1
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Wijetunga NA, Goglia AG, Weinhold N, Berger MF, Cislo M, Higginson DS, Chabot K, Osman AM, Schaff L, Pentsova E, Miller AM, Powell SN, Boire A, Yang JT. Dynamic Mutational Landscape of Cerebrospinal Fluid Circulating Tumor DNA and Predictors of Survival after Proton Craniospinal Irradiation for Leptomeningeal Metastases. Clin Cancer Res 2023; 29:775-783. [PMID: 36449664 PMCID: PMC9957915 DOI: 10.1158/1078-0432.ccr-22-2434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/05/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022]
Abstract
PURPOSE Proton craniospinal irradiation (pCSI) is a promising treatment for patients with solid tumor leptomeningeal metastasis (LM). We hypothesize that genetic characteristics before and changes resulting after pCSI will reflect clinical response to pCSI. We analyzed the cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) from patients receiving pCSI for LM and explored genetic variations associated with response. EXPERIMENTAL DESIGN We subjected CSF from 14 patients with LM before and after pCSI to cell-free DNA sequencing using a targeted-sequencing panel. In parallel, plasma ctDNA and primary tumors were subjected to targeted sequencing. Variant allele frequency (VAF) and cancer cell fraction (CCF) were calculated; clonality of observed mutations was determined. Kaplan-Meier analysis was used to associate genomic changes with survival. RESULTS The median overall survival (OS) for the cohort was 9 months [interquartile range (IQR), 5-21 months]. We showed clonal evolution between tumor and ctDNA of the CSF and plasma with unique mutations identified by compartment. Higher CSF ctDNA mean VAF before pCSI (VAFpre) had worse OS (6 months for VAFpre ≥ 0.32 vs. 9 months for VAFpre < 0.32; P = 0.05). Similarly, increased VAF after pCSI portended worse survival (6 vs. 18 months; P = 0.008). Higher mean CCF of subclonal mutations appearing after pCSI was associated with worse OS (8 vs. 17 months; P = 0.05). CONCLUSIONS In patients with solid tumor LM undergoing pCSI, we found unique genomic profiles associated with pCSI through CSF ctDNA analyses. Patients with reduced genomic diversity within the leptomeningeal compartment demonstrated improved OS after pCSI suggesting that CSF ctDNA analysis may have use in predicting pCSI response.
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Affiliation(s)
- N. Ari Wijetunga
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
| | | | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
| | | | - Michael Cislo
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
| | | | - Kiana Chabot
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Ahmed M. Osman
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Lauren Schaff
- Department of Neurology, Memorial Sloan Kettering Cancer Center
| | - Elena Pentsova
- Department of Neurology, Memorial Sloan Kettering Cancer Center
| | | | - Simon N. Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
| | - Adrienne Boire
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
- Department of Neurology, Memorial Sloan Kettering Cancer Center
| | - Jonathan T. Yang
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
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2
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Wijetunga N, Goglia A, Weinhold N, Cislo M, Berger M, Osman A, Pentsova E, Miller A, Powell S, Boire A, Yang J. The Dynamic Mutational Landscape of Cerebrospinal Fluid Circulating Tumor DNA can Predict Survival after Proton Craniospinal Irradiation for Leptomeningeal Metastasis. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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3
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Moore G, Majumdar R, Powell SN, Khan AJ, Weinhold N, Yin S, Higginson DS. Templated Insertions Are Associated Specifically with BRCA2 Deficiency and Overall Survival in Advanced Ovarian Cancer. Mol Cancer Res 2022; 20:1061-1070. [PMID: 35385581 PMCID: PMC9372910 DOI: 10.1158/1541-7786.mcr-21-1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 04/01/2022] [Indexed: 01/09/2023]
Abstract
Cancer cells defective in homologous recombination (HR) are responsive to DNA-crosslinking chemotherapies, PARP inhibitors, and inhibitors of polymerase theta (Pol θ), a key mediator of the backup pathway alternative end-joining. Such cancers include those with pathogenic biallelic alterations in core HR genes and another cohort of cases that exhibit sensitivity to the same agents and harbor genomic hallmarks of HR deficiency (HRD). These HRD signatures include a single-base substitution pattern, large rearrangements, characteristic tandem duplications, and small deletions. Here, we used what is now known about the backup pathway alternative end-joining (Alt-EJ) through the key factor Pol θ to design and test novel signatures of polymerase theta-mediated (TMEJ) repair. We generated two novel signatures; a signature composed of small deletions with microhomology and another consisting of small, templated insertions (TINS). We find that TINS consistent with TMEJ repair are highly specific to tumors with pathogenic biallelic mutations in BRCA2 and that high TINS genomic signature content in advanced ovarian cancers associate with overall survival following treatment with platinum agents. In addition, the combination of TINS with other HRD metrics significantly improves the association of platinum sensitivity with survival compared with current state-of-the-art signatures. IMPLICATIONS Small, templated insertions indicative of theta-mediated end-joining likely can be used in conjunction with other HRD mutational signatures as a prognostic tool for patient response to therapies targeting HR deficiency.
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Affiliation(s)
- Grace Moore
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Rahul Majumdar
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Simon N. Powell
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Atif J. Khan
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Shen Yin
- Epidemiology & Biostatistics, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Daniel S. Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065.,Corresponding author: Daniel S.
Higginson, Department of Radiation Oncology, Memorial Sloan Kettering Cancer
Center, 1275 York Ave Box #22, New York, NY 10065; Phone: (646) 888-3567;
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4
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Jones JR, Barber A, Le Bihan YV, Weinhold N, Ashby C, Walker BA, Wardell CP, Wang H, Kaiser MF, Jackson GH, Davies FE, Chopra R, Morgan GJ, Pawlyn C. Mutations in CRBN and other cereblon pathway genes are infrequently associated with acquired resistance to immunomodulatory drugs. Leukemia 2021; 35:3017-3020. [PMID: 34373585 PMCID: PMC8478640 DOI: 10.1038/s41375-021-01373-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023]
Affiliation(s)
- J R Jones
- The Institute of Cancer Research, London, UK.
- Brighton and Sussex Medical School, Brighton, UK.
- Kings College Hospital NHS Foundation Trust, London, UK.
| | - A Barber
- The Institute of Cancer Research, London, UK
| | | | - N Weinhold
- Department of Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany
| | - C Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Arkansas, USA
| | - B A Walker
- Indiana University School of Medicine, Indiana, USA
| | - C P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Arkansas, USA
| | - H Wang
- The Institute of Cancer Research, London, UK
| | - M F Kaiser
- The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - G H Jackson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - F E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, USA
| | - R Chopra
- The Institute of Cancer Research, London, UK
- Apple Tree Partners, London, UK
| | - G J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, USA
| | - C Pawlyn
- The Institute of Cancer Research, London, UK.
- The Royal Marsden Hospital, London, UK.
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5
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Marney CB, Anderson ES, Adnan M, Peng KL, Hu Y, Weinhold N, Schmitt AM. p53-intact cancers escape tumor suppression through loss of long noncoding RNA Dino. Cell Rep 2021; 35:109329. [PMID: 34192538 PMCID: PMC8287872 DOI: 10.1016/j.celrep.2021.109329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/15/2021] [Accepted: 06/09/2021] [Indexed: 02/08/2023] Open
Abstract
Many long noncoding RNA (lncRNA) genes exist near cancer-associated loci, yet evidence connecting lncRNA functions to recurrent genetic alterations in cancer are lacking. Here, we report that DINO, the lncRNA transcribed from the cancer-associated DINO/CDKN1A locus, suppresses tumor formation independent of p21, the protein encoded at the locus. Loss of one or two alleles of Dino impairs p53 signaling and apoptosis, resulting in a haplo-insufficient tumor suppressor phenotype in genetically defined mouse models of tumorigenesis. A discrete region of the DINO/CDKN1A locus is recurrently hypermethylated in human cancers, silencing DINO but not CDKN1A, the gene encoding p21. Hypermethylation silences DINO, impairs p53 signaling pathway in trans, and is mutually exclusive with TP53 alterations, indicating that DINO and TP53 comprise a common tumor suppressor module. Therefore, DINO encodes a lncRNA essential for tumor suppression that is recurrently silenced in human cancers as a mechanism to escape p53-dependent tumor suppression.
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Affiliation(s)
- Christina B Marney
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Erik S Anderson
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Mutayyaba Adnan
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Kai-Lin Peng
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Ya Hu
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Nils Weinhold
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Adam M Schmitt
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA.
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6
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Ratnakumar A, Weinhold N, Mar JC, Riaz N. Protein-Protein interactions uncover candidate 'core genes' within omnigenic disease networks. PLoS Genet 2020; 16:e1008903. [PMID: 32678846 PMCID: PMC7390454 DOI: 10.1371/journal.pgen.1008903] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 07/29/2020] [Accepted: 06/01/2020] [Indexed: 01/09/2023] Open
Abstract
Genome wide association studies (GWAS) of human diseases have generally identified many loci associated with risk with relatively small effect sizes. The omnigenic model attempts to explain this observation by suggesting that diseases can be thought of as networks, where genes with direct involvement in disease-relevant biological pathways are named ‘core genes’, while peripheral genes influence disease risk via their interactions or regulatory effects on core genes. Here, we demonstrate a method for identifying candidate core genes solely from genes in or near disease-associated SNPs (GWAS hits) in conjunction with protein-protein interaction network data. Applied to 1,381 GWAS studies from 5 ancestries, we identify a total of 1,865 candidate core genes in 343 GWAS studies. Our analysis identifies several well-known disease-related genes that are not identified by GWAS, including BRCA1 in Breast Cancer, Amyloid Precursor Protein (APP) in Alzheimer’s Disease, INS in A1C measurement and Type 2 Diabetes, and PCSK9 in LDL cholesterol, amongst others. Notably candidate core genes are preferentially enriched for disease relevance over GWAS hits and are enriched for both Clinvar pathogenic variants and known drug targets—consistent with the predictions of the omnigenic model. We subsequently use parent term annotations provided by the GWAS catalog, to merge related GWAS studies and identify candidate core genes in over-arching disease processes such as cancer–where we identify 109 candidate core genes. A recent theory suggests that only a small number of genes underpin the biology of a disease, these genes are called ‘core genes’, and for most diseases, these core genes remain unknown. The suggested methods for finding them requires complex and expensive experiments. We reasoned that if we merge currently available datasets in smart ways, we may be able to uncover these ‘core genes’. Our method finds “hub” proteins by merging lists of genes previously linked with disease to information on how proteins interact with each other. We found that many of these hub proteins have central roles in disease, such as insulin for both A1C measurement and Type 2 Diabetes, BRCA1 in Breast cancer, and Amyloid Precursor Protein in Alzheimer’s Disease. We think these ‘hub’ proteins are candidate ‘core genes’, and offer our method as a way to find ‘core genes’ by utilizing publicly available reference datasets.
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Affiliation(s)
- Abhirami Ratnakumar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Jessica C. Mar
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Australia
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
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7
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Mandal R, Samstein RM, Lee KW, Havel JJ, Wang H, Krishna C, Sabio EY, Makarov V, Kuo F, Blecua P, Ramaswamy AT, Durham JN, Bartlett B, Ma X, Srivastava R, Middha S, Zehir A, Hechtman JF, Morris LG, Weinhold N, Riaz N, Le DT, Diaz LA, Chan TA. Genetic diversity of tumors with mismatch repair deficiency influences anti-PD-1 immunotherapy response. Science 2019; 364:485-491. [PMID: 31048490 DOI: 10.1126/science.aau0447] [Citation(s) in RCA: 340] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 04/09/2019] [Indexed: 12/12/2022]
Abstract
Tumors with mismatch repair deficiency (MMR-d) are characterized by sequence alterations in microsatellites and can accumulate thousands of mutations. This high mutational burden renders tumors immunogenic and sensitive to programmed cell death-1 (PD-1) immune checkpoint inhibitors. Yet, despite their tumor immunogenicity, patients with MMR-deficient tumors experience highly variable responses, and roughly half are refractory to treatment. We present experimental and clinical evidence showing that the degree of microsatellite instability (MSI) and resultant mutational load, in part, underlies the variable response to PD-1 blockade immunotherapy in MMR-d human and mouse tumors. The extent of response is particularly associated with the accumulation of insertion-deletion (indel) mutational load. This study provides a rationale for the genome-wide characterization of MSI intensity and mutational load to better profile responses to anti-PD-1 immunotherapy across MMR-deficient human cancers.
