevertheless, this default reference is inadequate when the samples analysed are from people from Mexico, since population with a Hispanic genetic background are minimally represented. In this work, we describe the variation in the frequencies of four common CNVs in Mexican-Mestizo individuals. RESULTS In a cohort of 147 unrelated Mexican-Mestizo individuals, we found that the common CNVs 2p11.2 (99.6%), 8p11.22 (54.5%), 14q32.33 (100%), and 15q11.2 (71.1%) appeared with unexpectedly high frequencies when contrasted with the HapMap reference (ChAS). Yet, while when comparing to an ethnically related reference population, these differences were significantly reduced or even disappeared. CONCLUSION The findings in this work contribute to (1) a better description of the CNVs characteristics of the Mexican Mestizo population and enhance the knowledge of genome variation in different ethnic groups. (2) emphasize the importance of contrasting CNVs identified in studied individuals against a reference group that-as best as possible-share the same ethnicity while keeping this relevant information in mind when conducting CNV studies at the population or clinical level.
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Affiliation(s)
- Silvia Sánchez
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090, Ciudad de Mexico, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ulises Juárez
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090, Ciudad de Mexico, México
| | - Julieta Domínguez
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090, Ciudad de Mexico, México
| | - Bertha Molina
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090, Ciudad de Mexico, México
| | - Rehotbevely Barrientos
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090, Ciudad de Mexico, México
| | - Angélica Martínez-Hernández
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Alessandra Carnevale
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Patricia Grether-González
- Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología, Ciudad de Mexico, México
- Centro Médico ABC, Campus Santa Fe, Ciudad de Mexico, México
| | - Dora Gilda Mayen
- Unidad de Genética Aplicada. Hospital Ángeles Lomas, Huixquilucan, Edo. de México, México
| | - Camilo Villarroel
- Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Esther Lieberman
- Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Emiy Yokoyama
- Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | | | - Leda Torres
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090, Ciudad de Mexico, México.
| | - Sara Frias
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090, Ciudad de Mexico, México.
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México.
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3
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Encoded hydrogel microparticles with universal mismatch-incorporated DNA probes for highly specific multiplex detection of SNPs. Talanta 2022; 245:123480. [DOI: 10.1016/j.talanta.2022.123480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 11/22/2022]
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4
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Fanjul-Fernández M, Brown NJ, Hickey P, Diakumis P, Rafehi H, Bozaoglu K, Green CC, Rattray A, Young S, Alhuzaimi D, Mountford HS, Gillies G, Lukic V, Vick T, Finlay K, Coe BP, Eichler EE, Delatycki MB, Wilson SJ, Bahlo M, Scheffer IE, Lockhart PJ. A family study implicates GBE1 in the etiology of autism spectrum disorder. Hum Mutat 2022; 43:16-29. [PMID: 34633740 PMCID: PMC8720068 DOI: 10.1002/humu.24289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 09/17/2021] [Accepted: 10/07/2021] [Indexed: 11/06/2022]
Abstract
Autism spectrum disorders (ASD) are neurodevelopmental disorders with an estimated heritability of >60%. Family-based genetic studies of ASD have generally focused on multiple small kindreds, searching for de novo variants of major effect. We hypothesized that molecular genetic analysis of large multiplex families would enable the identification of variants of milder effects. We studied a large multigenerational family of European ancestry with multiple family members affected with ASD or the broader autism phenotype (BAP). We identified a rare heterozygous variant in the gene encoding 1,4-ɑ-glucan branching enzyme 1 (GBE1) that was present in seven of seven individuals with ASD, nine of ten individuals with the BAP, and none of four tested unaffected individuals. We genotyped a community-acquired cohort of 389 individuals with ASD and identified three additional probands. Cascade analysis demonstrated that the variant was present in 11 of 13 individuals with familial ASD/BAP and neither of the two tested unaffected individuals in these three families, also of European ancestry. The variant was not enriched in the combined UK10K ASD cohorts of European ancestry but heterozygous GBE1 deletion was overrepresented in large ASD cohorts, collectively suggesting an association between GBE1 and ASD.
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Affiliation(s)
- Miriam Fanjul-Fernández
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute Victoria, Parkville, Victoria, Australia
- Royal Children’s Hospital Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Barwon Health, Geelong, Victoria, Australia
| | - Peter Hickey
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Peter Diakumis
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Kiymet Bozaoglu
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cherie C Green
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Department of Psychology and Counselling, School of Psychology and Public Health, La Trobe University, Melbourne, Victoria, Australia
| | - Audrey Rattray
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Savannah Young
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dana Alhuzaimi
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hayley S Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Greta Gillies
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Vesna Lukic
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Tanya Vick
- Barwon Health, Geelong, Victoria, Australia
| | | | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington, USA
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sarah J Wilson
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Paul J Lockhart
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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5
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Jiang SH, Mercan S, Papa I, Moldovan M, Walters GD, Koina M, Fadia M, Stanley M, Lea-Henry T, Cook A, Ellyard J, McMorran B, Sundaram M, Thomson R, Canete PF, Hoy W, Hutton H, Srivastava M, McKeon K, de la Rúa Figueroa I, Cervera R, Faria R, D’Alfonso S, Gatto M, Athanasopoulos V, Field M, Mathews J, Cho E, Andrews TD, Kitching AR, Cook MC, Riquelme MA, Bahlo M, Vinuesa CG. Deletions in VANGL1 are a risk factor for antibody-mediated kidney disease. Cell Rep Med 2021; 2:100475. [PMID: 35028616 PMCID: PMC8714939 DOI: 10.1016/j.xcrm.2021.100475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/11/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022]
Abstract
We identify an intronic deletion in VANGL1 that predisposes to renal injury in high risk populations through a kidney-intrinsic process. Half of all SLE patients develop nephritis, yet the predisposing mechanisms to kidney damage remain poorly understood. There is limited evidence of genetic contribution to specific organ involvement in SLE.1,2 We identify a large deletion in intron 7 of Van Gogh Like 1 (VANGL1), which associates with nephritis in SLE patients. The same deletion occurs at increased frequency in an indigenous population (Tiwi Islanders) with 10-fold higher rates of kidney disease compared with non-indigenous populations. Vangl1 hemizygosity in mice results in spontaneous IgA and IgG deposition within the glomerular mesangium in the absence of autoimmune nephritis. Serum transfer into B cell-deficient Vangl1+/- mice results in mesangial IgG deposition indicating that Ig deposits occur in a kidney-intrinsic fashion in the absence of Vangl1. These results suggest that Vangl1 acts in the kidney to prevent Ig deposits and its deficiency may trigger nephritis in individuals with SLE.
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Affiliation(s)
- Simon H. Jiang
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
- Department of Renal Medicine, The Canberra Hospital, Canberra 2605, Australia
| | - Sevcan Mercan
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Department of Bioengineering, Kafkas University, Kars 36100, Turkey
| | - Ilenia Papa
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Max Moldovan
- Centre for Population Health Research, University of South Australia, South Australian Health and Medical Research Institute (SAHMRI), Adelaide 5001, Australia
- Australian Institute of Health Innovation, Macquarie University, Sydney 2109, Australia
| | - Giles D. Walters
- Department of Renal Medicine, The Canberra Hospital, Canberra 2605, Australia
| | - Mark Koina
- Department of Pathology, The Canberra Hospital, Canberra 2605, Australia
| | - Mitali Fadia
- Department of Pathology, The Canberra Hospital, Canberra 2605, Australia
| | - Maurice Stanley
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Tom Lea-Henry
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Amelia Cook
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Julia Ellyard
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
| | - Brendan McMorran
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Madhivanan Sundaram
- Department of Renal Medicine, Royal Darwin Hospital, Northern Territory 0811, Australia
| | - Russell Thomson
- Centre for Research in Mathematics and Data Science, School of Computer, Data and Mathematical Sciences, Western Sydney University, Parramatta 2150, NSW, Australia
| | - Pablo F. Canete
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
| | - Wendy Hoy
- Centre for Chronic Disease, Faculty of Health, The University of Queensland, Brisbane 4029, QLD, Australia
| | - Holly Hutton
- Centre for Inflammatory Diseases, Monash University, Melbourne 3168, VIC, Australia
| | - Monika Srivastava
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Kathryn McKeon
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
| | | | - Ricard Cervera
- Department of Autoimmune Diseases, Hospital Clinic, Barcelona 08036, Spain
| | - Raquel Faria
- Unidade de Imunologia Clinica, Centro Hospitalar Unisersitario do Porto, Porto 4099-001, Portugal
| | | | - Mariele Gatto
- Department of Rheumatology, University of Padova, Italy
| | - Vicki Athanasopoulos
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
| | - Matthew Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4870, QLD, Australia
| | - John Mathews
- School of Population and Global Health, University of Melbourne, Melbourne 3053, Australia
| | - Eun Cho
- Genome Informatics Laboratory, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - Thomas D. Andrews
- Genome Informatics Laboratory, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - A. Richard Kitching
- Centre for Inflammatory Diseases, Monash University, Melbourne 3168, VIC, Australia
- Departments Nephrology and Paediatric Nephrology. Monash Health, Melbourne 3168, Australia
| | - Matthew C. Cook
- Department of Immunology, The Canberra Hospital, Canberra 2605, Australia
| | - Marta Alarcon Riquelme
- Department of Medical Genomics, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, 18016, Spain
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010 VIC, Australia
| | - Carola G. Vinuesa
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
- China Australia Centre for Personalised Immunology, Renji Hospital Shanghai, JiaoTong University Shanghai 200001, China
- Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
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6
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Bartik Z, Sillén U, Östensson M, Fransson S, Djos A, Sjöberg R, Martinsson T. A genome‑wide scan to locate regions associated with familial vesicoureteral reflux. Exp Ther Med 2021; 23:92. [PMID: 34976134 PMCID: PMC8674978 DOI: 10.3892/etm.2021.11015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/06/2021] [Indexed: 11/05/2022] Open
Abstract
Vesicoureteral reflux (VUR) is a congenital malformation carrying a high risk of recurrent urinary tract infections (UTI) and, at worst, chronic renal failure. Familial clustering implies a genetic etiology, but studies during the past few decades have demonstrated a causal gene variant in <10% of patients with VUR. The aim of the present study was to search for fully or partially shared ancestral haplotypes in 14 families from south-western Sweden with at least three affected members. High-density single nucleotide polymorphism microarray was used for genotyping prior to analysis with a compatibility matching method developed in-house, and the analysis of copy number variations (CNV). No single unique haplotype was revealed to be shared by the families, thereby excluding a common ancestry and founder mutations as a probable cause of VUR. After evaluation of haplotypes shared by subsets of families, a haplotype shared by nine families was found to be of particular interest. This haplotype, located at chromosomal region 4q21.21, harbours two tentative candidate genes (bone morphogenetic protein 3 and fibroblast growth factor 5), both expressed in metanephros and with known functions during nephrogenesis. As to CNV, only one family had a specific CNV shared by all affected members. This was a focal deletion at 5q31.1 including follistatin-like 4, a gene without a previous known connection to VUR. These data demonstrated the genetic heterogeneity of VUR and indicated that an interaction of environmental and genetic factors, including non-coding and epigenetic regulators, all contribute to the complexity of VUR.
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Affiliation(s)
- Zsuzsa Bartik
- Department of Pediatric Surgery, Pediatric Uronephrology Center, The Queen Silvia Children's Hospital, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, SE‑41685 Gothenburg, Sweden
| | - Ulla Sillén
- Department of Pediatric Surgery, Pediatric Uronephrology Center, The Queen Silvia Children's Hospital, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, SE‑41685 Gothenburg, Sweden
| | - Malin Östensson
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
| | - Susanne Fransson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
| | - Anna Djos
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
| | - Rosmarie Sjöberg
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
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7
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Wang L, Lang GT, Xue MZ, Yang L, Chen L, Yao L, Li XG, Wang P, Hu X, Shao ZM. Dissecting the heterogeneity of the alternative polyadenylation profiles in triple-negative breast cancers. Am J Cancer Res 2020; 10:10531-10547. [PMID: 32929364 PMCID: PMC7482814 DOI: 10.7150/thno.40944] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is an aggressive malignancy with high heterogeneity. However, the alternative polyadenylation (APA) profiles of TNBC remain unknown. Here, we aimed to define the characteristics of the APA events at post-transcription level among TNBCs. Methods: Using transcriptome microarray data, we analyzed APA profiles of 165 TNBC samples and 33 paired normal tissues. A pooled short hairpin RNA screen targeting 23 core cleavage and polyadenylation (C/P) genes was used to identify key C/P factors. Results: We established an unconventional APA subtyping system composed of four stable subtypes: 1) luminal androgen receptor (LAR), 2) mesenchymal-like immune-activated (MLIA), 3) basal-like (BL), 4) suppressed (S) subtypes. Patients in the S subtype had the worst disease-free survival comparing to other patients (log-rank p = 0.021). Enriched clinically actionable pathways and putative therapeutic APA events were analyzed among each APA subtype. Furthermore, CPSF1 and PABPN1 were identified as the master C/P factors in regulating APA events and TNBC proliferation. The depletion of CPSF1 or PABPN1 weakened cell proliferation, enhanced apoptosis, resulted in cell cycle redistribution and a reversion of APA events of genes associated with tumorigenesis, proliferation, metastasis and chemosensitivity in breast cancer. Conclusions: Our findings advance the understanding of tumor heterogeneity regulation in APA and yield new insights into therapeutic target identification in TNBC.
