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Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell 2021; 183:197-210.e32. [PMID: 33007263 DOI: 10.1016/j.cell.2020.08.006] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 04/08/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022]
Abstract
Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g., deletion) or complex (e.g., chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early-replicating regions, superenhancers, and breast or ovarian cancers. Rigma comprise "chasms" of low-JCN deletions enriched in late-replicating fragile sites and gastrointestinal carcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold-back inversions associated with expressed protein-coding fusions, breakend hypermutation, and acral, but not cutaneous, melanomas. Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis.
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Affiliation(s)
- Kevin Hadi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Xiaotong Yao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Julie M Behr
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Aditya Deshpande
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Huasong Tian
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Sarah Kudman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joel Rosiene
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Madison Darmofal
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | | | - Emily M Adney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Alon Shaiber
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zoran Gajic
- New York Genome Center, New York, NY 10013, USA
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kenneth Eng
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeremiah A Wala
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Minita Shah
- New York Genome Center, New York, NY 10013, USA
| | | | | | - Mayu O Frank
- New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Robert B Darnell
- New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Franklin Huang
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sally Dewhurst
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - John Maciejowski
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Titia de Lange
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Jeremy Setton
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; 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
| | - Jorge S Reis-Filho
- 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
| | - Simon Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David A Knowles
- New York Genome Center, New York, NY 10013, USA; Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bud Mishra
- Departments of Computer Science, Mathematics and Cell Biology, Courant Institute and NYU School of Medicine, New York University, New York, NY 10012, USA
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | - Kenji M Oman
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Carissa A Sanchez
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lucian P Smith
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Patricia C Galipeau
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Thomas G Paulson
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Brian J Reid
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Xiaohong Li
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David Wilkes
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Olivier Elemento
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.
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Ganguli A, Mostafa A, Saavedra C, Kim Y, Le P, Faramarzi V, Feathers RW, Berger J, Ramos-Cruz KP, Adeniba O, Diaz GJP, Drnevich J, Wright CL, Hernandez AG, Lin W, Smith AM, Kosari F, Vasmatzis G, Anastasiadis PZ, Bashir R. Three-dimensional microscale hanging drop arrays with geometric control for drug screening and live tissue imaging. SCIENCE ADVANCES 2021; 7:7/17/eabc1323. [PMID: 33893093 PMCID: PMC8064630 DOI: 10.1126/sciadv.abc1323] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 03/05/2021] [Indexed: 05/09/2023]
Abstract
Existing three-dimensional (3D) culture techniques are limited by trade-offs between throughput, capacity for high-resolution imaging in living state, and geometric control. Here, we introduce a modular microscale hanging drop culture where simple design elements allow high replicates for drug screening, direct on-chip real-time or high-resolution confocal microscopy, and geometric control in 3D. Thousands of spheroids can be formed on our microchip in a single step and without any selective pressure from specific matrices. Microchip cultures from human LN229 glioblastoma and patient-derived mouse xenograft cells retained genomic alterations of originating tumors based on mate pair sequencing. We measured response to drugs over time with real-time microscopy on-chip. Last, by engineering droplets to form predetermined geometric shapes, we were able to manipulate the geometry of cultured cell masses. These outcomes can enable broad applications in advancing personalized medicine for cancer and drug discovery, tissue engineering, and stem cell research.
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Affiliation(s)
- A Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - A Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - C Saavedra
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Y Kim
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - P Le
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - V Faramarzi
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - R W Feathers
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - J Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - K P Ramos-Cruz
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - O Adeniba
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - G J Pagan Diaz
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - J Drnevich
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - C L Wright
- DNA Services Lab, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - A G Hernandez
- DNA Services Lab, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - W Lin
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - A M Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61820, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - F Kosari
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - G Vasmatzis
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - P Z Anastasiadis
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA.
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - R Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61820, USA
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3
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Abstract
Bladder cancer has been successfully treated with immunotherapy, whereas prostate cancer is a cold tumor with inadequate immune-related treatment response. A greater understanding of the tumor microenvironment and methods for harnessing the immune system to address tumor growth will be needed to improve immunotherapies for both prostate and bladder cancer. Here, we provide an overview of prostate and bladder cancer, including fundamental aspects of the disease and treatment, the elaborate cellular makeup of the tumor microenvironment, and methods for exploiting relevant pathways to develop more effective treatments.