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Affiliation(s)
- Rajarsi Mandal
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD 21287, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert M Samstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ken-Wing Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan J Havel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hao Wang
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erich Y Sabio
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pedro Blecua
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Apoorva T Ramaswamy
- Department of Otolaryngology-Head and Neck Surgery, Weill Cornell New York Presbyterian Hospital, New York, NY 10065, USA
| | - Jennifer N Durham
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA.,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA.,Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA
| | - Bjarne Bartlett
- Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA
| | - Xiaoxiao Ma
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Raghvendra Srivastava
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Luc Gt Morris
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dung T Le
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA.,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA.,Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA
| | - Luis A Diaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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8
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Anderson E, Marney C, Adnan M, Peng K, Weinhold N, Schmitt A. Dino Is a DNA Damage-Induced Tumor Suppressing Long Noncoding RNA. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Baertsch MA, Lutz R, Raab MS, Weinhold N, Goldschmidt H. Meeting report of the 7th Heidelberg Myeloma Workshop: today and tomorrow. J Cancer Res Clin Oncol 2019; 145:2445-2455. [PMID: 31407112 DOI: 10.1007/s00432-019-02998-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022]
Abstract
PURPOSE The 7th Heidelberg Myeloma Workshop was held on April 5th and 6th, 2019 at the University Hospital Heidelberg. METHODS AND RESULTS Main topics of the meeting were (1) diagnostics and prognostic factors, (2) role of immunotherapy in multiple myeloma (MM), (3) current therapy of MM, (4) biology and genomics of MM as well as (5) novel treatment concepts. A debate on the status of minimal residual disease (MRD) driven therapy was held. CONCLUSION Diagnostics and treatment of newly diagnosed and relapsed MM are continuously evolving. While advances in the field of (single cell) genetic analysis now allow for characterization of the disease at an unprecedented resolution, immunotherapeutic approaches and MRD testing are at the forefront of the current clinical trial landscape.
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Affiliation(s)
- M A Baertsch
- Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.
| | - R Lutz
- Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - M S Raab
- Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - N Weinhold
- Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - H Goldschmidt
- Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
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10
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Rasche L, Alapat D, Kumar M, Gershner G, McDonald J, Wardell CP, Samant R, Van Hemert R, Epstein J, Williams AF, Thanendrarajan S, Schinke C, Bauer M, Ashby C, Tytarenko RG, van Rhee F, Walker BA, Zangari M, Barlogie B, Davies FE, Morgan GJ, Weinhold N. Combination of flow cytometry and functional imaging for monitoring of residual disease in myeloma. Leukemia 2018; 33:1713-1722. [PMID: 30573775 PMCID: PMC6586541 DOI: 10.1038/s41375-018-0329-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/24/2018] [Accepted: 10/10/2018] [Indexed: 02/08/2023]
Abstract
The iliac crest is the sampling site for minimal residual disease (MRD) monitoring in multiple myeloma (MM). However, the disease distribution is often heterogeneous, and imaging can be used to complement MRD detection at a single site. We have investigated patients in complete remission (CR) during first-line or salvage therapy for whom MRD flow cytometry and the two imaging modalities positron emission tomography (PET) and diffusion-weighted magnetic resonance imaging (DW-MRI) were performed at the onset of CR. Residual focal lesions (FLs), detectable in 24% of first-line patients, were associated with short progression-free survival (PFS), with DW-MRI detecting disease in more patients. In some patients, FLs were only PET positive, indicating that the two approaches are complementary. Combining MRD and imaging improved prediction of outcome, with double-negative and double-positive features defining groups with excellent and dismal PFS, respectively. FLs were a rare event (12%) in first-line MRD-negative CR patients. In contrast, patients achieving an MRD-negative CR during salvage therapy frequently had FLs (50%). Multi-region sequencing and imaging in an MRD-negative patient showed persistence of spatially separated clones. In conclusion, we show that DW-MRI is a promising tool for monitoring residual disease that complements PET and should be combined with MRD.
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Affiliation(s)
- L Rasche
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - D Alapat
- Pathology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Kumar
- Radiology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - G Gershner
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J McDonald
- Radiology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C P Wardell
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R Samant
- Radiology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R Van Hemert
- Radiology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J Epstein
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A F Williams
- Pathology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - S Thanendrarajan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R G Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - F van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - B A Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - B Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - F E Davies
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - G J Morgan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - N Weinhold
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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11
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Chattopadhyay S, Thomsen H, Filho DS, Weinhold N, Broderick P, Morgan G, Goldscmidt H, Houlston R, Hemminki K, Försti A. PO-057 Genetic interaction and pathway based discovery of key regulators in multiple myeloma. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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12
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Riaz N, Blecua P, Lim RS, Shen R, Higginson DS, Weinhold N, Norton L, Weigelt B, Powell SN, Reis-Filho JS. Abstract PD8-09: Bi-allelic alterations in homologous recombination (HR) DNA repair-related genes as the basis for HR defects in human cancers: A pan-cancer genomics and functional analysis. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-pd8-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: BRCA1 and BRCA2 are involved in homologous recombination (HR) DNA repair and are germ-line cancer pre-disposition genes that result in the hereditary breast and ovarian cancer (HBOC) syndrome. Whether germ-line or somatic alterations in these genes or other members of the HR pathway and if mono- or bi-allelic alterations of HR-related genes have a phenotypic impact in breast and other cancers remains to be fully elucidated. Here we took a combined genomic and functional approach to identify the role of mutations in HR-related genes and their impact on HR DNA repair.
Methods: Whole-exome sequencing and Affymetrix SNP6 array data from 8,178 tumors, comprising 24 different cancer types including breast cancer, were retrieved from The Cancer Genome Atlas (TCGA). We identified the prevalence of missense and pathogenic (frame-shift, nonsense, start/stop codon and splice site variants) somatic and germline mutations in 102 HR-related genes curated from the literature. For each mutation, we determined if the alterations were bi-allelic. We evaluated genomic signatures of HR-deficiency in each tumor using large-scale state transitions (LSTs) and a mutational signature of HR-deficiency (signature 3). An independent set of 24 fresh sporadic breast cancer tissue specimens from our institution was subjected to i) an ex-vivo assay that assesses the ability of cancer cells to form RAD51 foci in response to ex-vivo irradiation (IR), and ii) whole exome-sequencing to define whether RAD51 deficient tumors would display LSTs, signature 3 and bi-allelic inactivation of HR-related genes.
Results: 13% and 5% of all TCGA cases displayed pathogenic mono- and bi-allelic alterations of HR-related genes, respectively. Of the biallelic alterations, only 45% occurred in traditional BRCA1/2 associated hereditary cancers (HBOCs, namely breast, ovarian and prostate cancer). Bi-allelic, but not mono-allelic, pathogenic genetic alterations in HR-related genes were significantly associated with genomic evidence of HR deficiency across cancer types, in HBOCs and within breast cancer. In HBOCs, bi-allelic alterations in HR-related genes were mutually exclusive (p=0.02). In breast cancer, bi-allelic inactivation of HR DNA repair-related genes was observed in 9.8%, of which 7.8% involved a germline pathogenic mutation and 2.0% were solely somatic. In breast cancer, in addition to BRCA1 and BRCA2, bi-allelic inactivation of PALB2 (0.2%), ATM (1.1%) and POLQ (0.3%) were found to be associated with genomic features of HR deficiency. In the 24 additional breast cancers, 9 were classified by the functional ex-vivo RAD51 assay as HR-deficient, 8 of which displayed bi-allelic inactivation of one HR-related gene, whereas only 1 of the 15 HR-proficient breast cancers harbored bi-allelic inactivation of HR-related genes (p<0.001).
Conclusion: Bi-allelic germline and somatic alterations of HR-related genes in addition to BRCA1 and BRCA2 are present in breast and other cancer types. Irrespective of the gene, these bi-allelic alterations are associated with HR deficiency as defined by genomic methods and functional assays, expanding the potential opportunities for therapies targeting HR DNA repair defects.
Citation Format: Riaz N, Blecua P, Lim RS, Shen R, Higginson DS, Weinhold N, Norton L, Weigelt B, Powell SN, Reis-Filho JS. Bi-allelic alterations in homologous recombination (HR) DNA repair-related genes as the basis for HR defects in human cancers: A pan-cancer genomics and functional analysis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-09.
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Affiliation(s)
- N Riaz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - P Blecua
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - RS Lim
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - R Shen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - DS Higginson
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - N Weinhold
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - L Norton
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - SN Powell
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY
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Crago AM, Socci ND, Qin LX, Wilder F, O'Connor R, Craig A, Houdt WV, Weinhold N, Kandoth C, Viale A, Antonescu C, Singer S. Abstract PR16: Multiplatform analysis of paired primary and recurrent well- and dedifferentiated liposarcoma samples defines copy number alterations as dominant drivers of initiation and progression. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.sarcomas17-pr16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Objective: Initiation of well-differentiated (WD) and dedifferentiated (DD) liposarcoma is driven by 12q13-15 amplification and consequent MDM2 and CDK4 overexpression, but mechanisms that regulate the variable biologic behavior of WD/DD tumors remain poorly understood. We used a multiplatform analysis of paired WD and DD samples to identify genomic events with potential to contribute to liposarcomagenesis.
Methods: From serial tumor resections performed on the same patient, we collected paired WD/DD (n=7) or WD/WD (n=2) test samples and normal tissue. Samples were analyzed using whole-exome sequencing, array comparative genomic hybridization (aCGH), Solexa small RNA sequencing, and, in a subset, RNA-seq. Findings were validated in WD/DD cohorts analyzed by custom capture array (n=201), aCGH (n=210), Affymetrix U133A microarrays (n=146), and Solexa (n=118). Lentivirus was used to deliver shRNA to WD cells in vitro; proliferation was assayed by CyQuant, differentiation by immunoblot/oil red O staining, and gene expression by Illumina microarrays.
Results: 12q13-15 amplification was observed in all WD/DD test and validation samples. Among WD samples, 1q21-24 and 6q23-25 amplifications were found in test samples and in 28% and 18% of the validation set, respectively. Of genes upregulated in WD vs. normal fat test samples, 465 were validated in the larger cohort [≥2-fold change (FC), FDR<0.05]. 53% of these genes lie within regions of copy number alteration (CNA); 8% were predicted targets of 12q-encoded miRNAs. shRNA targeting of MDM2 or drug inhibition of CDK4 in vitro negatively regulated 11% of the genes, including AURKA and its regulators TPX2 and KIF11. 6q23-25 amplification was associated with local recurrence (LR) after primary WD resection (HR 10.9, p<0.001) and with overexpression of CCDC28A and TAB2, an AP-1 regulator (1.7- and 1.9-FC, FDRs<0.05). In 6q23-25-amplified WD cells, shRNA-mediated TAB2 inhibition reduced proliferation by >90%. Comparison of matched WD/DD samples showed retained amplification of 12q13-15 and 6q23-25 after progression. In contrast to WD, DD showed strong association of the 6q23-25 CNA with increased expression of 6q genes TCF21 and HBS1L (16- and 4-FC, FDRs<0.001), but not TAB2 or CCDC28A, suggesting that additional progression events alter the oncogenic effects of initiation-associated CNAs in DD vs WD. Direct comparison of paired DD/WD test samples revealed recurrent 13q loss arising during dedifferentiation (n=3). 13q loss was found in 28% of the DD validation set and associated with reduced expression of 13q genes MYCBP2 and IRS2, regulators of insulin signaling. shRNA inhibition of MYCBP2 or IRS2 in vitro had little effect on WD differentiation, but inhibition of both genes decreased levels of PPARG, FABP4, PLIN and oil red O staining (70% reduction). Uncommon mutations in genes regulating steroid-hormone activation (e.g., NCOA6, KMT2C), adaptive immunity (e.g., LILRA1, NFKB1), and RTK signaling (e.g., NRG1, FGFR1) were identified in 11%, 6%, and 11% of WD/DD samples, respectively, but did not associate with differentiation.