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8
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Hsin CH, Stoffel MS, Gazzaz M, Schaeffeler E, Schwab M, Fuhr U, Taubert M. Combinations of common SNPs of the transporter gene ABCB1 influence apparent bioavailability, but not renal elimination of oral digoxin. Sci Rep 2020; 10:12457. [PMID: 32719417 PMCID: PMC7385621 DOI: 10.1038/s41598-020-69326-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
Effects of different genotypes on the pharmacokinetics of probe substrates may support their use as phenotyping agents for the activity of the respective enzyme or transporter. Digoxin is recommended as a probe substrate to assess the activity of the transporter P-glycoprotein (P-gp) in humans. Current studies on the individual effects of three commonly investigated single nucleotide polymorphisms (SNPs) of the ABCB1 gene encoding P-gp (C1236T, G2677T/A, and C3435T) on digoxin pharmacokinetics are inconclusive. Since SNPs are in incomplete linkage disequilibrium, considering combinations of these SNPs might be necessary to assess the role of polymorphisms in digoxin pharmacokinetics accurately. In this study, the relationship between SNP combinations and digoxin pharmacokinetics was explored via a population pharmacokinetic approach in 40 volunteers who received oral doses of 0.5 mg digoxin. Concerning the SNPs 1236/2677/3435, the following combinations were evaluated: CGC, CGT, and TTT. Carriers of CGC/CGT and TTT/TTT had 35% higher apparent bioavailability compared to the reference group CGC/CGC, while no difference was seen in CGC/TTT carriers. No significant effect on renal clearance was observed. The population pharmacokinetic model supports the use of oral digoxin as a phenotyping substrate of intestinal P-gp, but not to assess renal P-gp activity.
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Affiliation(s)
- Chih-Hsuan Hsin
- Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, University of Cologne, Cologne, Germany
| | - Marc S Stoffel
- Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, University of Cologne, Cologne, Germany
| | - Malaz Gazzaz
- Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, University of Cologne, Cologne, Germany.,Department of Clinical Pharmacy, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Elke Schaeffeler
- Dr. Margarete-Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete-Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Clinical Pharmacology, University of Tuebingen, Tuebingen, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Uwe Fuhr
- Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, University of Cologne, Cologne, Germany
| | - Max Taubert
- Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, University of Cologne, Cologne, Germany.
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9
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Yang J, Chen Y, Luo H, Cai H. The Landscape of Somatic Copy Number Alterations in Head and Neck Squamous Cell Carcinoma. Front Oncol 2020; 10:321. [PMID: 32226775 PMCID: PMC7080958 DOI: 10.3389/fonc.2020.00321] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/24/2020] [Indexed: 02/05/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Somatic copy number alterations (CNAs) play a significant role in the development of this lethal cancer. In this study, we present a meta-analysis of CNAs for a total of 1,395 HNSCC samples. Publicly available R packages and in-house scripts were used for genomic array data processing, including normalization, segmentation and CNA calling. We detected 125 regions of significant gains or losses using GISTIC algorithm and found several potential driver genes in these regions. The incidence of chromothripsis in HNSCC was estimated to be 6%, and the chromosome pulverization hotspot regions were detected. We determined 323 genomic locations significantly enriched for breakpoints, which indicate HNSCC-specific genomic instability regions. Unsupervised clustering of genome-wide CNA data revealed a sub-cluster predominantly composed of nasopharynx tumors and presented a large proportion of HPV-positive samples. These results will facilitate the discovery of therapeutic candidates and extend our molecular understanding of HNSCC.
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Affiliation(s)
- Jian Yang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi Chen
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Luo
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
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10
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Genome-wide somatic copy number alteration analysis and database construction for cervical cancer. Mol Genet Genomics 2020; 295:765-773. [PMID: 31901979 DOI: 10.1007/s00438-019-01636-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/06/2019] [Indexed: 12/24/2022]
Abstract
Cervical cancer is a common gynecological malignancy with high incidence and mortality. Somatic copy number alterations (CNAs) play an important role in identifying tumor suppressor genes and oncogenes and are a useful diagnostic indicator for many cancer types. However, the genomic landscape of CNAs in cervical cancer has not yet been comprehensively characterized. In the present study, we collected 974 cervical cancer samples from different data sources. All samples were analyzed by genomic arrays to obtain high-resolution CNAs. Focal genomic regions with CNA events and potential cancer driver genes were identified by GISTIC2.0. Meanwhile, we constructed a comprehensive cervical cancer database by PHP and self-written Perl and R scripts. In total, 54 recurrent regions of amplification and deletion were detected. Frequently altered tumor suppressor genes were found in these regions, including PIK3CA, ERBB2, EP300 and FBXW7. CNA hotspots and related enriched functional categories were also identified. The incidence of chromothripsis in cervical cancer was estimated to be 6.06%, and the chromosome pulverization hotspot regions were detected. Based on the curated data, we developed CNAdbCC (http://cailab.labshare.cn/CNAdbCC/), a comprehensive database for copy number alterations in cervical cancer. We provide a user-friendly Web interface for data mining and visualization. It is the most comprehensive public database devoted exclusively to genomic alterations in cervical cancer. These results extend our molecular understanding of cervical cancer. The database will enable researchers to explore specific CNA patterns in this lethal cancer and facilitate the discovery of therapeutic candidates.
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11
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Li Z, Zhang X, Hou C, Zhou Y, Chen J, Cai H, Ye Y, Liu J, Huang N. Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer. Int J Oncol 2019; 56:522-530. [PMID: 31894314 PMCID: PMC6959384 DOI: 10.3892/ijo.2019.4950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/30/2019] [Indexed: 12/27/2022] Open
Abstract
Triple‑negative breast cancer (TNBC) accounts for ~15% of all breast cancer diagnoses each year. Patients with TNBC tend to have a higher risk for early relapse and a worse prognosis. TNBC is characterized by extensive somatic copy number alterations (CNAs). However, the DNA CNA profile of TNBC remains to be extensively investigated. The present study assessed the genomic profile of CNAs in 201 TNBC samples, aiming to identify recurrent CNAs that may drive the pathogenesis of TNBC. In total, 123 regions of significant amplification and deletion were detected using the Genomic Identification of Significant Targets in Cancer algorithm, and potential driver genes for TNBC were identified. A total of 31 samples exhibited signs of chromothripsis and revealed chromosome pulverization hotspot regions. The present study further determined 199 genomic locations that were significantly enriched for breakpoints, which indicated TNBC‑specific genomic instability regions. Unsupervised hierarchical clustering of tumors resulted in three main subgroups that exhibited distinct CNA profiles, which may reveal the heterogeneity of molecular mechanisms in TNBC subgroups. These results will extend the molecular understanding of TNBC and will facilitate the discovery of therapeutic and diagnostic target candidates.
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Affiliation(s)
- Zaibing Li
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiao Zhang
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Chenxin Hou
- West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuqing Zhou
- West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Junli Chen
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Haoyang Cai
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio‑Resources and Eco‑Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Yifeng Ye
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Jinping Liu
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Ning Huang
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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12
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Rhie SK, Perez AA, Lay FD, Schreiner S, Shi J, Polin J, Farnham PJ. A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome. Nat Commun 2019; 10:4154. [PMID: 31515496 PMCID: PMC6742760 DOI: 10.1038/s41467-019-12079-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/15/2019] [Indexed: 12/27/2022] Open
Abstract
To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we develop high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer-promoter loop anchors. We also find that the chromatin structure surrounding the androgen receptor (AR) locus is altered in the prostate cancer cells with many cancer-specific enhancer-promoter loops. This creation of 3D epigenomic maps enables a better understanding of prostate cancer biology and mechanisms of gene regulation. In prostate cancer, chromatin structure can impact the transcriptome. Here, the authors develop high resolution chromatin interaction maps in prostate cancer cells using in situ Hi-C, revealing prostate cancer-specific TADs and enhancer-promoter loops surrounding the androgen receptor (AR) locus.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Andrew A Perez
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Fides D Lay
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jiani Shi
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jenevieve Polin
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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13
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Trueck C, Hsin CH, Scherf-Clavel O, Schaeffeler E, Lenssen R, Gazzaz M, Gersie M, Taubert M, Quasdorff M, Schwab M, Kinzig M, Sörgel F, Stoffel MS, Fuhr U. A Clinical Drug-Drug Interaction Study Assessing a Novel Drug Transporter Phenotyping Cocktail With Adefovir, Sitagliptin, Metformin, Pitavastatin, and Digoxin. Clin Pharmacol Ther 2019; 106:1398-1407. [PMID: 31247117 DOI: 10.1002/cpt.1564] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
A new probe drug cocktail containing substrates of important drug transporters was tested for mutual interactions in a clinical trial. The cocktail consisted of (predominant transporter; primary phenotyping metric): 10 mg adefovir-dipivoxil (OAT1; renal clearance (CLR )), 100 mg sitagliptin (OAT3; CLR ), 500 mg metformin (several renal transporters; CLR ), 2 mg pitavastatin (OATP1B1; clearance/F), and 0.5 mg digoxin (intestinal P-gp, renal P-gp, and OATP4C1; peak plasma concentration (Cmax ) and CLR ). Using a randomized six-period, open change-over design, single oral doses were administrated either concomitantly or separately to 24 healthy male and female volunteers. Phenotyping metrics were evaluated by noncompartmental analysis and compared between periods by the standard average bioequivalence approach (boundaries for ratios 0.80-1.25). Primary metrics supported the absence of relevant interactions, whereas secondary metrics suggested that mainly adefovir was a victim of minor drug-drug interactions (DDIs). All drugs were well tolerated. This cocktail may be another useful tool to assess transporter-based DDIs in vivo.
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Affiliation(s)
- Christina Trueck
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, Cologne, Germany
| | - Chih-Hsuan Hsin
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, Cologne, Germany
| | - Oliver Scherf-Clavel
- Institute for Biomedical and Pharmaceutical Research, Nürnberg-Heroldsberg, Germany
| | - Elke Schaeffeler
- Dr. Margarete-Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Rebekka Lenssen
- Hospital Pharmacy, University Hospital Cologne, Cologne, Germany
| | - Malaz Gazzaz
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, Cologne, Germany.,Department of Clinical Pharmacy, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Marleen Gersie
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, Cologne, Germany
| | - Max Taubert
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, Cologne, Germany
| | - Maria Quasdorff
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, Cologne, Germany
| | - Matthias Schwab
- University of Tuebingen, Tuebingen, Germany.,Department of Clinical Pharmacology, University Hospital Tuebingen, Tuebingen, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Martina Kinzig
- Institute for Biomedical and Pharmaceutical Research, Nürnberg-Heroldsberg, Germany
| | - Fritz Sörgel
- Institute for Biomedical and Pharmaceutical Research, Nürnberg-Heroldsberg, Germany.,Institute of Pharmacology, Faculty of Medicine, University Duisburg-Essen, Essen, Germany
| | - Marc S Stoffel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, Cologne, Germany
| | - Uwe Fuhr
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Pharmacology, Department I of Pharmacology, Cologne, Germany
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14
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Dogrusöz M, Ruschel Trasel A, Cao J, Ҫolak S, van Pelt SI, Kroes WGM, Teunisse AFAS, Alsafadi S, van Duinen SG, Luyten GPM, van der Velden PA, Amaro A, Pfeffer U, Jochemsen AG, Jager MJ. Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma. Cancers (Basel) 2019; 11:cancers11081104. [PMID: 31382494 PMCID: PMC6721581 DOI: 10.3390/cancers11081104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 01/20/2023] Open
Abstract
Expression of DNA repair genes was studied in uveal melanoma (UM) in order to identify genes that may play a role in metastases formation. We searched for genes that are differentially expressed between tumors with a favorable and unfavorable prognosis. Gene-expression profiling was performed on 64 primary UM from the Leiden University Medical Center (LUMC), Leiden, The Netherlands. The expression of 121 genes encoding proteins involved in DNA repair pathways was analyzed: a total of 44 genes differed between disomy 3 and monosomy 3 tumors. Results were validated in a cohort from Genoa and Paris and the The Cancer Genome Atlas (TCGA) cohort. Expression of the PRKDC, WDR48, XPC, and BAP1 genes was significantly associated with clinical outcome after validation. PRKDC was highly expressed in metastasizing UM (p < 0.001), whereas WDR48, XPC, and BAP1 were lowly expressed (p < 0.001, p = 0.006, p = 0.003, respectively). Low expression of WDR48 and XPC was related to a large tumor diameter (p = 0.01 and p = 0.004, respectively), and a mixed/epithelioid cell type (p = 0.007 and p = 0.03, respectively). We conclude that the expression of WDR48, XPC, and BAP1 is significantly lower in UM with an unfavorable prognosis, while these tumors have a significantly higher expression of PRKDC. Pharmacological inhibition of DNA-PKcs resulted in decreased survival of UM cells. PRKDC may be involved in proliferation, invasion and metastasis of UM cells. Unraveling the role of DNA repair genes may enhance our understanding of UM biology and result in the identification of new therapeutic targets.