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Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn 2020; 23:375-388. [PMID: 33387698 DOI: 10.1016/j.jmoldx.2020.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 11/22/2022] Open
Abstract
DNA junctions (DNAJs) frequently impact clinically relevant genes in tumors and are important for diagnostic and therapeutic purposes. Although routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single-gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole-genome sequencing. Structural variance analysis from whole-genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. Through optimized whole-genome sequencing and specialized bioinformatics algorithms, complete structural variance analysis is reported, including DNAJs, from formalin-fixed DNA. Selective library assembly from larger fragments (>500 bp) and economical sequencing depths (300 to 400 million reads) provide representative genomic coverage profiles and increased allelic coverage to levels compatible with DNAJ calling (40× to 60×). Although consistently fragmented, more recently formalin-fixed, specimens (<2 years' storage) revealed consistent populations of larger DNA fragments. Optimized bioinformatics efficiently detected >90% of DNAJs in two prostate tumors (approximately 60% tumor) previously analyzed by mate-pair sequencing on fresh frozen tissue, with evidence of at least one spanning-read in 99% of DNAJs. Rigorous masking with data from unrelated formalin-fixed tissue progressively eliminated many false-positive DNAJs, without loss of true positives, resulting in low numbers of false-positive passing current filters. This methodology enables more comprehensive clinical genomics testing on formalin-fixed clinical specimens.
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Murphy SJ, Harris FR, Smadbeck JB, Serla V, Karagouga G, Johnson SH, Kosari F, Pierson KE, Bungum AO, Edell ES, Mansfield AS, Wigle DA, Kipp BR, Vasmatzis G, Aubry MC. Optimizing clinical cytology touch preparations for next generation sequencing. Genomics 2020; 112:5313-5323. [PMID: 33144219 DOI: 10.1016/j.ygeno.2020.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 12/26/2022]
Abstract
Intraoperative diagnosis is routinely performed on cytology touch preparations (TPs) from core needle biopsies (CNBs). Current interest promotes their utility as an important source of patient tissue for clinical genomic testing. Herein we present whole genome structural variant analysis (SVA) from mate-pair sequencing (MPseq) and whole exome sequencing (WES) mutation calling in DNA directly whole genome amplified (WGA) from TPs. Chromosomal copy changes and somatic DNA junction detection from MPseq of TPs were highly consistent with associated CNBs and bulk resected tissues in all cases. While increased frequency coverage noise from limitations of amplification of limited sample input was significant, this was effectively compensated by natural tumor enrichment during the TP process, which also enhanced variant detection and loss of heterozygosity evaluations from WES. This novel TP methodology enables expanded utility of frequently limited CNB for both clinical and research genomic testing.
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Affiliation(s)
- Stephen J Murphy
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.
| | - Faye R Harris
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - James B Smadbeck
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Vishnu Serla
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States; Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Giannoula Karagouga
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Sarah H Johnson
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Farhad Kosari
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Karlyn E Pierson
- Departments of Thoracic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Aaron O Bungum
- Departments of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eric S Edell
- Departments of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Dennis A Wigle
- Departments of Thoracic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Benjamin R Kipp
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - George Vasmatzis
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.
| | - Marie Christine Aubry
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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6
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Murphy SJ, Harris FR, Kosari F, Barreto Siqueira Parrilha Terra S, Nasir A, Johnson SH, Serla V, Smadbeck JB, Halling GC, Karagouga G, Sukov WR, Leventakos K, Yang P, Peikert T, Mansfield AS, Wigle DA, Yi ES, Kipp BR, Vasmatzis G, Aubry MC. Using Genomics to Differentiate Multiple Primaries From Metastatic Lung Cancer. J Thorac Oncol 2019; 14:1567-1582. [PMID: 31103780 DOI: 10.1016/j.jtho.2019.05.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 04/01/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Genomic technologies present a promising mechanism of resolving the clinical dilemma of distinguishing independent primary tumors from intrapulmonary metastases in NSCLC. We evaluated the utility of discordant mapping somatic junctions from chromosomal rearrangements in diagnosing metastatic disease compared to the current standard histologic review. MATERIAL AND METHODS Mate-pair sequencing was performed on DNA extracted from 76 distinct tumors from 37 cases of multiple lung cancers. Discordant mapping junctions and chromosomal copy levels were assessed for each tumor. Blood-derived DNA was available on 22 of these cases for germline assessments. A lung cancer next-generation sequencing panel was additionally performed on tumor pairs from 17 patients. RESULTS Whereas mate-pair sequencing was able to classify lineage in all tumor pairs, histologic review appeared to misclassify lineage in 9 of 33 (27%) same-histology tumor pair comparisons. Based on disagreement between the reviewing pathologists, histopathologic lineage was classified as indeterminate in seven cases. In two cases where pathologists agreed on a metastatic call, no shared junctions were found suggesting independent primaries. Although germline junctions passing algorithmic filters were common, on average less than three were present and all had predictable structures of small focal rearrangements or transposons. Evaluation of shared chromosomal copy changes and driver mutations through a lung cancer next-generation sequencing panel, while informative, were nondefinitive in calling lineage in all cases. CONCLUSIONS The highly unique nature and prevalence of chromosomal rearrangement in lung cancers provide a useful and definitive technique for calling lineage in multifocal lung cancer.