Conclusions: Genes upregulated during WD initiation are commonly located in regions of CNA or regulated by 12q23-25 oncogenes MDM2 and CDK4 (e.g., AURKA, a potential therapeutic target). 6q23-26 amplification, observed in subsets of both WD and DD, associates with LR of WD, but expression of 6q23-26 genes with potential to modulate oncogenesis (e.g., TAB2 vs TCF21) differs in WD and DD tumors, suggesting that the CNA may differentially modulate early and late disease. Losses affecting broad chromosome regions such as 13q likely mediate progression by affecting multiple regulators of adipogenesis pathways (e.g., insulin signaling), while mutations have little effect on dedifferentiation.
Citation Format: Aimee M. Crago, Nicholas D. Socci, Li-Xuan Qin, Fatima Wilder, Rachael O'Connor, Amanda Craig, Willem van Houdt, Nils Weinhold, Cyriac Kandoth, Agnes Viale, Cristina Antonescu, Sam Singer. Multiplatform analysis of paired primary and recurrent well- and dedifferentiated liposarcoma samples defines copy number alterations as dominant drivers of initiation and progression [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr PR16.
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Affiliation(s)
| | | | - Li-Xuan Qin
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fatima Wilder
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Amanda Craig
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Nils Weinhold
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Sam Singer
- Memorial Sloan Kettering Cancer Center, New York, NY
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14
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Nargund AM, Pham CG, Dong Y, Wang PI, Osmangeyoglu HU, Xie Y, Aras O, Han S, Oyama T, Takeda S, Ray CE, Dong Z, Berge M, Hakimi AA, Monette S, Lekaye CL, Koutcher JA, Leslie CS, Creighton CJ, Weinhold N, Lee W, Tickoo SK, Wang Z, Cheng EH, Hsieh JJ. The SWI/SNF Protein PBRM1 Restrains VHL-Loss-Driven Clear Cell Renal Cell Carcinoma. Cell Rep 2017; 18:2893-2906. [PMID: 28329682 DOI: 10.1016/j.celrep.2017.02.074] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 01/23/2017] [Accepted: 02/24/2017] [Indexed: 02/07/2023] Open
Abstract
PBRM1 is the second most commonly mutated gene after VHL in clear cell renal cell carcinoma (ccRCC). However, the biological consequences of PBRM1 mutations for kidney tumorigenesis are unknown. Here, we find that kidney-specific deletion of Vhl and Pbrm1, but not either gene alone, results in bilateral, multifocal, transplantable clear cell kidney cancers. PBRM1 loss amplified the transcriptional outputs of HIF1 and STAT3 incurred by Vhl deficiency. Analysis of mouse and human ccRCC revealed convergence on mTOR activation, representing the third driver event after genetic inactivation of VHL and PBRM1. Our study reports a physiological preclinical ccRCC mouse model that recapitulates somatic mutations in human ccRCC and provides mechanistic and therapeutic insights into PBRM1 mutated subtypes of human ccRCC.
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Affiliation(s)
- Amrita M Nargund
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Can G Pham
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yiyu Dong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Patricia I Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hatice U Osmangeyoglu
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuchen Xie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Omer Aras
- Gerstner Sloan Kettering School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Song Han
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Toshinao Oyama
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shugaku Takeda
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chelsea E Ray
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zhenghong Dong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mathieu Berge
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - A Ari Hakimi
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carl L Lekaye
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jason A Koutcher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christina S Leslie
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chad J Creighton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - William Lee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Satish K Tickoo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zhong Wang
- Department of Cardiac Surgery, Cardiovascular Research Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily H Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - James J Hsieh
- Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA.
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15
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Riaz N, Havel JJ, Makarov V, Desrichard A, Urba WJ, Sims JS, Hodi FS, Martín-Algarra S, Mandal R, Sharfman WH, Bhatia S, Hwu WJ, Gajewski TF, Slingluff CL, Chowell D, Kendall SM, Chang H, Shah R, Kuo F, Morris LGT, Sidhom JW, Schneck JP, Horak CE, Weinhold N, Chan TA. Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab. Cell 2017; 171:934-949.e16. [PMID: 29033130 DOI: 10.1016/j.cell.2017.09.028] [Citation(s) in RCA: 1287] [Impact Index Per Article: 183.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/11/2017] [Accepted: 09/18/2017] [Indexed: 01/02/2023]
Abstract
The mechanisms by which immune checkpoint blockade modulates tumor evolution during therapy are unclear. We assessed genomic changes in tumors from 68 patients with advanced melanoma, who progressed on ipilimumab or were ipilimumab-naive, before and after nivolumab initiation (CA209-038 study). Tumors were analyzed by whole-exome, transcriptome, and/or T cell receptor (TCR) sequencing. In responding patients, mutation and neoantigen load were reduced from baseline, and analysis of intratumoral heterogeneity during therapy demonstrated differential clonal evolution within tumors and putative selection against neoantigenic mutations on-therapy. Transcriptome analyses before and during nivolumab therapy revealed increases in distinct immune cell subsets, activation of specific transcriptional networks, and upregulation of immune checkpoint genes that were more pronounced in patients with response. Temporal changes in intratumoral TCR repertoire revealed expansion of T cell clones in the setting of neoantigen loss. Comprehensive genomic profiling data in this study provide insight into nivolumab's mechanism of action.
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Affiliation(s)
- Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan J Havel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexis Desrichard
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Walter J Urba
- Earle A. Chiles Research Institute, Providence Cancer Center, Portland, OR 97213, USA
| | - Jennifer S Sims
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Salvador Martín-Algarra
- Medical Oncology, Clínica Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain
| | - Rajarsi Mandal
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - William H Sharfman
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Shailender Bhatia
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98105, USA
| | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Thomas F Gajewski
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Craig L Slingluff
- Department of Surgery and University of Virginia Cancer Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sviatoslav M Kendall
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Han Chang
- Bristol-Myers Squibb, Princeton, NJ 08648, USA
| | - Rachna Shah
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John-William Sidhom
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jonathan P Schneck
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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16
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Kirk IK, Weinhold N, Brunak S, Belling K. The impact of the protein interactome on the syntenic structure of mammalian genomes. PLoS One 2017; 12:e0179112. [PMID: 28910296 PMCID: PMC5598925 DOI: 10.1371/journal.pone.0179112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 05/10/2017] [Indexed: 02/06/2023] Open
Abstract
Conserved synteny denotes evolutionary preserved gene order across species. It is not well understood to which degree functional relationships between genes are preserved in syntenic blocks. Here we investigate whether protein-coding genes conserved in mammalian syntenic blocks encode gene products that serve the common functional purpose of interacting at protein level, i.e. connectivity. High connectivity among protein-protein interactions (PPIs) was only moderately associated with conserved synteny on a genome-wide scale. However, we observed a smaller subset of 3.6% of all syntenic blocks with high-confidence PPIs that had significantly higher connectivity than expected by random. Additionally, syntenic blocks with high-confidence PPIs contained significantly more chromatin loops than the remaining blocks, indicating functional preservation among these syntenic blocks. Conserved synteny is typically defined by sequence similarity. In this study, we also examined whether a functional relationship, here PPI connectivity, can identify syntenic blocks independently of orthology. While orthology-based syntenic blocks with high-confident PPIs and the connectivity-based syntenic blocks largely overlapped, the connectivity-based approach identified additional syntenic blocks that were not found by conventional sequence-based methods alone. Additionally, the connectivity-based approach enabled identification of potential orthologous genes between species. Our analyses demonstrate that subsets of syntenic blocks are associated with highly connected proteins, and that PPI connectivity can be used to detect conserved synteny even if sequence conservation drifts beyond what orthology algorithms normally can identify.
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Affiliation(s)
- Isa Kristina Kirk
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nils Weinhold
- Memorial Sloan Kettering Cancer Center, Computational Biology Program, New York, NY, United States of America
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kirstine Belling
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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17
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Besse A, Stolze SC, Rasche L, Weinhold N, Morgan GJ, Kraus M, Bader J, Overkleeft HS, Besse L, Driessen C. Carfilzomib resistance due to ABCB1/MDR1 overexpression is overcome by nelfinavir and lopinavir in multiple myeloma. Leukemia 2017; 32:391-401. [PMID: 28676669 PMCID: PMC5808083 DOI: 10.1038/leu.2017.212] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 06/21/2017] [Accepted: 06/26/2017] [Indexed: 12/18/2022]
Abstract
Proteasome inhibitor (PI) carfilzomib (CFZ) has activity superior to bortezomib (BTZ) and is increasingly incorporated in multiple myeloma (MM) frontline therapy and relapsed settings. Most MM patients ultimately experience PI-refractory disease, an unmet medical need with poorly understood biology and dismal outcome. Pharmacologic targeting of ABCB1 improved patient outcomes, including MM, but suffered from adverse drug effects and insufficient plasma concentrations. Proteomics analysis identified ABCB1 overexpression as the most significant change in CFZ-resistant MM cells. We addressed the functional role of ABCB1 overexpression in MM and observed significantly upregulated ABCB1 in peripheral blood malignant plasma cells (PCs) vs untreated patients' bone marrow PC. ABCB1 overexpression reduces the proteasome-inhibiting activity of CFZ due to drug efflux, in contrast to BTZ. Likewise, the cytotoxicity of established anti-MM drugs was significantly reduced in ABCB1-expressing MM cells. In search for potential drugs targeting ABCB1 in clinical trials, we identified the HIV protease inhibitors nelfinavir (NFV) and lopinavir (LPV) as potent functional modulators of ABCB1-mediated drug export, most likely via modulation of mitochondria permeability transition pore. NFV and LPV restored CFZ activity at therapeutically relevant drug levels and thus represent ready-to-use drugs to be tested in clinical trials to target ABCB1 and to re-sensitize PC to established myeloma drugs, in particular CFZ.
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Affiliation(s)
- A Besse
- Experimental Oncology and Hematology, Department of Oncology and Hematology, Kantonsspital St Gallen, St Gallen, Switzerland
| | - S C Stolze
- Gorlaeus Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Leiden, The Netherlands
| | - L Rasche
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - N Weinhold
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - G J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Kraus
- Experimental Oncology and Hematology, Department of Oncology and Hematology, Kantonsspital St Gallen, St Gallen, Switzerland
| | - J Bader
- Experimental Oncology and Hematology, Department of Oncology and Hematology, Kantonsspital St Gallen, St Gallen, Switzerland
| | - H S Overkleeft
- Gorlaeus Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Leiden, The Netherlands
| | - L Besse
- Experimental Oncology and Hematology, Department of Oncology and Hematology, Kantonsspital St Gallen, St Gallen, Switzerland
| | - C Driessen
- Experimental Oncology and Hematology, Department of Oncology and Hematology, Kantonsspital St Gallen, St Gallen, Switzerland
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18
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Chan TA, Riaz N, Havel JJ, Makarov V, Desrichard A, Sims JS, Hodi FS, Martín-Algarra S, Sharfman WH, Bhatia S, Hwu WJ, Gajewski TF, Slingluff CL, Kendall SM, Chang H, Sidhom JW, Schneck JP, Weinhold N, Horak CE, Urba WJ. Abstract 2988: Immunogenomic analyses of tumor cells and microenvironment in patients with advanced melanoma before and after treatment with nivolumab. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Response to checkpoint blockade may be dependent on tumor mutational load and the presence of antigen-specific effector T cells in the tumor microenvironment; however, how blockade modulates these features during therapy is unclear. We assessed genomic changes in tumors from patients (pts) with advanced melanoma receiving nivolumab (nivo) who progressed on ipilimumab (ipi-P) or were ipi-naive (ipi-N).
Methods: Tumor biopsies were collected pretreatment and 4 weeks post first nivo dose from ipi-N or ipi-P pts treated with nivo 3 mg/kg Q2W in the phase 1 open-label CA209-038 study (NCT01621490). Biopsies from 68 pts were analyzed by whole exome, transcriptome, and/or TCR sequencing (paired biopsies from 41, 42, and 34 pts, respectively).