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Affiliation(s)
- Mehmet Dogrusöz
- Department of Ophthalmology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
- Department of Ophthalmology, Amsterdam University Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Andrea Ruschel Trasel
- Department of Ophthalmology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
- Universidade Federal do Rio Grande do Sul, 90040-060 Porto Alegre, Brazil
| | - Jinfeng Cao
- Department of Ophthalmology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun 130012, China
| | - Selҫuk Ҫolak
- Department of Molecular Cell Biology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
- Center for Reproductive Medicine, Elisabeth-TweeSteden Hospital, 5022 GC Tilburg, The Netherlands
| | - Sake I van Pelt
- Department of Ophthalmology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
| | - Wilma G M Kroes
- Department of Clinical Genetics, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
| | - Amina F A S Teunisse
- Department of Clinical Genetics, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
| | - Samar Alsafadi
- Department of Translational Research, PSL Research University, Institute Curie, 75248 Paris, France
| | - Sjoerd G van Duinen
- Department of Pathology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
| | - Gregorius P M Luyten
- Department of Ophthalmology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
| | - Pieter A van der Velden
- Department of Ophthalmology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
| | - Adriana Amaro
- Laboratory of Tumor Epigenetics, Department of Integrated Oncology Therapies, IRCCS Ospedale Policlinico San Martino, 16133 Genoa, Italy
| | - Ulrich Pfeffer
- Laboratory of Tumor Epigenetics, Department of Integrated Oncology Therapies, IRCCS Ospedale Policlinico San Martino, 16133 Genoa, Italy
| | - Aart G Jochemsen
- Department of Molecular Cell Biology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, 2333 AZ Leiden, The Netherlands.
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15
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Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U. Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun 2018; 9:4446. [PMID: 30361538 PMCID: PMC6202389 DOI: 10.1038/s41467-018-06932-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 10/05/2018] [Indexed: 12/20/2022] Open
Abstract
In plants, transgenerational inheritance of some epialleles has been demonstrated but it remains controversial whether epigenetic variation is subject to selection and contributes to adaptation. Simulating selection in a rapidly changing environment, we compare phenotypic traits and epigenetic variation between Arabidopsis thaliana populations grown for five generations under selection and their genetically nearly identical ancestors. Selected populations of two distinct genotypes show significant differences in flowering time and plant architecture, which are maintained for at least 2–3 generations in the absence of selection. While we cannot detect consistent genetic changes, we observe a reduction of epigenetic diversity and changes in the methylation state of about 50,000 cytosines, some of which are associated with phenotypic changes. Thus, we propose that epigenetic variation is subject to selection and can contribute to rapid adaptive responses, although the extent to which epigenetics plays a role in adaptation is still unclear. Whether plant epigenetic variation is subject to selection and contributes to adaptation is under debate. Here, the authors compare DNA methylation and phenotypes of Arabidopsis lines subject to simulated selection and their nearly isogenic ancestors and provide evidence that epigenetic variation contributes to adaptive responses.
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Affiliation(s)
- Marc W Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Service and Support for Science IT, University of Zurich, Stampfenbachstrasse 73, 8006, Zurich, Switzerland.,MWSchmid GmbH, Möhrlistrasse 25, 8006, Zurich, Switzerland
| | - Christian Heichinger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,L. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Diana Coman Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Scientific IT Services, ETH Zurich, Weinbergstrasse 11, 8092, Zurich, Switzerland
| | - Daniela Guthörl
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Hochschulstrasse 6, 3012, Bern, Switzerland
| | - Sirisha Aluri
- Functional Genomics Center Zurich, ETH and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Bernhard Schmid
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lindsay A Turnbull
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland. .,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.
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16
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Aiderus A, Black MA, Dunbier AK. Fatty acid oxidation is associated with proliferation and prognosis in breast and other cancers. BMC Cancer 2018; 18:805. [PMID: 30092766 PMCID: PMC6085695 DOI: 10.1186/s12885-018-4626-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
Background Altered cellular metabolism is a hallmark of cancer but the association between utilisation of particular metabolic pathways in tumours and patient outcome is poorly understood. We sought to investigate the association between fatty acid metabolism and outcome in breast and other cancers. Methods Cox regression analysis and Gene Set Enrichment Analysis (GSEA) of a gene expression dataset from primary breast tumours with well annotated clinical and survival information was used to identify genesets associated with outcome. A geneset representing fatty acid oxidation (FAO) was then examined in other datasets. A doxycycline-inducible breast cancer cell line model overexpressing the rate-limiting enzyme in FAO, carnitine palmitoyl transferase 1A (CPT1A) was generated and analysed to confirm the association between FAO and cancer-associated characteristics in vitro. Results We identified a gene expression signature composed of 19 genes associated with fatty acid oxidation (FAO) that was significantly associated with patient outcome. We validated this observation in eight independent breast cancer datasets, and also observed the FAO signature to be prognostic in other cancer types. Furthermore, the FAO signature expression was significantly downregulated in tumours, compared to normal tissues from a variety of anatomic origins. In breast cancer, the expression of CPT1A was higher in oestrogen receptor (ER)-positive, compared to ER-negative tumours and cell lines. Importantly, overexpression of CPT1A significantly decreased the proliferation and wound healing migration rates of MDA-MB231 breast cancer cells, compared to basal expression control. Conclusions Our findings suggest that FAO is downregulated in multiple tumour types, and activation of this pathway may lower cancer cell proliferation, and is associated with improved outcomes in some cancers. Electronic supplementary material The online version of this article (10.1186/s12885-018-4626-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aziz Aiderus
- Centre for Translational Cancer Research and Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Michael A Black
- Centre for Translational Cancer Research and Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Anita K Dunbier
- Centre for Translational Cancer Research and Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand.
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17
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Patel N, Weekes D, Drosopoulos K, Gazinska P, Noel E, Rashid M, Mirza H, Quist J, Brasó-Maristany F, Mathew S, Ferro R, Pereira AM, Prince C, Noor F, Francesch-Domenech E, Marlow R, de Rinaldis E, Grigoriadis A, Linardopoulos S, Marra P, Tutt ANJ. Integrated genomics and functional validation identifies malignant cell specific dependencies in triple negative breast cancer. Nat Commun 2018; 9:1044. [PMID: 29535384 PMCID: PMC5849766 DOI: 10.1038/s41467-018-03283-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
Triple negative breast cancers (TNBCs) lack recurrent targetable driver mutations but demonstrate frequent copy number aberrations (CNAs). Here, we describe an integrative genomic and RNAi-based approach that identifies and validates gene addictions in TNBCs. CNAs and gene expression alterations are integrated and genes scored for pre-specified target features revealing 130 candidate genes. We test functional dependence on each of these genes using RNAi in breast cancer and non-malignant cells, validating malignant cell selective dependence upon 37 of 130 genes. Further analysis reveals a cluster of 13 TNBC addiction genes frequently co-upregulated that includes genes regulating cell cycle checkpoints, DNA damage response, and malignant cell selective mitotic genes. We validate the mechanism of addiction to a potential drug target: the mitotic kinesin family member C1 (KIFC1/HSET), essential for successful bipolar division of centrosome-amplified malignant cells and develop a potential selection biomarker to identify patients with tumors exhibiting centrosome amplification.
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Affiliation(s)
- Nirmesh Patel
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Daniel Weekes
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Konstantinos Drosopoulos
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Patrycja Gazinska
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Elodie Noel
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Mamun Rashid
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Hasan Mirza
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
- Cancer Bioinformatics, King's College London, London, SE1 9RT, UK
| | - Jelmar Quist
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
- Cancer Bioinformatics, King's College London, London, SE1 9RT, UK
| | - Fara Brasó-Maristany
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Sumi Mathew
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Riccardo Ferro
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Ana Mendes Pereira
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Cynthia Prince
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Farzana Noor
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Erika Francesch-Domenech
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Rebecca Marlow
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Emanuele de Rinaldis
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
- Precision Immunology Cluster, Sanofi, 640 Memorial Drive, Cambridge, MA, 02149, USA
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
- Cancer Bioinformatics, King's College London, London, SE1 9RT, UK
| | - Spiros Linardopoulos
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW7 3RP, UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Pierfrancesco Marra
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK
| | - Andrew N J Tutt
- Breast Cancer Now Research Unit, King's College London, London, SE1 9RT, UK.
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW7 3RP, UK.
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Hilberg F, Tontsch-Grunt U, Baum A, Le AT, Doebele RC, Lieb S, Gianni D, Voss T, Garin-Chesa P, Haslinger C, Kraut N. Triple Angiokinase Inhibitor Nintedanib Directly Inhibits Tumor Cell Growth and Induces Tumor Shrinkage via Blocking Oncogenic Receptor Tyrosine Kinases. J Pharmacol Exp Ther 2018; 364:494-503. [PMID: 29263244 PMCID: PMC6040086 DOI: 10.1124/jpet.117.244129] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022] Open
Abstract
The triple-angiokinase inhibitor nintedanib is an orally available, potent, and selective inhibitor of tumor angiogenesis by blocking the tyrosine kinase activities of vascular endothelial growth factor receptor (VEGFR) 1-3, platelet-derived growth factor receptor (PDGFR)-α and -β, and fibroblast growth factor receptor (FGFR) 1-3. Nintedanib has received regulatory approval as second-line treatment of adenocarcinoma non-small cell lung cancer (NSCLC), in combination with docetaxel. In addition, nintedanib has been approved for the treatment of idiopathic lung fibrosis. Here we report the results from a broad kinase screen that identified additional kinases as targets for nintedanib in the low nanomolar range. Several of these kinases are known to be mutated or overexpressed and are involved in tumor development (discoidin domain receptor family, member 1 and 2, tropomyosin receptor kinase A (TRKA) and C, rearranged during transfection proto-oncogene [RET proto oncogene]), as well as in fibrotic diseases (e.g., DDRs). In tumor cell lines displaying molecular alterations in potential nintedanib targets, the inhibitor demonstrates direct antiproliferative effects: in the NSCLC cell line NCI-H1703 carrying a PDGFRα amplification (ampl.); the gastric cancer cell line KatoIII and the breast cancer cell line MFM223, both driven by a FGFR2 amplification; AN3CA (endometrial carcinoma) bearing a mutated FGFR2; the acute myeloid leukemia cell lines MOLM-13 and MV-4-11-B with FLT3 mutations; and the NSCLC adenocarcinoma LC-2/ad harboring a CCDC6-RET fusion. Potent kinase inhibition does not, however, strictly translate into antiproliferative activity, as demonstrated in the TRKA-dependent cell lines CUTO-3 and KM-12. Importantly, nintedanib treatment of NCI-H1703 tumor xenografts triggered effective tumor shrinkage, indicating a direct effect on the tumor cells in addition to the antiangiogenic effect on the tumor stroma. These findings will be instructive in guiding future genome-based clinical trials of nintedanib.
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Affiliation(s)
- Frank Hilberg
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Ulrike Tontsch-Grunt
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Anke Baum
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Anh T Le
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Robert C Doebele
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Simone Lieb
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Davide Gianni
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Tilman Voss
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Pilar Garin-Chesa
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Christian Haslinger
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
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19
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ITGB1-dependent upregulation of Caveolin-1 switches TGFβ signalling from tumour-suppressive to oncogenic in prostate cancer. Sci Rep 2018; 8:2338. [PMID: 29402961 PMCID: PMC5799174 DOI: 10.1038/s41598-018-20161-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/15/2018] [Indexed: 01/10/2023] Open
Abstract
Caveolin-1 (CAV1) is over-expressed in prostate cancer (PCa) and is associated with adverse prognosis, but the molecular mechanisms linking CAV1 expression to disease progression are poorly understood. Extensive gene expression correlation analysis, quantitative multiplex imaging of clinical samples, and analysis of the CAV1-dependent transcriptome, supported that CAV1 re-programmes TGFβ signalling from tumour suppressive to oncogenic (i.e. induction of SLUG, PAI-1 and suppression of CDH1, DSP, CDKN1A). Supporting such a role, CAV1 knockdown led to growth arrest and inhibition of cell invasion in prostate cancer cell lines. Rationalized RNAi screening and high-content microscopy in search for CAV1 upstream regulators revealed integrin beta1 (ITGB1) and integrin associated proteins as CAV1 regulators. Our work suggests TGFβ signalling and beta1 integrins as potential therapeutic targets in PCa over-expressing CAV1, and contributes to better understand the paradoxical dual role of TGFβ in tumour biology.
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20
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Efremova M, Rieder D, Klepsch V, Charoentong P, Finotello F, Hackl H, Hermann-Kleiter N, Löwer M, Baier G, Krogsdam A, Trajanoski Z. Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution. Nat Commun 2018; 9:32. [PMID: 29296022 PMCID: PMC5750210 DOI: 10.1038/s41467-017-02424-0] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023] Open
Abstract
The cancer immunoediting hypothesis postulates a dual role of the immune system: protecting the host by eliminating tumor cells, and shaping the tumor by editing its genome. Here, we elucidate the impact of evolutionary and immune-related forces on editing the tumor in a mouse model for hypermutated and microsatellite-instable colorectal cancer. Analyses of wild-type and immunodeficient RAG1 knockout mice transplanted with MC38 cells reveal that upregulation of checkpoint molecules and infiltration by Tregs are the major tumor escape mechanisms. Our results show that the effects of immunoediting are weak and that neutral accumulation of mutations dominates. Targeting the PD-1/PD-L1 pathway using immune checkpoint blocker effectively potentiates immunoediting. The immunoediting effects are less pronounced in the CT26 cell line, a non-hypermutated/microsatellite-instable model. Our study demonstrates that neutral evolution is another force that contributes to sculpting the tumor and that checkpoint blockade effectively enforces T-cell-dependent immunoselective pressure. The cancer immunoediting hypothesis assumes the immune system sculpts the cancer genome. Here the authors show, in a mouse model, that neutral evolution outweighs the effects of immunoselection and that immune checkpoint blockade potentiates the immunoediting, switching the system to non-neutral evolution.