Results: Objective response rate (ORR) in the overall cohort (n=85) was 27% with similar ORR in ipi-N and ipi-P cohorts. In the genomic cohort (n=68), ORR was 23% with a similar number of complete or partial responses (CR/PR) in ipi-N and ipi-P pts (n=7 and n=8, respectively). Prior to treatment, mutational and neoantigen load were comparable, regardless of previous treatment. Following nivo treatment, both mutational and neoantigen load were reduced 5-fold in pts who responded (CR/PR; n=9) and 1.2-fold in pts with stable disease (SD, n=13) compared with a 1.1-fold increase in pts with progressive disease (PD, n=19). Intratumoral heterogeneity analysis before and after nivo demonstrated that CR/PR pts generally lost tumor mutation clones/subclones. Novel tumor mutation clones were observed in on-treatment samples from 2 CR/PR pts and all pts who progressed on nivo. Transcriptome analyses revealed significant increases in distinct tumor immune cell subsets (CD8+ T cells and NK cells) and immune checkpoint gene expression (LAG3, CTLA4, PCDC1, and CD274 [PD-L1]) following nivo, which were more pronounced in pts with CR/PR vs PD (log2 fold-changes of 1.24, 1.07, 1.71, and 0.74, respectively). Consistent with the transcriptome analyses, tumor-infiltrating lymphocytes, as assessed by immunohistochemistry, generally increased following nivo in pts who responded: 2.8 vs 1.9-fold change in CR/PR/SD vs PD in the ipi-P cohort; 4.8 vs 1.8-fold change in CR/PR/SD vs PD in the ipi-N cohort. Differences in treatment-related TCR repertoire diversity changes were apparent between pts who responded within the ipi-N and ipi-P cohorts: a decrease in the evenness of T-cell clonotype distribution was observed among pts with CR/PR/SD relative to pts with PD in the ipi-N cohort (P=0.036), but not in the ipi-P cohort.
Conclusion: Nivo and ipi modulate T-cell repertoire and tumor mutational heterogeneity in pts with advanced melanoma, presenting potential mechanisms of action underlying successful nivo therapy. These data also show that prior ipi treatment may influence biological response to nivo, but further investigation is warranted.
Citation Format: Timothy A. Chan, Nadeem Riaz, Jonathan J. Havel, Vladimir Makarov, Alexis Desrichard, Jennifer S. Sims, F. Stephen Hodi, Salvador Martín-Algarra, William H. Sharfman, Shailender Bhatia, Wen-Jen Hwu, Thomas F. Gajewski, Craig L. Slingluff, Sviatoslav M. Kendall, Han Chang, John-William Sidhom, Jonathan P. Schneck, Nils Weinhold, Christine E. Horak, Walter J. Urba. Immunogenomic analyses of tumor cells and microenvironment in patients with advanced melanoma before and after treatment with nivolumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2988. doi:10.1158/1538-7445.AM2017-2988
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Affiliation(s)
| | - Nadeem Riaz
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - William H. Sharfman
- 4The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Wen-Jen Hwu
- 6University of Texas MD Anderson Cancer Center, Houston, TX
| | - Thomas F. Gajewski
- 7University of Chicago Gordon Center for Integrative Science, Chicago, IL
| | | | | | - Han Chang
- 9Bristol-Myers Squibb, Princeton, NJ
| | | | | | - Nils Weinhold
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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19
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Went M, Sud A, Law PJ, Johnson DC, Weinhold N, Försti A, van Duin M, Mitchell JS, Chen B, Kuiper R, Stephens OW, Bertsch U, Campo C, Einsele H, Gregory WM, Henrion M, Hillengass J, Hoffmann P, Jackson GH, Lenive O, Nickel J, Nöthen MM, da Silva Filho MI, Thomsen H, Walker BA, Broyl A, Davies FE, Langer C, Hansson M, Kaiser M, Sonneveld P, Goldschmidt H, Hemminki K, Nilsson B, Morgan GJ, Houlston RS. Assessing the effect of obesity-related traits on multiple myeloma using a Mendelian randomisation approach. Blood Cancer J 2017; 7. [PMID: 28622301 PMCID: PMC5520395 DOI: 10.1038/bcj.2017.48] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- M Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - A Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - P J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - D C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - N Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - A Försti
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmo, Sweden
| | - M van Duin
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - J S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - B Chen
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - R Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - O W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - U Bertsch
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, Heidelberg, Germany
| | - C Campo
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - H Einsele
- Department of Internal Medicine II, Division of Hematology and Medical Oncology, University Hospital Würzburg, Würzburg, Germany
| | - W M Gregory
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - M Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - J Hillengass
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - P Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - G H Jackson
- Royal Victoria Infirmary, Newcastle upon Tyne, Newcastle, UK
| | - O Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - J Nickel
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - M M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - M I da Silva Filho
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - H Thomsen
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - B A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A Broyl
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - F E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Langer
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - M Hansson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Hematology Clinic, Skåne University Hospital, Lund, Sweden
| | - M Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - P Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - H Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, Heidelberg, Germany
| | - K Hemminki
- Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmo, Sweden
| | - B Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, Lund, Sweden
- Broad Institute, 7 Cambridge Center, Cambridge, MA, USA
| | - G J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- E-mail:
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20
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Casuscelli J, Weinhold N, Gundem G, Wang L, Zabor EC, Drill E, Wang PI, Nanjangud GJ, Redzematovic A, Nargund AM, Manley BJ, Arcila ME, Donin NM, Cheville JC, Thompson RH, Pantuck AJ, Russo P, Cheng EH, Lee W, Tickoo SK, Ostrovnaya I, Creighton CJ, Papaemmanuil E, Seshan VE, Hakimi AA, Hsieh JJ. Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma. JCI Insight 2017; 2:92688. [PMID: 28614790 PMCID: PMC5470887 DOI: 10.1172/jci.insight.92688] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/16/2017] [Indexed: 12/31/2022] Open
Abstract
Chromophobe renal cell carcinoma (chRCC) typically shows ~7 chromosome losses (1, 2, 6, 10, 13, 17, and 21) and ~31 exonic somatic mutations, yet carries ~5%-10% metastatic incidence. Since extensive chromosomal losses can generate proteotoxic stress and compromise cellular proliferation, it is intriguing how chRCC, a tumor with extensive chromosome losses and a low number of somatic mutations, can develop lethal metastases. Genomic features distinguishing metastatic from nonmetastatic chRCC are unknown. An integrated approach, including whole-genome sequencing (WGS), targeted ultradeep cancer gene sequencing, and chromosome analyses (FACETS, OncoScan, and FISH), was performed on 79 chRCC patients including 38 metastatic (M-chRCC) cases. We demonstrate that TP53 mutations (58%), PTEN mutations (24%), and imbalanced chromosome duplication (ICD, duplication of ≥ 3 chromosomes) (25%) were enriched in M-chRCC. Reconstruction of the subclonal composition of paired primary-metastatic chRCC tumors supports the role of TP53, PTEN, and ICD in metastatic evolution. Finally, the presence of these 3 genomic features in primary tumors of both The Cancer Genome Atlas kidney chromophobe (KICH) (n = 64) and M-chRCC (n = 35) cohorts was associated with worse survival. In summary, our study provides genomic insights into the metastatic progression of chRCC and identifies TP53 mutations, PTEN mutations, and ICD as high-risk features.
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Affiliation(s)
- Jozefina Casuscelli
- Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Urology, Ludwig-Maximilians University, Munich, Germany
| | | | | | | | | | | | - Patricia I. Wang
- Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Almedina Redzematovic
- Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, and
| | - Amrita M. Nargund
- Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Brandon J. Manley
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | | | | | | | | | - Paul Russo
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Emily H. Cheng
- Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pathology
| | | | | | | | - Chad J. Creighton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | | | - A. Ari Hakimi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James J. Hsieh
- Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University, St. Louis, Missouri, USA
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21
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Huhn S, Weinhold N, Nickel J, Pritsch M, Hielscher T, Hummel M, Bertsch U, Huegle-Doerr B, Vogel M, Angermund R, Hänel M, Salwender HJ, Weisel K, Dürig J, Görner M, Kirchner H, Peter N, Graeven U, Lordick F, Hoffmann M, Reimer P, Blau IW, Jauch A, Dembowsky K, Möhler T, Wuchter P, Goldschmidt H. Circulating tumor cells as a biomarker for response to therapy in multiple myeloma patients treated within the GMMG-MM5 trial. Bone Marrow Transplant 2017; 52:1194-1198. [PMID: 28504661 PMCID: PMC5543255 DOI: 10.1038/bmt.2017.91] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- S Huhn
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - N Weinhold
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J Nickel
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - M Pritsch
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - T Hielscher
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - M Hummel
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - U Bertsch
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
| | - B Huegle-Doerr
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - M Vogel
- Janssen-Cilag, Neuss, Germany
| | | | - M Hänel
- Department of Internal Medicine III, Klinikum Chemnitz gGmbH, Chemnitz, Germany
| | - H J Salwender
- Department of Hematology/Oncology, Asklepios Klinik Altona, Hamburg, Germany
| | - K Weisel
- Department of Internal Medicine II-Hematology and Oncology, Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - J Dürig
- Department of Hematology, University Hospital Essen, Essen, Germany
| | - M Görner
- Department of Hematology, Oncology and Palliative Care, Community Hospital Bielefeld, Bielefeld, Germany
| | - H Kirchner
- Medical Clinic III Hematology and Oncology, Städt. Krankenhaus Siloah, Hannover, Germany
| | - N Peter
- 2nd Medical Department, Academic Teaching Hospital of the Charité, Carl-Thiem-Klinikum Cottbus, Cottbus, Germany
| | - U Graeven
- Hematology, Oncology and Gastroenterology, Maria-Hilf-Krankenhaus, Mönchengladbach, Germany
| | - F Lordick
- 3rd Medical Department, Haematology and Oncology, Klinikum Braunschweig, Braunschweig, Germany.,University Cancer Center Leipzig (UCCL), University Medical Center Leipzig, Leipzig, Germany
| | - M Hoffmann
- Medical Clinic A, Klinikum der Stadt Ludwigshafen gGmbH, Ludwigshafen am Rhein, Germany
| | - P Reimer
- Hematology, Oncology and Stem Cell Transplantation, Evangelisches Krankenhaus Essen-Werden gGmbH, Essen, Germany
| | - I W Blau
- Medical Clinic III Hematology and Oncology, Charité University Medicine Berlin, Berlin, Germany
| | - A Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | | | - T Möhler
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,inVentiv Health, Boston, MA, USA
| | - P Wuchter
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Institute of Transfusion Medicine and Immunology, German Red Cross Blood Service Baden-Württemberg-Hessen, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - H Goldschmidt
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
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22
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Şenbabaoğlu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA. Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol 2017; 18:46. [PMID: 28249590 PMCID: PMC5333404 DOI: 10.1186/s13059-017-1180-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Yasin Şenbabaoğlu
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Present address: Swim Across America/Ludwig Collaborative Laboratory, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ron S Gejman
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Andrew G Winer
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ming Liu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Esther Drill
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Augustin Luna
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nils Weinhold
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William Lee
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brandon J Manley
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Danny N Khalil
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel D Kaffenberger
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yingbei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ludmila Danilova
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Martin H Voss
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan A Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Russo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Emily H Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David A Scheinberg
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James J Hsieh
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Ari Hakimi
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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23
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Chavan SS, He J, Tytarenko R, Deshpande S, Patel P, Bailey M, Stein CK, Stephens O, Weinhold N, Petty N, Steward D, Rasche L, Bauer M, Ashby C, Peterson E, Ali S, Ross J, Miller VA, Stephens P, Thanendrarajan S, Schinke C, Zangari M, van Rhee F, Barlogie B, Mughal TI, Davies FE, Morgan GJ, Walker BA. Bi-allelic inactivation is more prevalent at relapse in multiple myeloma, identifying RB1 as an independent prognostic marker. Blood Cancer J 2017; 7:e535. [PMID: 28234347 PMCID: PMC5386330 DOI: 10.1038/bcj.2017.12] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 01/13/2017] [Indexed: 12/21/2022] Open
Abstract
The purpose of this study is to identify prognostic markers and treatment targets using a clinically certified sequencing panel in multiple myeloma. We performed targeted sequencing of 578 individuals with plasma cell neoplasms using the FoundationOne Heme panel and identified clinically relevant abnormalities and novel prognostic markers. Mutational burden was associated with maf and proliferation gene expression groups, and a high-mutational burden was associated with a poor prognosis. We identified homozygous deletions that were present in multiple myeloma within key genes, including CDKN2C, RB1, TRAF3, BIRC3 and TP53, and that bi-allelic inactivation was significantly enriched at relapse. Alterations in CDKN2C, TP53, RB1 and the t(4;14) were associated with poor prognosis. Alterations in RB1 were predominantly homozygous deletions and were associated with relapse and a poor prognosis which was independent of other genetic markers, including t(4;14), after multivariate analysis. Bi-allelic inactivation of key tumor suppressor genes in myeloma was enriched at relapse, especially in RB1, CDKN2C and TP53 where they have prognostic significance.
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Affiliation(s)
- S S Chavan
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J He
- Foundation Medicine Inc., Cambridge, MA, USA
| | - R Tytarenko
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - S Deshpande
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - P Patel
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Bailey
- Foundation Medicine Inc., Cambridge, MA, USA
| | - C K Stein
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - O Stephens
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - N Weinhold
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - N Petty
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - D Steward
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - L Rasche
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Bauer
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Ashby
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - E Peterson
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - S Ali
- Foundation Medicine Inc., Cambridge, MA, USA
| | - J Ross
- Foundation Medicine Inc., Cambridge, MA, USA.,Albany Medical College, Albany, NY, USA
| | - V A Miller
- Foundation Medicine Inc., Cambridge, MA, USA
| | - P Stephens
- Foundation Medicine Inc., Cambridge, MA, USA
| | - S Thanendrarajan
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Schinke
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Zangari
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - F van Rhee
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - B Barlogie
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - T I Mughal
- Foundation Medicine Inc., Cambridge, MA, USA.,Tufts University Medical Center, Boston, MA, USA
| | - F E Davies
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - G J Morgan
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - B A Walker
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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24
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Kirk IK, Weinhold N, Belling K, Skakkebæk NE, Jensen TS, Leffers H, Juul A, Brunak S. Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations. Cell Syst 2017; 4:357-364.e3. [PMID: 28215527 DOI: 10.1016/j.cels.2017.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 10/23/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
Abstract
Gene copy-number changes influence phenotypes through gene-dosage alteration and subsequent changes of protein complex stoichiometry. Human trisomies where gene copy numbers are increased uniformly over entire chromosomes provide generic cases for studying these relationships. In most trisomies, gene and protein level alterations have fatal consequences. We used genome-wide protein-protein interaction data to identify chromosome-specific patterns of protein interactions. We found that some chromosomes encode proteins that interact infrequently with each other, chromosome 21 in particular. We combined the protein interaction data with transcriptome data from human brain tissue to investigate how this pattern of global interactions may affect cellular function. We identified highly connected proteins that also had coordinated gene expression. These proteins were associated with important neurological functions affecting the characteristic phenotypes for Down syndrome and have previously been validated in mouse knockout experiments. Our approach is general and applicable to other gene-dosage changes, such as arm-level amplifications in cancer.
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Affiliation(s)
- Isa Kristina Kirk
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nils Weinhold
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kirstine Belling
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Niels Erik Skakkebæk
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas Skøt Jensen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Henrik Leffers
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Brunak
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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25
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da Silva Filho MI, Försti A, Weinhold N, Meziane I, Campo C, Huhn S, Nickel J, Hoffmann P, Nöthen MM, Jöckel KH, Landi S, Mitchell JS, Johnson D, Morgan GJ, Houlston R, Goldschmidt H, Jauch A, Milani P, Merlini G, Rowcieno D, Hawkins P, Hegenbart U, Palladini G, Wechalekar A, Schönland SO, Hemminki K. Genome-wide association study of immunoglobulin light chain amyloidosis in three patient cohorts: comparison with myeloma. Leukemia 2016; 31:1735-1742. [PMID: 28025584 DOI: 10.1038/leu.2016.387] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/28/2016] [Accepted: 11/30/2016] [Indexed: 01/27/2023]
Abstract
Immunoglobulin light chain (AL) amyloidosis is characterized by tissue deposition of amyloid fibers derived from immunoglobulin light chain. AL amyloidosis and multiple myeloma (MM) originate from monoclonal gammopathy of undetermined significance. We wanted to characterize germline susceptibility to AL amyloidosis using a genome-wide association study (GWAS) on 1229 AL amyloidosis patients from Germany, UK and Italy, and 7526 healthy local controls. For comparison with MM, recent GWAS data on 3790 cases were used. For AL amyloidosis, single nucleotide polymorphisms (SNPs) at 10 loci showed evidence of an association at P<10-5 with homogeneity of results from the 3 sample sets; some of these were previously documented to influence MM risk, including the SNP at the IRF4 binding site. In AL amyloidosis, rs9344 at the splice site of cyclin D1, promoting translocation (11;14), reached the highest significance, P=7.80 × 10-11; the SNP was only marginally significant in MM. SNP rs79419269 close to gene SMARCD3 involved in chromatin remodeling was also significant (P=5.2 × 10-8). These data provide evidence for common genetic susceptibility to AL amyloidosis and MM. Cyclin D1 is a more prominent driver in AL amyloidosis than in MM, but the links to aggregation of light chains need to be demonstrated.
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Affiliation(s)
- M I da Silva Filho
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmo, Sweden
| | - N Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.,Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - I Meziane
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - C Campo
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - S Huhn
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - J Nickel
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - P Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - M M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Research Center, University of Bonn, Bonn, Germany
| | - K-H Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Germany
| | - S Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - J S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Surrey, UK
| | - D Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, Surrey, UK
| | - G J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Surrey, UK.,Division of Molecular Pathology, The Institute of Cancer Research, Surrey, UK
| | - H Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.,National Centre of Tumor Diseases, Heidelberg, Germany
| | - A Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - P Milani
- Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Foundation 'Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo', University of Pavia, Pavia, Italy
| | - G Merlini
- Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Foundation 'Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo', University of Pavia, Pavia, Italy
| | - D Rowcieno
- National Amyloidosis Centre, University College London Medical School, London UK
| | - P Hawkins
- National Amyloidosis Centre, University College London Medical School, London UK
| | - U Hegenbart
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - G Palladini
- Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Foundation 'Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo', University of Pavia, Pavia, Italy
| | - A Wechalekar
- National Amyloidosis Centre, University College London Medical School, London UK
| | - S O Schönland
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - K Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmo, Sweden
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26
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Hsieh JJ, Chen D, Wang PI, Marker M, Redzematovic A, Chen YB, Selcuklu SD, Weinhold N, Bouvier N, Huberman KH, Bhanot U, Chevinsky MS, Patel P, Pinciroli P, Won HH, You D, Viale A, Lee W, Hakimi AA, Berger MF, Socci ND, Cheng EH, Knox J, Voss MH, Voi M, Motzer RJ. Genomic Biomarkers of a Randomized Trial Comparing First-line Everolimus and Sunitinib in Patients with Metastatic Renal Cell Carcinoma. Eur Urol 2016; 71:405-414. [PMID: 27751729 DOI: 10.1016/j.eururo.2016.10.007] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/05/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND Metastatic renal cell carcinoma (RCC) patients are commonly treated with vascular endothelial growth factor (VEGF) inhibitors or mammalian target of rapamycin inhibitors. Correlations between somatic mutations and first-line targeted therapy outcomes have not been reported on a randomized trial. OBJECTIVE To evaluate the relationship between tumor mutations and treatment outcomes in RECORD-3, a randomized trial comparing first-line everolimus (mTOR inhibitor) followed by sunitinib (VEGF inhibitor) at progression with the opposite sequence in 471 metastatic RCC patients. DESIGN, SETTING, AND PARTICIPANTS Targeted sequencing of 341 cancer genes at ∼540× coverage was performed on available tumor samples from 258 patients; 220 with clear cell histology (ccRCC). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Associations between somatic mutations and median first-line progression free survival (PFS1L) and overall survival were determined in metastatic ccRCC using Cox proportional hazards models and log-rank tests. RESULTS AND LIMITATIONS Prevalent mutations (≥ 10%) were VHL (75%), PBRM1 (46%), SETD2 (30%), BAP1 (19%), KDM5C (15%), and PTEN (12%). With first-line everolimus, PBRM1 and BAP1 mutations were associated with longer (median [95% confidence interval {CI}] 12.8 [8.1, 18.4] vs 5.5 [3.1, 8.4] mo) and shorter (median [95% CI] 4.9 [2.9, 8.1] vs 10.5 [7.3, 12.9] mo) PFS1L, respectively. With first-line sunitinib, KDM5C mutations were associated with longer PFS1L (median [95% CI] of 20.6 [12.4, 27.3] vs 8.3 [7.8, 11.0] mo). Molecular subgroups of metastatic ccRCC based on PBRM1, BAP1, and KDM5C mutations could have predictive values for patients treated with VEGF or mTOR inhibitors. Most tumor DNA was obtained from primary nephrectomy samples (94%), which could impact correlation statistics. CONCLUSIONS PBRM1, BAP1, and KDM5C mutations impact outcomes of targeted therapies in metastatic ccRCC patients. PATIENT SUMMARY Large-scale genomic kidney cancer studies reported novel mutations and heterogeneous features among individual tumors, which could contribute to varied clinical outcomes. We demonstrated correlations between somatic mutations and treatment outcomes in clear cell renal cell carcinoma, supporting the value of genomic classification in prospective studies.
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Affiliation(s)
- James J Hsieh
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - David Chen
- Novartis Oncology, East Hanover, NJ, USA
| | | | | | | | - Ying-Bei Chen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Nils Weinhold
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Umesh Bhanot
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael S Chevinsky
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Barnes Jewish Hospital, St. Louis, MO, USA
| | | | - Patrizia Pinciroli
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Helen H Won
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daoqi You
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William Lee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Emily H Cheng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer Knox
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON, Canada
| | - Martin H Voss
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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27
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Johnson DC, Weinhold N, Mitchell J, Chen B, Stephens OW, Försti A, Nickel J, Kaiser M, Gregory WA, Cairns D, Jackson GH, Hoffmann P, Noethen MM, Hillengass J, Bertsch U, Barlogie B, Davis FE, Hemminki K, Goldschmidt H, Houlston RS, Morgan GJ. Genetic factors influencing the risk of multiple myeloma bone disease. Leukemia 2016; 30:883-8. [PMID: 26669972 PMCID: PMC4832071 DOI: 10.1038/leu.2015.342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/25/2015] [Accepted: 11/30/2015] [Indexed: 01/18/2023]
Abstract
A major complication of multiple myeloma (MM) is the development of osteolytic lesions, fractures and bone pain. To identify genetic variants influencing the development of MM bone disease (MBD), we analyzed MM patients of European ancestry (totaling 3774), which had been radiologically surveyed for MBD. Each patient had been genotyped for ~6 00 000 single-nucleotide polymorphisms with genotypes for six million common variants imputed using 1000 Genomes Project and UK10K as reference. We identified a locus at 8q24.12 for MBD (rs4407910, OPG/TNFRSF11B, odds ratio=1.38, P=4.09 × 10(-9)) and a promising association at 19q13.43 (rs74676832, odds ratio=1.97, P=9.33 × 10(-7)). Our findings demonstrate that germline variation influences MBD and highlights the importance of RANK/RANKL/OPG pathway in MBD development. These findings will contribute to the development of future strategies for prevention of MBD in the early precancerous phases of MM.