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Affiliation(s)
- Mirjana Efremova
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Victoria Klepsch
- Division of Translational Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Pornpimol Charoentong
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Francesca Finotello
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Martin Löwer
- TRON -Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Gottfried Baier
- Division of Translational Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
| | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
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21
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Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O. A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression. Methods Mol Biol 2018; 1702:247-276. [PMID: 29119509 DOI: 10.1007/978-1-4939-7456-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Unraveling mechanisms underlying diseases has motivated the development of systems biology approaches. The key challenges for the development of mathematical models and computational tool are (1) the size of molecular networks, (2) the nonlinear nature of spatio-temporal interactions, and (3) feedback loops in the structure of interaction networks. We here propose an integrative workflow that combines structural analyses of networks, high-throughput data, and mechanistic modeling. As an illustration of the workflow, we use prostate cancer as a case study with the aim of identifying key functional components associated with primary to metastasis transitions. Analysis carried out by the workflow revealed that HOXD10, BCL2, and PGR are the most important factors affected in primary prostate samples, whereas, in the metastatic state, STAT3, JUN, and JUNB are playing a central role. The identified key elements of each network are validated using patient survival analysis. The workflow presented here allows experimentalists to use heterogeneous data sources for the identification of diagnostic and prognostic signatures.
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Affiliation(s)
- Faiz M Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Mehdi Sadeghi
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
| | - Shailendra K Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany.,Chhattisgarh Swami Vivekanand Technical University, Bhilai, Chhattisgarh, India
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany. .,Chhattisgarh Swami Vivekanand Technical University, Bhilai, Chhattisgarh, India. .,Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre, Stellenbosch University, Stellenbosch, South Africa.
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22
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Jabs V, Edlund K, König H, Grinberg M, Madjar K, Rahnenführer J, Ekman S, Bergkvist M, Holmberg L, Ickstadt K, Botling J, Hengstler JG, Micke P. Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer. PLoS One 2017; 12:e0187246. [PMID: 29112949 PMCID: PMC5675410 DOI: 10.1371/journal.pone.0187246] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 10/17/2017] [Indexed: 12/27/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) represents a genomically unstable cancer type with extensive copy number aberrations. The relationship of gene copy number alterations and subsequent mRNA levels has only fragmentarily been described. The aim of this study was to conduct a genome-wide analysis of gene copy number gains and corresponding gene expression levels in a clinically well annotated NSCLC patient cohort (n = 190) and their association with survival. While more than half of all analyzed gene copy number-gene expression pairs showed statistically significant correlations (10,296 of 18,756 genes), high correlations, with a correlation coefficient >0.7, were obtained only in a subset of 301 genes (1.6%), including KRAS, EGFR and MDM2. Higher correlation coefficients were associated with higher copy number and expression levels. Strong correlations were frequently based on few tumors with high copy number gains and correspondingly increased mRNA expression. Among the highly correlating genes, GO groups associated with posttranslational protein modifications were particularly frequent, including ubiquitination and neddylation. In a meta-analysis including 1,779 patients we found that survival associated genes were overrepresented among highly correlating genes (61 of the 301 highly correlating genes, FDR adjusted p<0.05). Among them are the chaperone CCT2, the core complex protein NUP107 and the ubiquitination and neddylation associated protein CAND1. In conclusion, in a comprehensive analysis we described a distinct set of highly correlating genes. These genes were found to be overrepresented among survival-associated genes based on gene expression in a large collection of publicly available datasets.
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Affiliation(s)
- Verena Jabs
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at Dortmund University, Dortmund, Germany
| | - Helena König
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | | | - Katrin Madjar
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | | | - Simon Ekman
- Department of Oncology, Karolinska University Hospital, Stockholm, Sweden
| | | | - Lars Holmberg
- Regional Cancer Center Uppsala-Örebro, Uppsala, Sweden
- King’s College London, Faculty of Life Sciences and Medicine, Division of Cancer Studies, London, United Kingdom
| | - Katja Ickstadt
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Johan Botling
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at Dortmund University, Dortmund, Germany
| | - Patrick Micke
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- * E-mail:
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23
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Danziger SA, Miller LR, Singh K, Whitney GA, Peskind ER, Li G, Lipshutz RJ, Aitchison JD, Smith JJ. An indicator cell assay for blood-based diagnostics. PLoS One 2017; 12:e0178608. [PMID: 28594877 PMCID: PMC5464608 DOI: 10.1371/journal.pone.0178608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 05/16/2017] [Indexed: 11/30/2022] Open
Abstract
We have established proof of principle for the Indicator Cell Assay Platform™ (iCAP™), a broadly applicable tool for blood-based diagnostics that uses specifically-selected, standardized cells as biosensors, relying on their innate ability to integrate and respond to diverse signals present in patients' blood. To develop an assay, indicator cells are exposed in vitro to serum from case or control subjects and their global differential response patterns are used to train reliable, disease classifiers based on a small number of features. In a feasibility study, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value = 3.81E-6) and correctly identified samples from a murine Huntington's disease model as non-carriers of ALS. Beyond the mouse model, in a preliminary human disease study, the iCAP detected early stage Alzheimer's disease with 72% cross-validated accuracy (p-Value = 3.10E-3). For both assays, iCAP features were enriched for disease-related genes, supporting the assay's relevance for disease research.
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Affiliation(s)
- Samuel A. Danziger
- Institute for Systems Biology, Seattle, WA, United States of America
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, United States of America
| | - Leslie R. Miller
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Karanbir Singh
- Institute for Systems Biology, Seattle, WA, United States of America
| | | | - Elaine R. Peskind
- Northwest Network (VISN-20) Mental Illness, Research, Education, and Clinical Center (MIRECC), VA Puget Sound, Seattle, WA, United States of America
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States of America
| | - Ge Li
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States of America
- Geriatric Research, Education, and Clinical Center, Veterans Affairs (VA) Puget Sound Health Care System (VA Puget Sound), Seattle, WA, United States of America
| | - Robert J. Lipshutz
- Institute for Systems Biology, Seattle, WA, United States of America
- PreCyte Inc., Seattle, WA, United States of America
| | - John D. Aitchison
- Institute for Systems Biology, Seattle, WA, United States of America
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, United States of America
| | - Jennifer J. Smith
- Institute for Systems Biology, Seattle, WA, United States of America
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, United States of America
- PreCyte Inc., Seattle, WA, United States of America
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24
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Aure MR, Vitelli V, Jernström S, Kumar S, Krohn M, Due EU, Haukaas TH, Leivonen SK, Vollan HKM, Lüders T, Rødland E, Vaske CJ, Zhao W, Møller EK, Nord S, Giskeødegård GF, Bathen TF, Caldas C, Tramm T, Alsner J, Overgaard J, Geisler J, Bukholm IRK, Naume B, Schlichting E, Sauer T, Mills GB, Kåresen R, Mælandsmo GM, Lingjærde OC, Frigessi A, Kristensen VN, Børresen-Dale AL, Sahlberg KK. Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome. Breast Cancer Res 2017; 19:44. [PMID: 28356166 PMCID: PMC5372339 DOI: 10.1186/s13058-017-0812-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 02/05/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Breast cancer is a heterogeneous disease at the clinical and molecular level. In this study we integrate classifications extracted from five different molecular levels in order to identify integrated subtypes. METHODS Tumor tissue from 425 patients with primary breast cancer from the Oslo2 study was cut and blended, and divided into fractions for DNA, RNA and protein isolation and metabolomics, allowing the acquisition of representative and comparable molecular data. Patients were stratified into groups based on their tumor characteristics from five different molecular levels, using various clustering methods. Finally, all previously identified and newly determined subgroups were combined in a multilevel classification using a "cluster-of-clusters" approach with consensus clustering. RESULTS Based on DNA copy number data, tumors were categorized into three groups according to the complex arm aberration index. mRNA expression profiles divided tumors into five molecular subgroups according to PAM50 subtyping, and clustering based on microRNA expression revealed four subgroups. Reverse-phase protein array data divided tumors into five subgroups. Hierarchical clustering of tumor metabolic profiles revealed three clusters. Combining DNA copy number and mRNA expression classified tumors into seven clusters based on pathway activity levels, and tumors were classified into ten subtypes using integrative clustering. The final consensus clustering that incorporated all aforementioned subtypes revealed six major groups. Five corresponded well with the mRNA subtypes, while a sixth group resulted from a split of the luminal A subtype; these tumors belonged to distinct microRNA clusters. Gain-of-function studies using MCF-7 cells showed that microRNAs differentially expressed between the luminal A clusters were important for cancer cell survival. These microRNAs were used to validate the split in luminal A tumors in four independent breast cancer cohorts. In two cohorts the microRNAs divided tumors into subgroups with significantly different outcomes, and in another a trend was observed. CONCLUSIONS The six integrated subtypes identified confirm the heterogeneity of breast cancer and show that finer subdivisions of subtypes are evident. Increasing knowledge of the heterogeneity of the luminal A subtype may add pivotal information to guide therapeutic choices, evidently bringing us closer to improved treatment for this largest subgroup of breast cancer.
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Affiliation(s)
- Miriam Ragle Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Valeria Vitelli
- Oslo Center for Biostatistics and Epidemiology, Institute of Basic Medical Science, University of Oslo, Oslo, Norway
| | - Sandra Jernström
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Surendra Kumar
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Marit Krohn
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eldri U. Due
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tonje Husby Haukaas
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Suvi-Katri Leivonen
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Hans Kristian Moen Vollan
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torben Lüders
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Einar Rødland
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | | | - Wei Zhao
- Department of Systems Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Elen K. Møller
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guro F. Giskeødegård
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Tone Frost Bathen
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Carlos Caldas
- Cambridge University Hospitals Trust, Addenbrookes Hospital, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Trine Tramm
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jan Alsner
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Overgaard
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jürgen Geisler
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ida R. K. Bukholm
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Surgery, Akershus University Hospital, Lørenskog, Norway
| | - Bjørn Naume
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Ellen Schlichting
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Breast and Endocrine Surgery, Oslo University Hospital, Oslo, Norway
| | - Torill Sauer
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
| | - Gordon B. Mills
- Department of Systems Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Rolf Kåresen
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Breast and Endocrine Surgery, Oslo University Hospital, Oslo, Norway
| | - Gunhild M. Mælandsmo
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Ole Christian Lingjærde
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Computer Science, University of Oslo, Oslo, Norway
| | - Arnoldo Frigessi
- Oslo Center for Biostatistics and Epidemiology, Institute of Basic Medical Science, University of Oslo, Oslo, Norway
- Oslo Center for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Vessela N. Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kristine K. Sahlberg
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Research, Vestre Viken Hospital Trust, Drammen, Norway
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25
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van de Ven RA, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K, van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer MW, Sahai E, Derksen PW. p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. Nat Commun 2016; 7:13874. [PMID: 28004812 PMCID: PMC5192218 DOI: 10.1038/ncomms13874] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/07/2016] [Indexed: 02/07/2023] Open
Abstract
Spatiotemporal activation of RhoA and actomyosin contraction underpins cellular adhesion and division. Loss of cell-cell adhesion and chromosomal instability are cardinal events that drive tumour progression. Here, we show that p120-catenin (p120) not only controls cell-cell adhesion, but also acts as a critical regulator of cytokinesis. We find that p120 regulates actomyosin contractility through concomitant binding to RhoA and the centralspindlin component MKLP1, independent of cadherin association. In anaphase, p120 is enriched at the cleavage furrow where it binds MKLP1 to spatially control RhoA GTPase cycling. Binding of p120 to MKLP1 during cytokinesis depends on the N-terminal coiled-coil domain of p120 isoform 1A. Importantly, clinical data show that loss of p120 expression is a common event in breast cancer that strongly correlates with multinucleation and adverse patient survival. In summary, our study identifies p120 loss as a driver event of chromosomal instability in cancer.
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Affiliation(s)
- Robert A.H. van de Ven
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Jolien S. de Groot
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Danielle Park
- Tumour Cell Biology Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Robert van Domselaar
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Danielle de Jong
- Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Elsken van der Wall
- Department of Internal Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - H. Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Paul J. van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Martin W. Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Erik Sahai
- Tumour Cell Biology Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Patrick W.B. Derksen
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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26
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van Essen TH, van Pelt SI, Bronkhorst IHG, Versluis M, Némati F, Laurent C, Luyten GPM, van Hall T, van den Elsen PJ, van der Velden PA, Decaudin D, Jager MJ. Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes. PLoS One 2016; 11:e0164292. [PMID: 27764126 PMCID: PMC5072555 DOI: 10.1371/journal.pone.0164292] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 09/22/2016] [Indexed: 12/22/2022] Open
Abstract
Introduction Uveal melanoma (UM) with an inflammatory phenotype, characterized by infiltrating leukocytes and increased human leukocyte antigen (HLA) expression, carry an increased risk of death due to metastases. These tumors should be ideal for T-cell based therapies, yet it is not clear why prognostically-infaust tumors have a high HLA expression. We set out to determine whether the level of HLA molecules in UM is associated with other genetic factors, HLA transcriptional regulators, or microenvironmental factors. Methods 28 enucleated UM were used to study HLA class I and II expression, and several regulators of HLA by immunohistochemistry, PCR microarray, qPCR and chromosome SNP-array. Fresh tumor samples of eight primary UM and four metastases were compared to their corresponding xenograft in SCID mice, using a PCR microarray and SNP array. Results Increased expression levels of HLA class I and II showed no dosage effect of chromosome 6p, but, as expected, were associated with monosomy of chromosome 3. Increased HLA class I and II protein levels were positively associated with their gene expression and with raised levels of the peptide-loading gene TAP1, and HLA transcriptional regulators IRF1, IRF8, CIITA, and NLRC5, revealing a higher transcriptional activity in prognostically-bad tumors. Implantation of fresh human tumor samples into SCID mice led to a loss of infiltrating leukocytes, and to a decreased expression of HLA class I and II genes, and their regulators. Conclusion Our data provides evidence for a proper functioning HLA regulatory system in UM, offering a target for T-cell based therapies.
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Affiliation(s)
| | - Sake I van Pelt
- Department of Medical Statistics, LUMC, Leiden, the Netherlands
| | | | - Mieke Versluis
- Department of Ophthalmology, LUMC, Leiden, the Netherlands
| | - Fariba Némati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
| | - Cécile Laurent
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
| | | | | | - Peter J van den Elsen
- Department of Immunohematology and Blood Transfusion, LUMC, Leiden, the Netherlands.,Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France.,Department of Clinical Hematology, Institut Curie, Paris France
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27
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Kanojia D, Nagata Y, Garg M, Lee DH, Sato A, Yoshida K, Sato Y, Sanada M, Mayakonda A, Bartenhagen C, Klein HU, Doan NB, Said JW, Mohith S, Gunasekar S, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Myklebost O, Yang H, Dugas M, Meza-Zepeda LA, Silberman AW, Forscher C, Tyner JW, Ogawa S, Koeffler HP. Genomic landscape of liposarcoma. Oncotarget 2016; 6:42429-44. [PMID: 26643872 PMCID: PMC4767443 DOI: 10.18632/oncotarget.6464] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/26/2015] [Indexed: 01/09/2023] Open
Abstract
Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.
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Affiliation(s)
- Deepika Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manoj Garg
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Dhong Hyun Lee
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA
| | - Aiko Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Sanada
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Hans-Ulrich Klein
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Ngan B Doan
- Department of Pathology and Laboratory Medicine, Santa Monica-University of California-Los Angeles Medical Center, Los Angeles, California, USA
| | - Jonathan W Said
- Department of Pathology and Laboratory Medicine, Santa Monica-University of California-Los Angeles Medical Center, Los Angeles, California, USA
| | - S Mohith
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Swetha Gunasekar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ola Myklebost
- Norwegian Cancer Genomics Consortium and Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Department of Molecular Bioscience, University of Oslo, Oslo, Norway
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Leonardo A Meza-Zepeda
- Norwegian Cancer Genomics Consortium and Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Allan W Silberman
- Department of Surgery, Cedars Sinai Medical Center, Division of Surgical Oncology, Los Angeles, California, USA
| | - Charles Forscher
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Cell and Developmental Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA.,National University Cancer Institute, National University Hospital, Singapore
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28
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Yang J, Liu J, Ouyang L, Chen Y, Liu B, Cai H. CTLPScanner: a web server for chromothripsis-like pattern detection. Nucleic Acids Res 2016; 44:W252-8. [PMID: 27185889 PMCID: PMC4987951 DOI: 10.1093/nar/gkw434] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/08/2016] [Indexed: 02/05/2023] Open
Abstract
Chromothripsis is a recently observed phenomenon in cancer cells in which one or several chromosomes shatter into pieces with subsequent inaccurate reassembly and clonal propagation. This type of event generates a potentially vast number of mutations within a relatively short-time period, and has been considered as a new paradigm in cancer development. Despite recent advances, much work is still required to better understand the molecular mechanisms of this phenomenon, and thus an easy-to-use tool is in urgent need for automatically detecting and annotating chromothripsis. Here we present CTLPScanner, a web server for detection of chromothripsis-like pattern (CTLP) in genomic array data. The output interface presents intuitive graphical representations of detected chromosome pulverization region, as well as detailed results in table format. CTLPScanner also provides additional information for associated genes in chromothripsis region to help identify the potential candidates involved in tumorigenesis. To assist in performing meta-data analysis, we integrated over 50 000 pre-processed genomic arrays from The Cancer Genome Atlas and Gene Expression Omnibus into CTLPScanner. The server allows users to explore the presence of chromothripsis signatures from public data resources, without carrying out any local data processing. CTLPScanner is freely available at http://cgma.scu.edu.cn/CTLPScanner/.
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Affiliation(s)
- Jian Yang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Jixiang Liu
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China
| | - Yi Chen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Bo Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
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29
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Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Res 2016; 26:719-31. [PMID: 27053337 PMCID: PMC4889976 DOI: 10.1101/gr.201517.115] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/04/2016] [Indexed: 12/29/2022]
Abstract
A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type–specific gene expression profiles. Here, we performed Hi-C chromosome conformation capture sequencing to investigate how three-dimensional chromatin organization is disrupted in the context of copy-number variation, long-range epigenetic remodeling, and atypical gene expression programs in prostate cancer. We find that cancer cells retain the ability to segment their genomes into megabase-sized topologically associated domains (TADs); however, these domains are generally smaller due to establishment of additional domain boundaries. Interestingly, a large proportion of the new cancer-specific domain boundaries occur at regions that display copy-number variation. Notably, a common deletion on 17p13.1 in prostate cancer spanning the TP53 tumor suppressor locus results in bifurcation of a single TAD into two distinct smaller TADs. Change in domain structure is also accompanied by novel cancer-specific chromatin interactions within the TADs that are enriched at regulatory elements such as enhancers, promoters, and insulators, and associated with alterations in gene expression. We also show that differential chromatin interactions across regulatory regions occur within long-range epigenetically activated or silenced regions of concordant gene activation or repression in prostate cancer. Finally, we present a novel visualization tool that enables integrated exploration of Hi-C interaction data, the transcriptome, and epigenome. This study provides new insights into the relationship between long-range epigenetic and genomic dysregulation and changes in higher-order chromatin interactions in cancer.
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30
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Cutcutache I, Wu AY, Suzuki Y, McPherson JR, Lei Z, Deng N, Zhang S, Wong WK, Soo KC, Chan WH, Ooi LL, Welsch R, Tan P, Rozen SG. Abundant copy-number loss of CYCLOPS and STOP genes in gastric adenocarcinoma. Gastric Cancer 2016; 19. [PMID: 26205786 PMCID: PMC4824836 DOI: 10.1007/s10120-015-0514-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer, a leading cause of cancer death worldwide, has been little studied compared with other cancers that impose similar health burdens. Our goal is to assess genomic copy-number loss and the possible functional consequences and therapeutic implications thereof across a large series of gastric adenocarcinomas. METHODS We used high-density single-nucleotide polymorphism microarrays to determine patterns of copy-number loss and allelic imbalance in 74 gastric adenocarcinomas. We investigated whether suppressor of tumorigenesis and/or proliferation (STOP) genes are associated with genomic copy-number loss. We also analyzed the extent to which copy-number loss affects Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes-genes that may be attractive targets for therapeutic inhibition when partially deleted. RESULTS The proportion of the genome subject to copy-number loss varies considerably from tumor to tumor, with a median of 5.5 %, and a mean of 12 % (range 0-58.5 %). On average, 91 STOP genes were subject to copy-number loss per tumor (median 35, range 0-452), and STOP genes tended to have lower copy-number compared with the rest of the genes. Furthermore, on average, 1.6 CYCLOPS genes per tumor were both subject to copy-number loss and downregulated, and 51.4 % of the tumors had at least one such gene. CONCLUSIONS The enrichment of STOP genes in regions of copy-number loss indicates that their deletion may contribute to gastric carcinogenesis. Furthermore, the presence of several deleted and downregulated CYCLOPS genes in some tumors suggests potential therapeutic targets in these tumors.
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Affiliation(s)
- Ioana Cutcutache
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Alice Yingting Wu
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
| | - Yuka Suzuki
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - John Richard McPherson
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Zhengdeng Lei
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Niantao Deng
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Shenli Zhang
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Wai Keong Wong
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
| | - Khee Chee Soo
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
- />Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Weng Hoong Chan
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
| | - London Lucien Ooi
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
- />Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Roy Welsch
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
- />Engineering Systems Division and Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Patrick Tan
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
- />Duke-NUS Genome Biology Facility, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Genome Institute of Singapore, A* STAR, Singapore, Singapore
| | - Steven G. Rozen
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
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31
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Kanojia D, Nagata Y, Garg M, Lee DH, Sato A, Yoshida K, Sato Y, Sanada M, Mayakonda A, Bartenhagen C, Klein HU, Doan NB, Said JW, Mohith S, Gunasekar S, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Myklebost O, Yang H, Dugas M, Meza-Zepeda LA, Silberman AW, Forscher C, Tyner JW, Ogawa S, Koeffler HP. Genomic landscape of liposarcoma. Oncotarget 2015. [PMID: 26643872 DOI: 10.1832/oncotarget.3575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.
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Affiliation(s)
- Deepika Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manoj Garg
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Dhong Hyun Lee
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA
| | - Aiko Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Sanada
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Hans-Ulrich Klein
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Ngan B Doan
- Department of Pathology and Laboratory Medicine, Santa Monica-University of California-Los Angeles Medical Center, Los Angeles, California, USA
| | - Jonathan W Said
- Department of Pathology and Laboratory Medicine, Santa Monica-University of California-Los Angeles Medical Center, Los Angeles, California, USA
| | - S Mohith
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Swetha Gunasekar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ola Myklebost
- Norwegian Cancer Genomics Consortium and Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Molecular Bioscience, University of Oslo, Oslo, Norway
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Leonardo A Meza-Zepeda
- Norwegian Cancer Genomics Consortium and Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Allan W Silberman
- Department of Surgery, Cedars Sinai Medical Center, Division of Surgical Oncology, Los Angeles, California, USA
| | - Charles Forscher
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Cell and Developmental Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA
- National University Cancer Institute, National University Hospital, Singapore
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32
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Ng J, Fass JN, Durbin-Johnson B, Smith DG, Kanthaswamy S. Identifying rhesus macaque gene orthologs using heterospecific human CNV probes. GENOMICS DATA 2015; 6:202-7. [PMID: 26697375 PMCID: PMC4664757 DOI: 10.1016/j.gdata.2015.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/12/2015] [Indexed: 12/14/2022]
Abstract
We used the Affymetrix(®) Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.
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Affiliation(s)
- Jillian Ng
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA
| | - Joseph N. Fass
- Genome Center Bioinformatics Core, University of California, Davis, CA, USA
| | | | - David Glenn Smith
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Sree Kanthaswamy
- California National Primate Research Center, University of California, Davis, CA, USA
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA
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33
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Mihailovich M, Bremang M, Spadotto V, Musiani D, Vitale E, Varano G, Zambelli F, Mancuso FM, Cairns DA, Pavesi G, Casola S, Bonaldi T. miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nat Commun 2015; 6:8725. [PMID: 26555894 PMCID: PMC4667639 DOI: 10.1038/ncomms9725] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/22/2015] [Indexed: 01/07/2023] Open
Abstract
The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 3′ untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c-MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 3′ UTR shortening at different stages of tumorigenesis. The synergism between c-MYC and miR-17-19b plays an important role in lymphoma initiation. In this study, the authors identify a panel of targets co-regulated by miR-17-19b and in MYC-driven lymphoma and unravel the molecular mechanism through which miR-17-19b inhibits MYC translation.
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Affiliation(s)
- Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Valeria Spadotto
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Daniele Musiani
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Elena Vitale
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Gabriele Varano
- Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | | | - Francesco M Mancuso
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - David A Cairns
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Giulio Pavesi
- Department of Biosciences, Milan University, Milan 20133, Italy
| | - Stefano Casola
- Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
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34
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Petrovics G, Li H, Stümpel T, Tan SH, Young D, Katta S, Li Q, Ying K, Klocke B, Ravindranath L, Kohaar I, Chen Y, Ribli D, Grote K, Zou H, Cheng J, Dalgard CL, Zhang S, Csabai I, Kagan J, Takeda D, Loda M, Srivastava S, Scherf M, Seifert M, Gaiser T, McLeod DG, Szallasi Z, Ebner R, Werner T, Sesterhenn IA, Freedman M, Dobi A, Srivastava S. A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men. EBioMedicine 2015; 2:1957-64. [PMID: 26844274 PMCID: PMC4703707 DOI: 10.1016/j.ebiom.2015.10.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/22/2015] [Accepted: 10/29/2015] [Indexed: 02/03/2023] Open
Abstract
Evaluation of cancer genomes in global context is of great interest in light of changing ethnic distribution of the world population. We focused our study on men of African ancestry because of their disproportionately higher rate of prostate cancer (CaP) incidence and mortality. We present a systematic whole genome analyses, revealing alterations that differentiate African American (AA) and Caucasian American (CA) CaP genomes. We discovered a recurrent deletion on chromosome 3q13.31 centering on the LSAMP locus that was prevalent in tumors from AA men (cumulative analyses of 435 patients: whole genome sequence, 14; FISH evaluations, 101; and SNP array, 320 patients). Notably, carriers of this deletion experienced more rapid disease progression. In contrast, PTEN and ERG common driver alterations in CaP were significantly lower in AA prostate tumors compared to prostate tumors from CA. Moreover, the frequency of inter-chromosomal rearrangements was significantly higher in AA than CA tumors. These findings reveal differentially distributed somatic mutations in CaP across ancestral groups, which have implications for precision medicine strategies.