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Affiliation(s)
- D C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - N Weinhold
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - J Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - B Chen
- German Cancer Research Center, Heidelberg, Germany
| | - O W Stephens
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A Försti
- German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - J Nickel
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - M Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - W A Gregory
- Leeds Institute of Molecular Medicine, Section of Clinical Trials Research, University of Leeds, Leeds, UK
| | - D Cairns
- Leeds Institute of Molecular Medicine, Section of Clinical Trials Research, University of Leeds, Leeds, UK
| | - G H Jackson
- Department of Haematology, Newcastle University, Newcastle-Upon-Tyne, UK
| | - P Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - M M Noethen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - J Hillengass
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - U Bertsch
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - B Barlogie
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - F E Davis
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - K Hemminki
- German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - H Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center of Tumor Diseases, Heidelberg, Germany
| | - R S Houlston
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - G J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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28
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Brat DJ, Verhaak RGW, Aldape KD, Yung WKA, Salama SR, Cooper LAD, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DPC, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 2015; 372:2481-98. [PMID: 26061751 PMCID: PMC4530011 DOI: 10.1056/nejmoa1402121] [Citation(s) in RCA: 2125] [Impact Index Per Article: 236.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. METHODS We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. RESULTS Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. CONCLUSIONS The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).
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29
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Erson-Omay EZ, Çağlayan AO, Schultz N, Weinhold N, Omay SB, Özduman K, Köksal Y, Li J, Serin Harmancı A, Clark V, Carrión-Grant G, Baranoski J, Çağlar C, Barak T, Coşkun S, Baran B, Köse D, Sun J, Bakırcıoğlu M, Moliterno Günel J, Pamir MN, Mishra-Gorur K, Bilguvar K, Yasuno K, Vortmeyer A, Huttner AJ, Sander C, Günel M. Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis. Neuro Oncol 2015; 17:1356-64. [PMID: 25740784 DOI: 10.1093/neuonc/nov027] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/03/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Malignant high-grade gliomas (HGGs), including the most aggressive form, glioblastoma multiforme, show significant clinical and genomic heterogeneity. Despite recent advances, the overall survival of HGGs and their response to treatment remain poor. In order to gain further insight into disease pathophysiology by correlating genomic landscape with clinical behavior, thereby identifying distinct HGG molecular subgroups associated with improved prognosis, we performed a comprehensive genomic analysis. METHODS We analyzed and compared 720 exome-sequenced gliomas (136 from Yale, 584 from The Cancer Genome Atlas) based on their genomic, histological, and clinical features. RESULTS We identified a subgroup of HGGs (6 total, 4 adults and 2 children) that harbored a statistically significantly increased number of somatic mutations (mean = 9257.3 vs 76.2, P = .002). All of these "ultramutated" tumors harbored somatic mutations in the exonuclease domain of the polymerase epsilon gene (POLE), displaying a distinctive genetic profile, characterized by genomic stability and increased C-to-A transversions. Histologically, they all harbored multinucleated giant or bizarre cells, some with predominant infiltrating immune cells. One adult and both pediatric patients carried homozygous germline mutations in the mutS homolog 6 (MSH6) gene. In adults, POLE mutations were observed in patients younger than 40 years and were associated with a longer progression-free survival. CONCLUSIONS We identified a genomically, histologically, and clinically distinct subgroup of HGGs that harbored somatic POLE mutations and carried an improved prognosis. Identification of distinctive molecular and pathological HGG phenotypes has implications not only for improved classification but also for potential targeted treatments.
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Affiliation(s)
- E Zeynep Erson-Omay
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Ahmet Okay Çağlayan
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Nikolaus Schultz
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Nils Weinhold
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - S Bülent Omay
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Koray Özduman
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Yavuz Köksal
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Jie Li
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Akdes Serin Harmancı
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Victoria Clark
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Geneive Carrión-Grant
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Jacob Baranoski
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Caner Çağlar
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Tanyeri Barak
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Süleyman Coşkun
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Burçin Baran
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Doğan Köse
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Jia Sun
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Mehmet Bakırcıoğlu
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Jennifer Moliterno Günel
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - M Necmettin Pamir
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Ketu Mishra-Gorur
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Kaya Bilguvar
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Katsuhito Yasuno
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Alexander Vortmeyer
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Anita J Huttner
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Chris Sander
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Murat Günel
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
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Shinbrot E, Henninger EE, Weinhold N, Covington KR, Göksenin AY, Schultz N, Chao H, Doddapaneni H, Muzny DM, Gibbs RA, Sander C, Pursell ZF, Wheeler DA. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Res 2014; 24:1740-50. [PMID: 25228659 PMCID: PMC4216916 DOI: 10.1101/gr.174789.114] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilon (POLE-exo*) exhibit a novel mutator phenotype, with markedly elevated TCT→TAT and TCG→TTG mutations and overall mutation frequencies often exceeding 100 mutations/Mb. Here, we identify POLE-exo* tumors in numerous cancers and classify them into two groups, A and B, according to their mutational properties. Group A mutants are found only in POLE, whereas Group B mutants are found in POLE and POLD1 and appear to be nonfunctional. In Group A, cell-free polymerase assays confirm that mutations in the exonuclease domain result in high mutation frequencies with a preference for C→A mutation. We describe the patterns of amino acid substitutions caused by POLE-exo* and compare them to other tumor types. The nucleotide preference of POLE-exo* leads to increased frequencies of recurrent nonsense mutations in key tumor suppressors such as TP53, ATM, and PIK3R1. We further demonstrate that strand-specific mutation patterns arise from some of these POLE-exo* mutants during genome duplication. This is the first direct proof of leading strand-specific replication by human POLE, which has only been demonstrated in yeast so far. Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication.
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Affiliation(s)
- Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erin E Henninger
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - Nils Weinhold
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Kyle R Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - A Yasemin Göksenin
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - Nikolaus Schultz
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chris Sander
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
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Waizenegger JS, Ben-Batalla I, Weinhold N, Meissner T, Wroblewski M, Janning M, Riecken K, Binder M, Atanackovic D, Taipaleenmaeki H, Schewe D, Sawall S, Gensch V, Cubas-Cordova M, Seckinger A, Fiedler W, Hesse E, Kröger N, Fehse B, Hose D, Klein B, Raab MS, Pantel K, Bokemeyer C, Loges S. Role of Growth arrest-specific gene 6-Mer axis in multiple myeloma. Leukemia 2014; 29:696-704. [PMID: 25102945 DOI: 10.1038/leu.2014.236] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/11/2014] [Accepted: 07/28/2014] [Indexed: 11/09/2022]
Abstract
Multiple myeloma is a mostly incurable malignancy characterized by the expansion of a malignant plasma cell (PC) clone in the human bone marrow (BM). Myeloma cells closely interact with the BM stroma, which secretes soluble factors that foster myeloma progression and therapy resistance. Growth arrest-specific gene 6 (Gas6) is produced by BM-derived stroma cells and can promote malignancy. However, the role of Gas6 and its receptors Axl, Tyro3 and Mer (TAM receptors) in myeloma is unknown. We therefore investigated their expression in myeloma cell lines and in the BM of myeloma patients and healthy donors. Gas6 showed increased expression in sorted BMPCs of myeloma patients compared with healthy controls. The fraction of Mer(+) BMPCs was increased in myeloma patients in comparison with healthy controls whereas Axl and Tyro3 were not expressed by BMPCs in the majority of patients. Downregulation of Gas6 and Mer inhibited the proliferation of different myeloma cell lines, whereas knocking down Axl or Tyro3 had no effect. Inhibition of the Gas6 receptor Mer or therapeutic targeting of Gas6 by warfarin reduced myeloma burden and improved survival in a systemic model of myeloma. Thus, the Gas6-Mer axis represents a novel candidate for therapeutic intervention in this incurable malignancy.
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Affiliation(s)
- J S Waizenegger
- 1] Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany [2] Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - I Ben-Batalla
- 1] Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany [2] Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - N Weinhold
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - T Meissner
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - M Wroblewski
- 1] Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany [2] Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - M Janning
- 1] Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany [2] Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - K Riecken
- Department of Stem Cell Transplantation, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - M Binder
- Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - D Atanackovic
- Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - H Taipaleenmaeki
- Heisenberg-Group for Molecular Skeletal Biology, Department of Trauma, Hand and Reconstructive Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - D Schewe
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - S Sawall
- 1] Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany [2] Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - V Gensch
- 1] Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany [2] Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - M Cubas-Cordova
- 1] Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany [2] Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - A Seckinger
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - W Fiedler
- Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - E Hesse
- Heisenberg-Group for Molecular Skeletal Biology, Department of Trauma, Hand and Reconstructive Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - N Kröger
- Department of Stem Cell Transplantation, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - B Fehse
- Department of Stem Cell Transplantation, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - D Hose
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - B Klein
- Institute of Research in Biotherapy, University Hospital of Montpellier (CHU), Montpellier, France
| | - M S Raab
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - K Pantel
- Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - C Bokemeyer
- Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - S Loges
- 1] Department of Hematology and Oncology, BMT with Section of Pneumology, Hubertus Wald Tumorzentrum, University Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany [2] Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Weinhold N, Försti A, da Silva Filho MI, Nickel J, Campo C, Hoffmann P, Nöthen MM, Hose D, Goldschmidt H, Jauch A, Langer C, Hegenbart U, Schönland SO, Hemminki K. Immunoglobulin light-chain amyloidosis shares genetic susceptibility with multiple myeloma. Leukemia 2014; 28:2254-6. [DOI: 10.1038/leu.2014.208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Morgan GJ, Johnson DC, Weinhold N, Goldschmidt H, Landgren O, Lynch HT, Hemminki K, Houlston RS. Inherited genetic susceptibility to multiple myeloma. Leukemia 2014; 28:518-24. [PMID: 24247655 DOI: 10.1038/leu.2013.344] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/15/2013] [Accepted: 10/17/2013] [Indexed: 12/29/2022]
Abstract
Although the familial clustering of multiple myeloma (MM) supports the role of inherited susceptibility, only recently has direct evidence for genetic predisposition been demonstrated. A meta-analysis of two genome-wide association (GWA) studies has identified single-nucleotide polymorphisms (SNPs) localising to a number of genomic regions that are robustly associated with MM risk. In this review, we provide an overview of the evidence supporting a genetic contribution to the predisposition to MM and MGUS (monoclonal gammopathy of unknown significance), and the insight this gives into the biological basis of disease aetiology. We also highlight the promise of future approaches to identify further specific risk factors and their potential clinical utility.
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Affiliation(s)
- G J Morgan
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Institute of Cancer Research, Surrey, UK
| | - D C Johnson
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Institute of Cancer Research, Surrey, UK
| | - N Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - H Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - O Landgren
- Multiple Myeloma Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - H T Lynch
- Department of Preventive Medicine, Creighton's Hereditary Cancer Center, Omaha, NE, USA
| | - K Hemminki
- 1] Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany [2] Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - R S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Surrey, UK
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34
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Iyer G, Al-Ahmadie H, Schultz N, Hanrahan AJ, Ostrovnaya I, Balar AV, Kim PH, Lin O, Weinhold N, Sander C, Zabor EC, Janakiraman M, Garcia-Grossman IR, Heguy A, Viale A, Bochner BH, Reuter VE, Bajorin DF, Milowsky MI, Taylor BS, Solit DB. Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer. J Clin Oncol 2013; 31:3133-40. [PMID: 23897969 DOI: 10.1200/jco.2012.46.5740] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE We sought to define the prevalence and co-occurrence of actionable genomic alterations in patients with high-grade bladder cancer to serve as a platform for therapeutic drug discovery. PATIENTS AND METHODS An integrative analysis of 97 high-grade bladder tumors was conducted to identify actionable drug targets, which are defined as genomic alterations that have been clinically validated in another cancer type (eg, BRAF mutation) or alterations for which a selective inhibitor of the target or pathway is under clinical investigation. DNA copy number alterations (CNAs) were defined by using array comparative genomic hybridization. Mutation profiling was performed by using both mass spectroscopy-based genotyping and Sanger sequencing. RESULTS Sixty-one percent of tumors harbored potentially actionable genomic alterations. A core pathway analysis of the integrated data set revealed a nonoverlapping pattern of mutations in the RTK-RAS-RAF and phosphoinositide 3-kinase/AKT/mammalian target of rapamycin pathways and regulators of G1-S cell cycle progression. Unsupervised clustering of CNAs defined two distinct classes of bladder tumors that differed in the degree of their CNA burden. Integration of mutation and copy number analyses revealed that mutations in TP53 and RB1 were significantly more common in tumors with a high CNA burden (P < .001 and P < .003, respectively). CONCLUSION High-grade bladder cancer possesses substantial genomic heterogeneity. The majority of tumors harbor potentially tractable genomic alterations that may predict for response to target-selective agents. Given the genomic diversity of bladder cancers, optimal development of target-specific agents will require pretreatment genomic characterization.