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Affiliation(s)
- Gyorgy Petrovics
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Hua Li
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | | | - Shyh-Han Tan
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Denise Young
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Shilpa Katta
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Qiyuan Li
- Medical College, Xiamen University, Xiamen 361102, China; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kai Ying
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | | | - Lakshmi Ravindranath
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Indu Kohaar
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Yongmei Chen
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Dezső Ribli
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest H-1117, Hungary; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, DK -2800, Denmark
| | | | - Hua Zou
- CytoTest Inc., Rockville, MD 20850, USA
| | | | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Shimin Zhang
- Genitourinary Pathology, Joint Pathology Center, Silver Spring, MD 20910, USA
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest H-1117, Hungary; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, DK -2800, Denmark
| | - Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Takeda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Massimo Loda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA
| | | | | | - Timo Gaiser
- Pathologisches Institut, Universitätsmedizin Mannheim, Medizinische Fakultät Mannheim der Universität Heidelberg, Mannheim D-68167, Germany
| | - David G McLeod
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; Urology Service, Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, DK -2800, Denmark; Children's Hospital Informatics Program at the Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 20115, USA; MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, 2nd Department of Pathology, Semmelweis University, Budapest H-1091, Hungary
| | | | - Thomas Werner
- Genomatix Software GmbH, MünchenE D-80335, Germany; Internal Medicine, Nephrology Division and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Matthew Freedman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Albert Dobi
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
| | - Shiv Srivastava
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA
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35
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Torabi K, Miró R, Fernández-Jiménez N, Quintanilla I, Ramos L, Prat E, del Rey J, Pujol N, Killian JK, Meltzer PS, Fernández PL, Ried T, Lozano JJ, Camps J, Ponsa I. Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer. Carcinogenesis 2015; 36:1103-10. [PMID: 26243311 PMCID: PMC4598814 DOI: 10.1093/carcin/bgv115] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/06/2015] [Accepted: 07/29/2015] [Indexed: 01/17/2023] Open
Abstract
Colorectal cancer (CRC) is characterized by specific patterns of copy number alterations (CNAs), which helped with the identification of driver oncogenes and tumor suppressor genes (TSGs). More recently, the usage of single nucleotide polymorphism arrays provided information of copy number neutral loss of heterozygosity, thus suggesting the occurrence of somatic uniparental disomy (UPD) and uniparental polysomy (UPP) events. The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs and CNAs in sporadic CRC. Our results indicate that regions showing high frequencies of UPD/UPP mostly coincide with regions typically involved in genomic losses. Among them, chromosome arms 3p, 5q, 9q, 10q, 14q, 17p, 17q, 20p, 21q and 22q preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. Several regions affected by recurrent UPDs/UPPs contain well-known TSGs, as well as novel candidates such as ARID1A, DLC1, TCF7L2 and DMBT1. In addition, VCAN, FLT4, SFRP1 and GAS7 were also frequently involved in regions of UPD/UPP and displayed high levels of methylation. Finally, sequencing and fluorescence in situ hybridization analysis of the gene APC underlined that a somatic UPD event might represent the second hit to achieve biallelic inactivation of this TSG in colorectal tumors. In summary, our data define a profile of somatic UPDs/UPPs in sporadic CRC and highlights the importance of these events as a mechanism to achieve the inactivation of TSGs.
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Affiliation(s)
- Keyvan Torabi
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain
| | - Rosa Miró
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain
| | - Nora Fernández-Jiménez
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Present address: Epigenetics Group, International Agency for Research on Cancer 69008, Lyon, France
| | - Isabel Quintanilla
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Catalonia 08036, Spain
| | - Laia Ramos
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Present address: Unitat de Genòmica i Bioinformàtica, Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Catalonia 08916, Spain
| | - Esther Prat
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Present address: Laboratori de Genètica Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Catalonia 08908, Spain
| | - Javier del Rey
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain
| | - Núria Pujol
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain
| | - J Keith Killian
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro Luis Fernández
- Department of Pathology, Hospital Clínic/IDIBAPS, Universitat de Barcelona, Barcelona, Catalonia 08036, Spain and
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan José Lozano
- Bioinformatics Unit, CIBERehd, Barcelona, Catalonia 08036, Spain
| | - Jordi Camps
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Catalonia 08036, Spain, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Immaculada Ponsa
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain,
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36
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Alentorn A, Dehais C, Ducray F, Carpentier C, Mokhtari K, Figarella-Branger D, Chinot O, Cohen-Moyal E, Ramirez C, Loiseau H, Elouahdani-Hamdi S, Beauchesne P, Langlois O, Desenclos C, Guillamo JS, Dam-Hieu P, Ghiringhelli F, Colin P, Godard J, Parker F, Dhermain F, Carpentier AF, Frenel JS, Menei P, Bauchet L, Faillot T, Fesneau M, Fontaine D, Motuo-Fotso MJ, Vauleon E, Gaultier C, Le Guerinel C, Gueye EM, Noel G, Desse N, Durando X, Barrascout E, Wager M, Ricard D, Carpiuc I, Delattre JY, Idbaih A. Allelic loss of 9p21.3 is a prognostic factor in 1p/19q codeleted anaplastic gliomas. Neurology 2015; 85:1325-31. [PMID: 26385879 DOI: 10.1212/wnl.0000000000002014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 06/17/2015] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES We aimed to study the potential clinical relevance of 9p allelic loss, with or without copy number variation, in 1p/19q codeleted anaplastic oligodendroglial tumors (AOTs). METHODS This study enrolled 216 patients with 1p/19q codeleted AOT. The prognostic value of 9p allelic loss was investigated using a French nation-wide prospective registry, POLA (prise en charge des tumeurs oligodendrogliales anaplasiques) and high-density single nucleotide polymorphism arrays. We validated our results using the Repository of Molecular Brain Neoplasia Data (REMBRANDT) dataset. RESULTS The minimal common region of allelic loss in chromosome arm 9p was 9p21.3. Allelic loss of 9p21.3, detected in 41.7% of tumors, was associated with shorter progression-free and overall survival rates in univariate (p = 0.008 and p < 0.001, respectively) and multivariate analyses (p = 0.009 and p = 0.009, respectively). This finding was validated in the REMBRANDT dataset in univariate and multivariate analysis (p = 0.01 and p = 0.01, respectively). CONCLUSION Our study highlights a novel potential prognostic biomarker in 1p/19q codeleted AOT. Further prospective studies are warranted to investigate our finding.
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Affiliation(s)
| | | | | | | | | | | | - Olivier Chinot
- Authors' affiliations are listed at the end of the article
| | | | - Carole Ramirez
- Authors' affiliations are listed at the end of the article
| | - Hugues Loiseau
- Authors' affiliations are listed at the end of the article
| | | | | | | | | | | | - Phong Dam-Hieu
- Authors' affiliations are listed at the end of the article
| | | | - Philippe Colin
- Authors' affiliations are listed at the end of the article
| | - Joel Godard
- Authors' affiliations are listed at the end of the article
| | - Fabrice Parker
- Authors' affiliations are listed at the end of the article
| | | | | | | | - Philippe Menei
- Authors' affiliations are listed at the end of the article
| | - Luc Bauchet
- Authors' affiliations are listed at the end of the article
| | | | | | - Denys Fontaine
- Authors' affiliations are listed at the end of the article
| | | | - Elodie Vauleon
- Authors' affiliations are listed at the end of the article
| | | | | | | | - Georges Noel
- Authors' affiliations are listed at the end of the article
| | - Nicolas Desse
- Authors' affiliations are listed at the end of the article
| | - Xavier Durando
- Authors' affiliations are listed at the end of the article
| | | | - Michel Wager
- Authors' affiliations are listed at the end of the article
| | - Damien Ricard
- Authors' affiliations are listed at the end of the article
| | - Ioana Carpiuc
- Authors' affiliations are listed at the end of the article
| | | | - Ahmed Idbaih
- Authors' affiliations are listed at the end of the article.
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Chen C, Zhang Y, Loomis MM, Upton MP, Lohavanichbutr P, Houck JR, Doody DR, Mendez E, Futran N, Schwartz SM, Wang P. Genome-Wide Loss of Heterozygosity and DNA Copy Number Aberration in HPV-Negative Oral Squamous Cell Carcinoma and Their Associations with Disease-Specific Survival. PLoS One 2015; 10:e0135074. [PMID: 26247464 PMCID: PMC4527746 DOI: 10.1371/journal.pone.0135074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 07/17/2015] [Indexed: 01/15/2023] Open
Abstract
Oral squamous cell cancer of the oral cavity and oropharynx (OSCC) is associated with high case-fatality. For reasons that are largely unknown, patients with the same clinical and pathologic staging have heterogeneous response to treatment and different probability of recurrence and survival, with patients with Human Papillomavirus (HPV)-positive oropharyngeal tumors having the most favorable survival. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we used Affymtrix 6.0 SNP arrays to examine paired DNA from peripheral blood and tumor cell populations isolated by laser capture microdissection to assess genome-wide loss of heterozygosity (LOH) and DNA copy number aberration (CNA) and their associations with risk factors, tumor characteristics, and oral cancer-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p and 11q that seem to play an important role in oral cancer biology and survival from this disease. If confirmed, these findings could assist in designing personalized treatment or in the creation of models to predict survival in patients with HPV-negative OSCC.
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Affiliation(s)
- Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Yuzheng Zhang
- Program in Biostatistics and Biomathematics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Melissa M. Loomis
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Melissa P. Upton
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Pawadee Lohavanichbutr
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John R. Houck
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David R. Doody
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eduardo Mendez
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Neal Futran
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
| | - Stephen M. Schwartz
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Pei Wang
- Program in Biostatistics and Biomathematics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genetics and Genomics Sciences, Mt. Sinai School of Medicine, New York, New York, United States of America
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Nutsua ME, Fischer A, Nebel A, Hofmann S, Schreiber S, Krawczak M, Nothnagel M. Family-Based Benchmarking of Copy Number Variation Detection Software. PLoS One 2015. [PMID: 26197066 PMCID: PMC4510559 DOI: 10.1371/journal.pone.0133465] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The analysis of structural variants, in particular of copy-number variations (CNVs), has proven valuable in unraveling the genetic basis of human diseases. Hence, a large number of algorithms have been developed for the detection of CNVs in SNP array signal intensity data. Using the European and African HapMap trio data, we undertook a comparative evaluation of six commonly used CNV detection software tools, namely Affymetrix Power Tools (APT), QuantiSNP, PennCNV, GLAD, R-gada and VEGA, and assessed their level of pair-wise prediction concordance. The tool-specific CNV prediction accuracy was assessed in silico by way of intra-familial validation. Software tools differed greatly in terms of the number and length of the CNVs predicted as well as the number of markers included in a CNV. All software tools predicted substantially more deletions than duplications. Intra-familial validation revealed consistently low levels of prediction accuracy as measured by the proportion of validated CNVs (34-60%). Moreover, up to 20% of apparent family-based validations were found to be due to chance alone. Software using Hidden Markov models (HMM) showed a trend to predict fewer CNVs than segmentation-based algorithms albeit with greater validity. PennCNV yielded the highest prediction accuracy (60.9%). Finally, the pairwise concordance of CNV prediction was found to vary widely with the software tools involved. We recommend HMM-based software, in particular PennCNV, rather than segmentation-based algorithms when validity is the primary concern of CNV detection. QuantiSNP may be used as an additional tool to detect sets of CNVs not detectable by the other tools. Our study also reemphasizes the need for laboratory-based validation, such as qPCR, of CNVs predicted in silico.
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Affiliation(s)
- Marcel Elie Nutsua
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Annegret Fischer
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Sylvia Hofmann
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - Michael Nothnagel
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany; Cologne Center for Genomics, University of Cologne, Cologne, Germany
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39
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Mohammed H, Russell IA, Stark R, Rueda OM, Hickey TE, Tarulli GA, Serandour AAA, Birrell SN, Bruna A, Saadi A, Menon S, Hadfield J, Pugh M, Raj GV, Brown GD, D’Santos C, Robinson JLL, Silva G, Launchbury R, Perou CM, Stingl J, Caldas C, Tilley WD, Carroll JS. Progesterone receptor modulates ERα action in breast cancer. Nature 2015; 523:313-7. [PMID: 26153859 PMCID: PMC4650274 DOI: 10.1038/nature14583] [Citation(s) in RCA: 482] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/22/2015] [Indexed: 01/27/2023]
Abstract
Progesterone receptor (PR) expression is used as a biomarker of oestrogen receptor-α (ERα) function and breast cancer prognosis. Here we show that PR is not merely an ERα-induced gene target, but is also an ERα-associated protein that modulates its behaviour. In the presence of agonist ligands, PR associates with ERα to direct ERα chromatin binding events within breast cancer cells, resulting in a unique gene expression programme that is associated with good clinical outcome. Progesterone inhibited oestrogen-mediated growth of ERα(+) cell line xenografts and primary ERα(+) breast tumour explants, and had increased anti-proliferative effects when coupled with an ERα antagonist. Copy number loss of PGR, the gene coding for PR, is a common feature in ERα(+) breast cancers, explaining lower PR levels in a subset of cases. Our findings indicate that PR functions as a molecular rheostat to control ERα chromatin binding and transcriptional activity, which has important implications for prognosis and therapeutic interventions.