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Affiliation(s)
- Gopa Iyer
- Memorial Sloan-Kettering Cancer Center, Cornell University, New York, NY, USA
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Shinbrot E, Weinhold N, Schultz N, Donehower LA, Drummond J, Chang K, Gibbs R, Sander C, Wheeler DA. Abstract 1114: Polymerase epsilon (POLE) mutations and mutator phenotypes in colorectal and endometrial tumors. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colorectal rectal and endometrial cancers are divided into microsatellite instable (MSI) and microsatellite stable (MSS) types. MSS tumors have chromosome instability with mutation rates of 1-10/Mb. MSI patients have a better prognosis than MSS patients and are treated less aggressively. These tumors exhibit microsatellite instability (MSI), and the CpG island methylator phenotype (CIMP), an increased mutation rate (10-100/Mb, hypermutated). Here we demonstrate a novel class of tumor in these two diseases exhibiting an ultramutator phenotype with mutation rates exceeding 100/ Mb, MSS and chromosome stable. The ultra-high mutation rates appear to be caused by recurrent mutations in the exonuclease domain of DNA polymerase epsilon (POLE).
Matched tumor and normal whole exomes for 512 colorectal and 248 endometrial cancers (TCGA data control center) were evaluated for mutation frequency and MSI status. Among the colorectal tumors, 70/512(14%) were hyper mutated, endometroid tumors had 65/248(26%) hypermutated tumors. Within the hypermutated tumors, we identified tumors with extremely high mutation rates (100 mutations/Mb) termed “ultramutated”. 14 (3%) colorectal and 17 (7%) endometrial were ultramutated. 100% of the colorectal and endometrial ultramutated contain an exonuclease domain mutation in POLE with three recurrently mutated positions: P286R/H/S and V411L and S459F, these mutations are found exclusively in ultramutated samples. The functional relevance of these mutations has been demonstrated by previous mutational analysis of the exonuclease domain in bacteria phage (T4) yeast,and mice. Disruption of residues in the active site leads to high error rates, a mutator phenotype and tumor formation. The defined exonuclease active site aligns closely with the recurrent mutation found in the ultramutated tumors.
The ultramuted tumors have a distinct mutation spectrum, occur in context and exhibit strand biases. POLE exonuclease domain mutation tumors have high rates of C to A and T to G mutations with low rates of C to G and T to A. Changes of C to A occur predominately in context of 3’ and 5’ flanking T bases. This mutation spectrum and context of flanking bases suggests replicative strand bias. We found that mutations on the leading strand, exhibited a preference for C to A over G to T (60:40). Suggesting transcription-coupled repair (TCR) plays a role in ultramutation.
Our results demonstrate that ultra mutated tumors are driven by recurrent mutations in the exonuclease domain of DNA polymerase epsilon. The distinct mutation spectrum, strand bias and mutation context all suggest TCR is involved in ultramutated tumors. We describe a previously unknown role of POLE in colorectal tumors as well as identification of a previously undescribed hot spot for cancer mutations.
Citation Format: Eve Shinbrot, Nils Weinhold, Nikolaus Schultz, Lawrence A. Donehower, Jennifer Drummond, Kyle Chang, Richard Gibbs, Chris Sander, David A. Wheeler. Polymerase epsilon (POLE) mutations and mutator phenotypes in colorectal and endometrial tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1114. doi:10.1158/1538-7445.AM2013-1114
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Affiliation(s)
| | - Nils Weinhold
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Kyle Chang
- 1Baylor College of Medicine, Houston, TX
| | | | - Chris Sander
- 2Memorial Sloan Kettering Cancer Center, New York, NY
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Edsgärd D, Dalgaard MD, Weinhold N, Wesolowska-Andersen A, Rajpert-De Meyts E, Ottesen AM, Juul A, Skakkebæk NE, Skøt Jensen T, Gupta R, Leffers H, Brunak S. Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer. Front Endocrinol (Lausanne) 2013; 4:2. [PMID: 23372565 PMCID: PMC3557397 DOI: 10.3389/fendo.2013.00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 01/07/2013] [Indexed: 01/09/2023] Open
Abstract
Testicular germ cell cancer (TGCC) is one of the most heritable forms of cancer. Previous genome-wide association studies have focused on single nucleotide polymorphisms, largely ignoring the influence of copy number variants (CNVs). Here we present a genome-wide study of CNV on a cohort of 212 cases and 437 controls from Denmark, which was genotyped at ∼1.8 million markers, half of which were non-polymorphic copy number markers. No association of common variants were found, whereas analysis of rare variants (present in less than 1% of the samples) initially indicated a single gene with significantly higher accumulation of rare CNVs in cases as compared to controls, at the gene PTPN1 (P = 3.8 × 10(-2), 0.9% of cases and 0% of controls). However, the CNV could not be verified by qPCR in the affected samples. Further, the CNV calling of the array-data was validated by sequencing of the GSTM1 gene, which showed that the CNV frequency was in complete agreement between the two platforms. This study therefore disconfirms the hypothesis that there exists a single CNV locus with a major effect size that predisposes to TGCC. Genome-wide pathway association analysis indicated a weak association of rare CNVs related to cell migration (false-discovery rate = 0.021, 1.8% of cases and 1.1% of controls). Dysregulation during migration of primordial germ cells has previously been suspected to be a part of TGCC development and this set of multiple rare variants may thereby have a minor contribution to an increased susceptibility of TGCCs.
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Affiliation(s)
- Daniel Edsgärd
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | | | - Nils Weinhold
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | | | | | - Anne Marie Ottesen
- Department of Growth and Reproduction, RigshospitaletCopenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, RigshospitaletCopenhagen, Denmark
| | - Niels E. Skakkebæk
- Department of Growth and Reproduction, RigshospitaletCopenhagen, Denmark
| | - Thomas Skøt Jensen
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | - Ramneek Gupta
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | - Henrik Leffers
- Department of Growth and Reproduction, RigshospitaletCopenhagen, Denmark
| | - Søren Brunak
- Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
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Dalgaard MD, Weinhold N, Edsgärd D, Silver JD, Pers TH, Nielsen JE, Jørgensen N, Juul A, Gerds TA, Giwercman A, Giwercman YL, Cohn-Cedermark G, Virtanen HE, Toppari J, Daugaard G, Jensen TS, Brunak S, Rajpert-De Meyts E, Skakkebæk NE, Leffers H, Gupta R. A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation. J Med Genet 2011; 49:58-65. [PMID: 22140272 PMCID: PMC3284313 DOI: 10.1136/jmedgenet-2011-100174] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Background Testicular dysgenesis syndrome (TDS) is a common disease that links testicular germ cell cancer, cryptorchidism and some cases of hypospadias and male infertility with impaired development of the testis. The incidence of these disorders has increased over the last few decades, and testicular cancer now affects 1% of the Danish and Norwegian male population. Methods To identify genetic variants that span the four TDS phenotypes, the authors performed a genome-wide association study (GWAS) using Affymetrix Human SNP Array 6.0 to screen 488 patients with symptoms of TDS and 439 selected controls with excellent reproductive health. Furthermore, they developed a novel integrative method that combines GWAS data with other TDS-relevant data types and identified additional TDS markers. The most significant findings were replicated in an independent cohort of 671 Nordic men. Results Markers located in the region of TGFBR3 and BMP7 showed association with all TDS phenotypes in both the discovery and replication cohorts. An immunohistochemistry investigation confirmed the presence of transforming growth factor β receptor type III (TGFBR3) in peritubular and Leydig cells, in both fetal and adult testis. Single-nucleotide polymorphisms in the KITLG gene showed significant associations, but only with testicular cancer. Conclusions The association of single-nucleotide polymorphisms in the TGFBR3 and BMP7 genes, which belong to the transforming growth factor β signalling pathway, suggests a role for this pathway in the pathogenesis of TDS. Integrating data from multiple layers can highlight findings in GWAS that are biologically relevant despite having border significance at currently accepted statistical levels.
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Affiliation(s)
- Marlene D Dalgaard
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
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Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood 2011; 118:3559-69. [PMID: 21828137 PMCID: PMC3186332 DOI: 10.1182/blood-2011-06-357996] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 07/29/2011] [Indexed: 11/20/2022] Open
Abstract
The phenotype of germinal center (GC) B cells includes the unique ability to tolerate rapid proliferation and the mutagenic actions of activation induced cytosine deaminase (AICDA). Given the importance of epigenetic patterning in determining cellular phenotypes, we examined DNA methylation and the role of DNA methyltransferases in the formation of GCs. DNA methylation profiling revealed a marked shift in DNA methylation patterning in GC B cells versus resting/naive B cells. This shift included significant differential methylation of 235 genes, with concordant inverse changes in gene expression affecting most notably genes of the NFkB and MAP kinase signaling pathways. GC B cells were predominantly hypomethylated compared with naive B cells and AICDA binding sites were highly overrepresented among hypomethylated loci. GC B cells also exhibited greater DNA methylation heterogeneity than naive B cells. Among DNA methyltransferases (DNMTs), only DNMT1 was significantly up-regulated in GC B cells. Dnmt1 hypomorphic mice displayed deficient GC formation and treatment of mice with the DNA methyltransferase inhibitor decitabine resulted in failure to form GCs after immune stimulation. Notably, the GC B cells of Dnmt1 hypomorphic animals showed evidence of increased DNA damage, suggesting dual roles for DNMT1 in DNA methylation and double strand DNA break repair.
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Affiliation(s)
- Rita Shaknovich
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
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Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgärd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI. ChemProt: a disease chemical biology database. Nucleic Acids Res 2010; 39:D367-72. [PMID: 20935044 PMCID: PMC3013776 DOI: 10.1093/nar/gkq906] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical–protein annotation resources, as well as disease-associated protein–protein interactions (PPIs). We assembled more than 700 000 unique chemicals with biological annotation for 30 578 proteins. We gathered over 2-million chemical–protein interactions, which were integrated in a quality scored human PPI network of 428 429 interactions. The PPI network layer allows for studying disease and tissue specificity through each protein complex. ChemProt can assist in the in silico evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram, an antidepressant, with osteogenesis imperfect and leukemia and bisphenol A, an endocrine disruptor, with certain types of cancer, respectively. The server can be accessed at http://www.cbs.dtu.dk/services/ChemProt/.
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Affiliation(s)
- Olivier Taboureau
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, DK-2800 Denmark.
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Audouze K, Juncker AS, Roque FJSSA, Krysiak-Baltyn K, Weinhold N, Taboureau O, Jensen TS, Brunak S. Deciphering diseases and biological targets for environmental chemicals using toxicogenomics networks. PLoS Comput Biol 2010; 6:e1000788. [PMID: 20502671 PMCID: PMC2873901 DOI: 10.1371/journal.pcbi.1000788] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 04/15/2010] [Indexed: 11/27/2022] Open
Abstract
Exposure to environmental chemicals and drugs may have a negative effect on human health. A better understanding of the molecular mechanism of such compounds is needed to determine the risk. We present a high confidence human protein-protein association network built upon the integration of chemical toxicology and systems biology. This computational systems chemical biology model reveals uncharacterized connections between compounds and diseases, thus predicting which compounds may be risk factors for human health. Additionally, the network can be used to identify unexpected potential associations between chemicals and proteins. Examples are shown for chemicals associated with breast cancer, lung cancer and necrosis, and potential protein targets for di-ethylhexyl-phthalate, 2,3,7,8-tetrachlorodibenzo-p-dioxin, pirinixic acid and permethrine. The chemical-protein associations are supported through recent published studies, which illustrate the power of our approach that integrates toxicogenomics data with other data types. Exposure to environmental chemicals and drugs may have a negative effect on human health. An essential step towards understanding the effect of chemicals on human health is to identify all possible molecular targets of a given chemical. Recently, various network-oriented chemical pharmacology approaches have been published. However, these methods limit the protein prediction to already known molecular drug targets. New findings can for example be made by using high-confidence protein-protein association databases. Here, we describe a generic, computational systems biology model with the aim of understanding the underlying molecular mechanisms of chemicals and the biological pathways they perturb. We present a novel and complementary approach to existing models by integrating toxicogenomics data, chemical structures, protein-protein interaction data, disease information and functional annotation of proteins. The high confidence protein-protein association network proposed reveals unexpected connections between chemicals and diseases or human proteins. We provide literature support to demonstrate the validity of some predictions, and thereby illustrate the power of an approach that integrates toxicogenomics data with other data types.
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Affiliation(s)
- Karine Audouze
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Agnieszka Sierakowska Juncker
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Francisco J. S. S. A. Roque
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Konrad Krysiak-Baltyn
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Nils Weinhold
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Olivier Taboureau
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Skøt Jensen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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Wesolowska A, Dalgaard MD, Borst L, Gautier L, Bak M, Weinhold N, Nielsen BF, Nersting J, Tommerup N, Brunak S, Ponten T, Leffers H, Schmiegelow K, Gupta R. Relating genomic variation to drug response in childhood acute lymphoblastic leukemia by multiplexed targeted sequencing. Genome Biol 2010. [DOI: 10.1186/1465-6906-11-s1-p41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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Wesolowska A, Dalgaard MD, Borst L, Gautier L, Bak M, Weinhold N, Nielsen BF, Nersting J, Tommerup N, Brunak S, Ponten TS, Leffers H, Schmiegelow K, Gupta R. Relating genomic variation to drug response in childhood acute lymphoblastic leukemia by multiplexed targeted sequencing. Genome Biol 2010. [PMCID: PMC3026272 DOI: 10.1186/gb-2010-11-s1-p41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Agata Wesolowska
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Marlene D Dalgaard
- Pediatric Oncology labs and Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
| | - Louise Borst
- Pediatric Oncology labs and Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
| | - Laurent Gautier
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Mads Bak
- Institute for Cellular and Molecular Medicine, Panum Institute, Copenhagen, Denmark
| | - Nils Weinhold
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Betina F Nielsen
- Pediatric Oncology labs and Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
| | - Jacob Nersting
- Pediatric Oncology labs and Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
| | - Niels Tommerup
- Institute for Cellular and Molecular Medicine, Panum Institute, Copenhagen, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | | | - Henrik Leffers
- Pediatric Oncology labs and Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Pediatric Oncology labs and Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
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Juncker AS, Larsen MV, Weinhold N, Nielsen M, Brunak S, Lund O. Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands. PLoS One 2009; 4:e7448. [PMID: 19826487 PMCID: PMC2758592 DOI: 10.1371/journal.pone.0007448] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 09/23/2009] [Indexed: 11/27/2022] Open
Abstract
Background Presentation of peptides on Major Histocompatibility Complex (MHC) molecules is the cornerstone in immune system activation and increased knowledge of the characteristics of MHC ligands and their source proteins is highly desirable. Methodology/Principal Finding In the present large-scale study, we used a large data set of proteins containing experimentally identified MHC class I or II ligands and examined the proteins according to their expression profiles at the mRNA level and their Gene Ontology (GO) classification within the cellular component ontology. Proteins encoded by highly abundant mRNA were found to be much more likely to be the source of MHC ligands. Of the 2.5% most abundant mRNAs as much as 41% of the proteins encoded by these mRNAs contained MHC class I ligands. For proteins containing MHC class II ligands, the corresponding percentage was 11%. Furthermore, we found that most proteins containing MHC class I ligands were localised to the intracellular parts of the cell including the cytoplasm and nucleus. MHC class II ligand donors were, on the other hand, mostly membrane proteins. Conclusions/Significance The results contribute to the ongoing debate concerning the nature of MHC ligand-containing proteins and can be used to extend the existing methods for MHC ligand predictions by including the source protein's localisation and expression profile. Improving the current methods is important in the growing quest for epitopes that can be used for vaccine or diagnostic purposes, especially when it comes to large DNA viruses and cancer.
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Affiliation(s)
- Agnieszka S. Juncker
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Mette V. Larsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
| | - Nils Weinhold
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
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Vogl TJ, Mack MG, Scholz WR, Müller P, Weinhold N, Philipp C, Bouttcher H, Roggan A, Felix R. MR imaging-guided laser-induced thermotherapy. MINIM INVASIV THER 2009. [DOI: 10.3109/13645709609153298] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Wolf K, Mass R, Kiefer F, Eckert K, Weinhold N, Wiedemann K, Naber D. The influence of olanzapine on facial expression of emotions in schizophrenia – An improved facial EMG study. Pharmacopsychiatry 2004. [DOI: 10.1055/s-2003-825564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Vogl TJ, Weinhold N, Mack MG, Müller PK, Scholz WR, Straub R, Roggan A, Felix R. [Verification of MR thermometry by means of an in vivo intralesional, fluoroptic temperature measurement for laser-induced thermotherapy ov liver metastases]. ROFO-FORTSCHR RONTG 1998; 169:182-8. [PMID: 9739370 DOI: 10.1055/s-2007-1015071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE To evaluate the correlation of MR-measured changes of signal intensity and invasive fluoroptic temperature measurements during MR-guided LITT of liver metastases. MATERIALS AND METHODS In 15 patients with proven liver metastases of colorectal carcinoma, MR-guided LITT was performed with a percutaneous approach in a multiapplicator technique. Two temperature sensitive T1-weighted sequences (FLASH-2D- and TurboFLASH-sequences) were used to map the spatial and temporal distribution of Nd:YAG laser effects. Parallel fluoroptic temperature measurements were carried out by means of an inserted probe in a distance of 5-26 mm (mean: 14 mm) from the laser applicator. RESULTS In both sequences a gradually increasing signal loss could be documented during laser application which proved to be reversible after cessation of energy deposition. the percentage of decrease in signal intensity correlated directly with the measured increase of temperature. Invasive fluoroptical evaluation of temperature distribution after 10 min exposure time showed at 5 mm distance from the applicator an increase of temperature of 35 degrees C, in 10 mm distance a mean increase of 9 degrees C +/- 1.7, in 15 mm a mean increase of 7 degrees C +/- 1.6 and in 20 mm a mean increase of 3 degrees C +/- 0.5. This is evidence of thermal tissue damage up to 3 cm in diameter with laser monoapplication. The qualitative evaluation revealed a reproducible correlation of the extent of signal loss around the applicator and the finally induced degree of necrosis. CONCLUSION Invasive fluoroptical temperature measurements prove the diagnostic reliability of MR thermometry for the online monitoring of LITT of liver metastases.
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Affiliation(s)
- T J Vogl
- Strahlenklinik und Poliklinik, Virchow-Klinikum der Humboldt-Universität Berlin
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Vogl TJ, Mack MG, Hirsch HH, Müller P, Weinhold N, Wust P, Philipp C, Roggan A, Felix R. [In vitro evaluation of MR thermometry in the implementation of laser-induced thermotherapy]. ROFO-FORTSCHR RONTG 1997; 167:638-44. [PMID: 9465961 DOI: 10.1055/s-2007-1015595] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE To optimize the MR sequences parameter for monitoring hyperthermic effects in the tissue during laser induced thermotherapy (LITT). MATERIAL AND METHODS Experimental studies were performed for the evaluation of MR-thermometry using a contrast-agent-water solution and a pig-liver. A T1-weighted TurboFLASH sequence and a FLASH-2D sequence were used. The TurboFLASH sequence was used with various T1 settings (between 100 and 1250 ms). MR findings were correlated with temperature measurements using a fluoride optical temperature measuring system in a distance of 1, 2, and 5 cm from the laser applicator. RESULTS Using the contrast-agent-water solution demonstrated the temperature sensitivity of both sequences. In vitro evaluations using pig liver demonstrated a near linear increase of signal versus increasing tissue temperatures in a distance of 1 cm to the tip of the laser applicator. Optimal visualization of the temperature effects was obtained using a T1 between 100 ms and 400 ms. Using the FLASH-2D sequence a signal loss was documented at a TR of 110 ms. CONCLUSION MR-thermometry using sequentially TurboFLASH and FLASH-2D sequences allowed a non-invasive monitoring of the laser induced temperature changes.
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Affiliation(s)
- T J Vogl
- Strahlenklinik und Poliklinik, Virchow-Klinikum, Humboldt-Universität zu Berlin
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Vogl TJ, Weinhold N, Müller P, Mack M, Scholz W, Philipp C, Roggan A, Felix R. [MR-controlled laser-induced thermotherapy (LITT) of liver metastases: clinical evaluation]. Rontgenpraxis 1996; 49:161-168. [PMID: 8928047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- T J Vogl
- Strahlenklinik und Poliklinik, Virchow-Klinikum, HU Berlin
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Vogl TJ, Weinhold N, Müller P, Phillip C, Roggan A, Mack MG, Balzer JO, Eichstädt H, Blumhardt G, Lobeck H, Felix R. [Early clinical experiences with MR-guided laser-induced thermotherapy (LITT) of liver metastases in preoperative care]. ROFO-FORTSCHR RONTG 1996; 164:413-21. [PMID: 8634403 DOI: 10.1055/s-2007-1015681] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
PURPOSE To evaluate the LITT-induced changes with the aid of MRT and correlate these with histopathological findings. MATERIAL AND METHODS Five patients with solitary colorectal liver metastases were treated by means of MR-guided LITT before liver resection. Application time and energy of the Nd:YAG laser (1064 nm) was 10-20 minutes and 4.5-8.8 W. MRT monitoring during the LITT was carried out with temperature-sensitive T1 weighted sequences (FLASH-2-D, turbo FLASH). The extent of the induced necrosis as seen on MR was compared with the unfixed specimen and with the histopathological findings. RESULTS The extent of necrosis visible by MRT correlated with the histopathological findings with an accuracy of 95.3% +/- 4.2%. Following single treatments (three cases) the metastases suffered a reduction of 24%-55% of their original volume. In two patients a second application produced laser-induced necrosis of 78% and 98% of volume. In these two patients a temperature sound was used for measuring regional heating and showed an exact correlation with MR thermometry. CONCLUSION The results of pre-operative MR-guided LITT indicates the potential of this form of treatment for obtaining reproducible tumor necrosis of liver metastases.
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Affiliation(s)
- T J Vogl
- Strahlenklinik, Virchow-Klinikum, HU Berlin
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Vogl TJ, Müller PK, Hammerstingl R, Weinhold N, Mack MG, Philipp C, Deimling M, Beuthan J, Pegios W, Riess H. Malignant liver tumors treated with MR imaging-guided laser-induced thermotherapy: technique and prospective results. Radiology 1995; 196:257-65. [PMID: 7540310 DOI: 10.1148/radiology.196.1.7540310] [Citation(s) in RCA: 263] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
PURPOSE To evaluate magnetic resonance (MR) imaging-guided laser-induced thermotherapy (LITT) of liver metastases. MATERIALS AND METHODS In a phase II study, 20 patients with 33 metastases from colorectal carcinoma (75%) or other primary tumors (25%) underwent LITT. MR thermometry performed with fast low-angle shot sequences was used to monitor therapy on-line, and dynamic and static contrast material-enhanced MR images enabled estimation of the degree of resultant necrosis. Follow-up studies were performed 3 months after thermotherapy. RESULTS The thermosequences enabled accurate on-line monitoring in 85% of lesions. In 69% of lesions 20 mm in diameter or smaller, contrast-enhanced MR images depicted substantial necrosis, with a local tumor control rate of 69% after 6 months and 44% after 12 months. Among lesions larger than 20 mm, necrosis was frequently incomplete, with a local control rate of only 41% after 6 months and 27% after 12 months. CONCLUSION MR imaging-guided LITT of liver metastases is a safe and promising therapy for liver metastases.
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Affiliation(s)
- T J Vogl
- Department of Radiology, University of Berlin, Germany
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