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Affiliation(s)
- Hisham Mohammed
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - I. Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Rory Stark
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Theresa E. Hickey
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, SA 5005, Australia
| | - Gerard A. Tarulli
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, SA 5005, Australia
| | - Aurelien A. A. Serandour
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Stephen N. Birrell
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Amel Saadi
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - James Hadfield
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Michelle Pugh
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ganesh V. Raj
- Department of Urology, University of Texas, Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Gordon D. Brown
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Clive D’Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jessica L. L. Robinson
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Grace Silva
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB7295, Chapel Hill, NC, 27599, USA
| | - Rosalind Launchbury
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB7295, Chapel Hill, NC, 27599, USA
| | - John Stingl
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge, CB2 0RE
| | - Wayne D. Tilley
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jason S. Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
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40
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Liu Y, Li A, Feng H, Wang M. TAFFYS: An Integrated Tool for Comprehensive Analysis of Genomic Aberrations in Tumor Samples. PLoS One 2015; 10:e0129835. [PMID: 26111017 PMCID: PMC4482394 DOI: 10.1371/journal.pone.0129835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 05/13/2015] [Indexed: 01/13/2023] Open
Abstract
Background Tumor single nucleotide polymorphism (SNP) array is a common platform for investigating the cancer genomic aberration and the functionally important altered genes. Original SNP array signals are usually corrupted by noise, and need to be de-convoluted into absolute copy number profile by analytical methods. Unfortunately, in contrast with the popularity of tumor Affymetrix SNP array, the methods that are specifically designed for this platform are still limited. The complicated characteristics of noise in signals is one of the difficulties for dissecting tumor Affymetrix SNP array data, as they inevitably blur the distinction between aberrations and create an obstacle for the copy number aberration (CNA) identification. Results We propose a tool named TAFFYS for comprehensive analysis of tumor Affymetrix SNP array data. TAFFYS introduce a wavelet-based de-noising approach and copy number-specific signal variance model for suppressing and modelling the noise in signals. Then a hidden Markov model is employed for copy number inference. Finally, by using the absolute copy number profile, statistical significance of each aberration region is calculated in term of different aberration types, including amplification, deletion and loss of heterozygosity (LOH). The result shows that copy number specific-variance model and wavelet de-noising algorithm fits well with the Affymetrix SNP array signals, leading to more accurate estimation for diluted tumor sample (even with only 30% of cancer cells) than other existed methods. Results of examinations also demonstrate a good compatibility and extensibility for different Affymetrix SNP array platforms. Application on the 35 breast tumor samples shows that TAFFYS can automatically dissect the tumor samples and reveal statistically significant aberration regions where cancer-related genes locate. Conclusions TAFFYS provide an efficient and convenient tool for identifying the copy number alteration and allelic imbalance and assessing the recurrent aberrations for the tumor Affymetrix SNP array data.
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Affiliation(s)
- Yuanning Liu
- School of Information Science and Technology, University of Science and Technology of China, Hefei, AH230027, China
| | - Ao Li
- School of Information Science and Technology, University of Science and Technology of China, Hefei, AH230027, China
- Research centres for Biomedical Engineering, University of Science and Technology of China, Hefei, AH230027, China
- * E-mail:
| | - Huanqing Feng
- School of Information Science and Technology, University of Science and Technology of China, Hefei, AH230027, China
| | - Minghui Wang
- School of Information Science and Technology, University of Science and Technology of China, Hefei, AH230027, China
- Research centres for Biomedical Engineering, University of Science and Technology of China, Hefei, AH230027, China
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41
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Marquard AM, Eklund AC, Joshi T, Krzystanek M, Favero F, Wang ZC, Richardson AL, Silver DP, Szallasi Z, Birkbak NJ. Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs. Biomark Res 2015; 3:9. [PMID: 26015868 PMCID: PMC4443545 DOI: 10.1186/s40364-015-0033-4] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/25/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Ovarian and triple-negative breast cancers with BRCA1 or BRCA2 loss are highly sensitive to treatment with PARP inhibitors and platinum-based cytotoxic agents and show an accumulation of genomic scars in the form of gross DNA copy number aberrations. Cancers without BRCA1 or BRCA2 loss but with accumulation of similar genomic scars also show increased sensitivity to platinum-based chemotherapy. Therefore, reliable biomarkers to identify DNA repair-deficient cancers prior to treatment may be useful for directing patients to platinum chemotherapy and possibly PARP inhibitors. Recently, three SNP array-based signatures of chromosomal instability were published that each quantitate a distinct type of genomic scar considered likely to be caused by improper DNA repair. They measure telomeric allelic imbalance (named NtAI), large scale transition (named LST), and loss of heterozygosity (named HRD-LOH), and it is suggested that these signatures may act as biomarkers for the state of DNA repair deficiency in a given cancer. RESULTS We explored the pan-cancer distribution of scores of the three signatures utilizing a panel of 5371 tumors representing 15 cancer types from The Cancer Genome Atlas, and found a good correlation between scores of the three signatures (Spearman's ρ 0.73-0.87). In addition we found that cancer types ordinarily receiving platinum as standard of care have higher median scores of all three signatures. Interestingly, we also found that smaller subpopulations of high-scoring tumors exist in most cancer types, including those for which platinum chemotherapy is not standard therapy. CONCLUSIONS Within several cancer types that are not ordinarily treated with platinum chemotherapy, we identified tumors with high levels of the three genomic biomarkers. These tumors represent identifiable subtypes of patients which may be strong candidates for clinical trials with PARP inhibitors or platinum-based chemotherapeutic regimens.
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Affiliation(s)
- Andrea M Marquard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Aron C Eklund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Tejal Joshi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Marcin Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Francesco Favero
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Zhigang C Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, 02215 Boston, Massachusetts USA.,Department of Surgery, Brigham and Women's Hospital, 75 Francis Street, 02115 Boston, Massachusetts USA
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, 02115 Boston, Massachusetts USA
| | - Daniel P Silver
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, 02215 Boston, Massachusetts USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, 02215 Boston, Massachusetts USA
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark.,Harvard Medical School, Children's Hospital Informatics Program at the Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology (CHIP@HST), 320 Longwood Avenue, Boston, Massachusetts USA
| | - Nicolai J Birkbak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
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42
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McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci Transl Med 2015; 7:283ra54. [PMID: 25877892 PMCID: PMC4636056 DOI: 10.1126/scitranslmed.aaa1408] [Citation(s) in RCA: 534] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deciphering whether actionable driver mutations are found in all or a subset of tumor cells will likely be required to improve drug development and precision medicine strategies. We analyzed nine cancer types to determine the subclonal frequencies of driver events, to time mutational processes during cancer evolution, and to identify drivers of subclonal expansions. Although mutations in known driver genes typically occurred early in cancer evolution, we also identified later subclonal "actionable" mutations, including BRAF (V600E), IDH1 (R132H), PIK3CA (E545K), EGFR (L858R), and KRAS (G12D), which may compromise the efficacy of targeted therapy approaches. More than 20% of IDH1 mutations in glioblastomas, and 15% of mutations in genes in the PI3K (phosphatidylinositol 3-kinase)-AKT-mTOR (mammalian target of rapamycin) signaling axis across all tumor types were subclonal. Mutations in the RAS-MEK (mitogen-activated protein kinase kinase) signaling axis were less likely to be subclonal than mutations in genes associated with PI3K-AKT-mTOR signaling. Analysis of late mutations revealed a link between APOBEC-mediated mutagenesis and the acquisition of subclonal driver mutations and uncovered putative cancer genes involved in subclonal expansions, including CTNNA2 and ATXN1. Our results provide a pan-cancer census of driver events within the context of intratumor heterogeneity and reveal patterns of tumor evolution across cancers. The frequent presence of subclonal driver mutations suggests the need to stratify targeted therapy response according to the proportion of tumor cells in which the driver is identified.
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Affiliation(s)
- Nicholas McGranahan
- Cancer Research UK London Research Institute, London WC2A 3LY, UK. Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, UK
| | - Francesco Favero
- Cancer System Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Elza C de Bruin
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley Street, London WC1E 6DD, UK
| | - Nicolai Juul Birkbak
- Cancer Research UK London Research Institute, London WC2A 3LY, UK. Cancer System Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark. UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley Street, London WC1E 6DD, UK
| | - Zoltan Szallasi
- Cancer System Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark. Children's Hospital Informatics Program, Harvard Medical School, Boston, MA 02115, USA
| | - Charles Swanton
- Cancer Research UK London Research Institute, London WC2A 3LY, UK. UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley Street, London WC1E 6DD, UK.
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43
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Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RGW. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution. Genome Res 2015; 25:316-27. [PMID: 25650244 PMCID: PMC4352879 DOI: 10.1101/gr.180612.114] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glioblastoma (GBM) is a prototypical heterogeneous brain tumor refractory to conventional therapy. A small residual population of cells escapes surgery and chemoradiation, resulting in a typically fatal tumor recurrence ∼7 mo after diagnosis. Understanding the molecular architecture of this residual population is critical for the development of successful therapies. We used whole-genome sequencing and whole-exome sequencing of multiple sectors from primary and paired recurrent GBM tumors to reconstruct the genomic profile of residual, therapy resistant tumor initiating cells. We found that genetic alteration of the p53 pathway is a primary molecular event predictive of a high number of subclonal mutations in glioblastoma. The genomic road leading to recurrence is highly idiosyncratic but can be broadly classified into linear recurrences that share extensive genetic similarity with the primary tumor and can be directly traced to one of its specific sectors, and divergent recurrences that share few genetic alterations with the primary tumor and originate from cells that branched off early during tumorigenesis. Our study provides mechanistic insights into how genetic alterations in primary tumors impact the ensuing evolution of tumor cells and the emergence of subclonal heterogeneity.
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Affiliation(s)
- Hoon Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Siyuan Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Seyed S Amini
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Selene M Virk
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Tom Mikkelsen
- Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Daniel J Brat
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Jonna Grimsby
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Florian Muller
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jian Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA; Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, Cleveland, Ohio 44106, USA
| | - Mark L Cohen
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA; Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA
| | - Erwin G Van Meir
- Department of Neurosurgery and Hematology and Medical Oncology, Winship Cancer Institute and School of Medicine, Emory University, Atlanta, Georgia 30322, USA
| | - Lisa Scarpace
- Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Eric S Lander
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stacey Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Lynda Chin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Roel G W Verhaak
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
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Khaled WT, Choon Lee S, Stingl J, Chen X, Raza Ali H, Rueda OM, Hadi F, Wang J, Yu Y, Chin SF, Stratton M, Futreal A, Jenkins NA, Aparicio S, Copeland NG, Watson CJ, Caldas C, Liu P. BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells. Nat Commun 2015; 6:5987. [PMID: 25574598 PMCID: PMC4338552 DOI: 10.1038/ncomms6987] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/28/2014] [Indexed: 01/03/2023] Open
Abstract
Triple-negative breast cancer (TNBC) has poor prognostic outcome compared with other types of breast cancer. The molecular and cellular mechanisms underlying TNBC pathology are not fully understood. Here, we report that the transcription factor BCL11A is overexpressed in TNBC including basal-like breast cancer (BLBC) and that its genomic locus is amplified in up to 38% of BLBC tumours. Exogenous BCL11A overexpression promotes tumour formation, whereas its knockdown in TNBC cell lines suppresses their tumourigenic potential in xenograft models. In the DMBA-induced tumour model, Bcl11a deletion substantially decreases tumour formation, even in p53-null cells and inactivation of Bcl11a in established tumours causes their regression. At the cellular level, Bcl11a deletion causes a reduction in the number of mammary epithelial stem and progenitor cells. Thus, BCL11A has an important role in TNBC and normal mammary epithelial cells. This study highlights the importance of further investigation of BCL11A in TNBC-targeted therapies.
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Affiliation(s)
- Walid T. Khaled
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
- These authors contributed equally to this work
| | - Song Choon Lee
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
- These authors contributed equally to this work
| | - John Stingl
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Xiongfeng Chen
- SAIC-Frederic, National Cancer Institute-Frederick, Frederick, Maryland 21701, USA
| | - H. Raza Ali
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Fazal Hadi
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Juexuan Wang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Yong Yu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mike Stratton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Andy Futreal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Nancy A. Jenkins
- The Methodist Hospital Research Institute, 6670 Bertner Street, Houston, Texas 77030, USA
| | - Sam Aparicio
- Molecular Oncology Department, BC Cancer Agency Research Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Neal G. Copeland
- The Methodist Hospital Research Institute, 6670 Bertner Street, Houston, Texas 77030, USA
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK
- Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
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Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. Proc Natl Acad Sci U S A 2015; 112:851-6. [PMID: 25561528 DOI: 10.1073/pnas.1320611111] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is a cancer comprised of morphologically, genetically, and phenotypically diverse cells. However, an understanding of the functional significance of intratumoral heterogeneity is lacking. We devised a method to isolate and functionally profile tumorigenic clones from patient glioblastoma samples. Individual clones demonstrated unique proliferation and differentiation abilities. Importantly, naïve patient tumors included clones that were temozolomide resistant, indicating that resistance to conventional GBM therapy can preexist in untreated tumors at a clonal level. Further, candidate therapies for resistant clones were detected with clone-specific drug screening. Genomic analyses revealed genes and pathways that associate with specific functional behavior of single clones. Our results suggest that functional clonal profiling used to identify tumorigenic and drug-resistant tumor clones will lead to the discovery of new GBM clone-specific treatment strategies.
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46
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Vollan HKM, Rueda OM, Chin SF, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, Brenton JD, Pharoah PDP, Børresen-Dale AL, Aparicio S, Caldas C. A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Mol Oncol 2015; 9:115-27. [PMID: 25169931 PMCID: PMC4286124 DOI: 10.1016/j.molonc.2014.07.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 01/27/2023] Open
Abstract
Complex focal chromosomal rearrangements in cancer genomes, also called "firestorms", can be scored from DNA copy number data. The complex arm-wise aberration index (CAAI) is a score that captures DNA copy number alterations that appear as focal complex events in tumors, and has potential prognostic value in breast cancer. This study aimed to validate this DNA-based prognostic index in breast cancer and test for the first time its potential prognostic value in ovarian cancer. Copy number alteration (CNA) data from 1950 breast carcinomas (METABRIC cohort) and 508 high-grade serous ovarian carcinomas (TCGA dataset) were analyzed. Cases were classified as CAAI positive if at least one complex focal event was scored. Complex alterations were frequently localized on chromosome 8p (n = 159), 17q (n = 176) and 11q (n = 251). CAAI events on 11q were most frequent in estrogen receptor positive (ER+) cases and on 17q in estrogen receptor negative (ER-) cases. We found only a modest correlation between CAAI and the overall rate of genomic instability (GII) and number of breakpoints (r = 0.27 and r = 0.42, p < 0.001). Breast cancer specific survival (BCSS), overall survival (OS) and ovarian cancer progression free survival (PFS) were used as clinical end points in Cox proportional hazard model survival analyses. CAAI positive breast cancers (43%) had higher mortality: hazard ratio (HR) of 1.94 (95%CI, 1.62-2.32) for BCSS, and of 1.49 (95%CI, 1.30-1.71) for OS. Representations of the 70-gene and the 21-gene predictors were compared with CAAI in multivariable models and CAAI was independently significant with a Cox adjusted HR of 1.56 (95%CI, 1.23-1.99) for ER+ and 1.55 (95%CI, 1.11-2.18) for ER- disease. None of the expression-based predictors were prognostic in the ER- subset. We found that a model including CAAI and the two expression-based prognostic signatures outperformed a model including the 21-gene and 70-gene signatures but excluding CAAI. Inclusion of CAAI in the clinical prognostication tool PREDICT significantly improved its performance. CAAI positive ovarian cancers (52%) also had worse prognosis: HRs of 1.3 (95%CI, 1.1-1.7) for PFS and 1.3 (95%CI, 1.1-1.6) for OS. This study validates CAAI as an independent predictor of survival in both ER+ and ER- breast cancer and reveals a significant prognostic value for CAAI in high-grade serous ovarian cancer.
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Affiliation(s)
- Hans Kristian Moen Vollan
- Cancer Research UK, Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Oncology, Division for Surgery, Cancer and Transplantation, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Christina Curtis
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Gulisa Turashvili
- Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, British Colombia V6T 2B5, Canada; Molecular Oncology, British Colombia Cancer Research Center, Vancouver, British Columbia V5Z 1L3, Canada
| | - Sohrab Shah
- Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, British Colombia V6T 2B5, Canada; Molecular Oncology, British Colombia Cancer Research Center, Vancouver, British Columbia V5Z 1L3, Canada
| | - Ole Christian Lingjærde
- The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Biomedical Informatics Division, Department of Computer Science, University of Oslo, Oslo, Norway; Center for Cancer Biomedicine, University of Oslo, Norway
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB, London, UK
| | - Charlotte K Ng
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mark J Dunning
- Cancer Research UK, Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Ed Dicks
- Strangeways Research Laboratories, University of Cambridge, Cambridge CB1 9RN, UK
| | - Elena Provenzano
- Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
| | - Stephen Sammut
- Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
| | - Steven McKinney
- Molecular Oncology, British Colombia Cancer Research Center, Vancouver, British Columbia V5Z 1L3, Canada
| | - Ian O Ellis
- Department of Histopathology, School of Molecular Medical Sciences, University of Nottingham, Nottingham, NG5 1PB, UK
| | - Sarah Pinder
- King's College London, Breakthrough Breast Cancer Research Unit, London WC2R 2LS, UK; NIHR Comprehensive Biomedical Research Centre at Guy's and St. Thomas NHS Foundation Trust and King's College London, London WC2R 2LS, UK
| | - Arnie Purushotham
- King's College London, Breakthrough Breast Cancer Research Unit, London WC2R 2LS, UK; NIHR Comprehensive Biomedical Research Centre at Guy's and St. Thomas NHS Foundation Trust and King's College London, London WC2R 2LS, UK
| | - Leigh C Murphy
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Manitoba R3E 0V9, Canada
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital, Lørenskog, Norway
| | - James D Brenton
- Cancer Research UK, Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK; Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
| | - Paul D P Pharoah
- Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK; Strangeways Research Laboratories, University of Cambridge, Cambridge CB1 9RN, UK; Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, British Colombia V6T 2B5, Canada; Molecular Oncology, British Colombia Cancer Research Center, Vancouver, British Columbia V5Z 1L3, Canada.
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK; Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK.
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Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol 2015; 26:64-70. [PMID: 25319062 PMCID: PMC4269342 DOI: 10.1093/annonc/mdu479] [Citation(s) in RCA: 542] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Exome or whole-genome deep sequencing of tumor DNA along with paired normal DNA can potentially provide a detailed picture of the somatic mutations that characterize the tumor. However, analysis of such sequence data can be complicated by the presence of normal cells in the tumor specimen, by intratumor heterogeneity, and by the sheer size of the raw data. In particular, determination of copy number variations from exome sequencing data alone has proven difficult; thus, single nucleotide polymorphism (SNP) arrays have often been used for this task. Recently, algorithms to estimate absolute, but not allele-specific, copy number profiles from tumor sequencing data have been described. MATERIALS AND METHODS We developed Sequenza, a software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. We applied Sequenza, as well as two previously published algorithms, to exome sequence data from 30 tumors from The Cancer Genome Atlas. We assessed the performance of these algorithms by comparing their results with those generated using matched SNP arrays and processed by the allele-specific copy number analysis of tumors (ASCAT) algorithm. RESULTS Comparison between Sequenza/exome and SNP/ASCAT revealed strong correlation in cellularity (Pearson's r = 0.90) and ploidy estimates (r = 0.42, or r = 0.94 after manual inspecting alternative solutions). This performance was noticeably superior to previously published algorithms. In addition, in artificial data simulating normal-tumor admixtures, Sequenza detected the correct ploidy in samples with tumor content as low as 30%. CONCLUSIONS The agreement between Sequenza and SNP array-based copy number profiles suggests that exome sequencing alone is sufficient not only for identifying small scale mutations but also for estimating cellularity and inferring DNA copy number aberrations.
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Affiliation(s)
- F Favero
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - T Joshi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - A M Marquard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - N J Birkbak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - M Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Q Li
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Medical School, Xiamen University, Xiamen, China
| | - Z Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, USA
| | - A C Eklund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
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48
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Grimonprez Q, Celisse A, Blanck S, Cheok M, Figeac M, Marot G. MPAgenomics: an R package for multi-patient analysis of genomic markers. BMC Bioinformatics 2014; 15:394. [PMID: 25495450 PMCID: PMC4269855 DOI: 10.1186/s12859-014-0394-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/19/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. RESULTS MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic markers from multi-patient copy number and SNP data profiles. It provides wrappers from commonly used packages to streamline their repeated (sometimes difficult) manipulation, offering an easy-to-use pipeline for beginners in R.The segmentation of successive multiple profiles (finding losses and gains) is performed with an automatic choice of parameters involved in the wrapped packages. Considering multiple profiles in the same time, MPAgenomics wraps efficient penalized regression methods to select relevant markers associated with a given outcome. CONCLUSIONS MPAgenomics provides an easy tool to analyze data from SNP arrays in R. The R-package MPAgenomics is available on CRAN.
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49
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Rall K, Eisenbeis S, Barresi G, Rückner D, Walter M, Poths S, Wallwiener D, Riess O, Bonin M, Brucker S. Mayer-Rokitansky-Küster-Hauser syndrome discordance in monozygotic twins: matrix metalloproteinase 14, low-density lipoprotein receptor-related protein 10, extracellular matrix, and neoangiogenesis genes identified as candidate genes in a tissue-specific mosaicism. Fertil Steril 2014; 103:494-502.e3. [PMID: 25492683 DOI: 10.1016/j.fertnstert.2014.10.053] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To find a potential underlying cause for Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) discordance in monozygotic twins. DESIGN Prospective comparative study. SETTING University hospital. PATIENT(S) Our study genetically analyzed 5 MRKHS-discordant monozygotic twin pairs with the unique opportunity to include saliva and rudimentary uterine tissue. INTERVENTION(S) Blood, saliva, or rudimentary uterine tissue from five MRKHS-discordant twins was analyzed and compared between twin pairs as well as within the same individual where applicable. We used copy number variations (CNVs) to identify differences. MAIN OUTCOME MEASURE(S) CNVs in blood, rudimentary uterine tissue, and saliva, network analysis, and review of the literature. RESULT(S) One duplication found in the affected twin included two genes, matrix metalloproteinase 14 (MMP14) and low-density lipoprotein receptor-related protein 10 (LRP10), which have known functions in the embryonic development of the uterus and endometrium. The duplicated region was detected in rudimentary uterine tissue from the same individual but not in saliva, making a tissue-specific mosaicism a possible explanation for twin discordance. Additional network analysis revealed important connections to differentially expressed genes from previous studies. These genes encode several molecules involved in extracellular matrix (ECM) remodeling and neoangiogenesis. CONCLUSION(S) MMP-14, LRP-10, ECM, and neoangiogenesis genes are identified as candidate genes in a tissue-specific mosaicism. The detected clusters provide evidence of deficient vascularization during uterine development and/or disturbed reorganization of ECM components, potentially during müllerian duct elongation signaled by the embryologically relevant phosphatidylinositol 3-kinase/protein kinase B pathway. Therefore, we consider these genes to be new candidates in the manifestation of MRKHS.
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Affiliation(s)
- Katharina Rall
- Department of Obstetrics and Gynecology and Center for Rare Female Genital Malformations, Tübingen, Germany.
| | - Simone Eisenbeis
- Department of Obstetrics and Gynecology and Center for Rare Female Genital Malformations, Tübingen, Germany
| | - Gianmaria Barresi
- Department of Obstetrics and Gynecology and Center for Rare Female Genital Malformations, Tübingen, Germany
| | - Daniel Rückner
- Department of Obstetrics and Gynecology and Center for Rare Female Genital Malformations, Tübingen, Germany
| | - Michael Walter
- Department of Medical Genetics, Microarray Facility, Tübingen University Hospital, Tübingen, Germany
| | - Sven Poths
- Department of Medical Genetics, Microarray Facility, Tübingen University Hospital, Tübingen, Germany
| | - Diethelm Wallwiener
- Department of Obstetrics and Gynecology and Center for Rare Female Genital Malformations, Tübingen, Germany
| | - Olaf Riess
- Department of Medical Genetics, Microarray Facility, Tübingen University Hospital, Tübingen, Germany
| | - Michael Bonin
- Department of Medical Genetics, Microarray Facility, Tübingen University Hospital, Tübingen, Germany
| | - Sara Brucker
- Department of Obstetrics and Gynecology and Center for Rare Female Genital Malformations, Tübingen, Germany
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50
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Cai H, Gupta S, Rath P, Ai N, Baudis M. arrayMap 2014: an updated cancer genome resource. Nucleic Acids Res 2014; 43:D825-30. [PMID: 25428357 PMCID: PMC4383937 DOI: 10.1093/nar/gku1123] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Somatic copy number aberrations (CNA) represent a mutation type encountered in the majority of cancer genomes. Here, we present the 2014 edition of arrayMap (http://www.arraymap.org), a publicly accessible collection of pre-processed oncogenomic array data sets and CNA profiles, representing a vast range of human malignancies. Since the initial release, we have enhanced this resource both in content and especially with regard to data mining support. The 2014 release of arrayMap contains more than 64 000 genomic array data sets, representing about 250 tumor diagnoses. Data sets included in arrayMap have been assembled from public repositories as well as additional resources, and integrated by applying custom processing pipelines. Online tools have been upgraded for a more flexible array data visualization, including options for processing user provided, non-public data sets. Data integration has been improved by mapping to multiple editions of the human reference genome, with the majority of the data now being available for the UCSC hg18 as well as GRCh37 versions. The large amount of tumor CNA data in arrayMap can be freely downloaded by users to promote data mining projects, and to explore special events such as chromothripsis-like genome patterns.
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Affiliation(s)
- Haoyang Cai
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Saumya Gupta
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Prisni Rath
- Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland Centre for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ni Ai
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Michael Baudis
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
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