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Affiliation(s)
- Stephen J Murphy
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Faye R Harris
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Farhad Kosari
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Simone Barreto Siqueira Parrilha Terra
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Aqsa Nasir
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Vishnu Serla
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - James B Smadbeck
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Geoffrey C Halling
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Giannoula Karagouga
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Tobias Peikert
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Dennis A Wigle
- Department of General Thoracic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Eunhee S Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
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7
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Bochtler T, Kartal‐Kaess M, Granzow M, Hielscher T, Cosenza MR, Herold‐Mende C, Jauch A, Krämer A. Micronucleus formation in human cancer cells is biased by chromosome size. Genes Chromosomes Cancer 2019; 58:392-395. [DOI: 10.1002/gcc.22707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 01/22/2023] Open
Affiliation(s)
- Tilmann Bochtler
- Clinical Cooperation Unit Molecular Hematology/OncologyGerman Cancer Research Center (DKFZ) Heidelberg Germany
- Department of Internal Medicine VUniversity of Heidelberg Heidelberg Germany
| | - Mutlu Kartal‐Kaess
- Clinical Cooperation Unit Molecular Hematology/OncologyGerman Cancer Research Center (DKFZ) Heidelberg Germany
- Institute of Human Genetics, University Heidelberg Heidelberg Germany
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, InselspitalUniversity Hospital, University of Bern Bern Switzerland
| | - Martin Granzow
- Institute of Human Genetics, University Heidelberg Heidelberg Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Marco R. Cosenza
- Clinical Cooperation Unit Molecular Hematology/OncologyGerman Cancer Research Center (DKFZ) Heidelberg Germany
| | - Christel Herold‐Mende
- Division of Experimental Neurosurgery, Department of NeurosurgeryUniversity of Heidelberg Heidelberg Germany
| | - Anna Jauch
- Institute of Human Genetics, University Heidelberg Heidelberg Germany
| | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/OncologyGerman Cancer Research Center (DKFZ) Heidelberg Germany
- Department of Internal Medicine VUniversity of Heidelberg Heidelberg Germany
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8
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Vasmatzis G, Kosari F, Murphy SJ, Terra S, Kovtun IV, Harris FR, Zarei S, Smadbeck JB, Johnson SH, Gaitatzes AG, Therneau TM, Rangel LJ, Knudson RA, Greipp P, Sukov WR, Knutson DL, Kloft-Nelson SM, Karnes RJ, Cheville JC. Large Chromosomal Rearrangements Yield Biomarkers to Distinguish Low-Risk From Intermediate- and High-Risk Prostate Cancer. Mayo Clin Proc 2019; 94:27-36. [PMID: 30611450 DOI: 10.1016/j.mayocp.2018.06.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/07/2018] [Accepted: 06/18/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To test the hypothesis that chromosomal rearrangements (CRs) can distinguish low risk of progression (LRP) from intermediate and high risk of progression (IHRP) to prostate cancer (PCa) and if these CRs have the potential to identify men with LRP on needle biopsy that harbor IHRP PCa in the prostate gland. PATIENTS AND METHODS Mate pair sequencing of amplified DNA from pure populations of Gleason patterns in 154 frozen specimens from 126 patients obtained between August 14, 2001, and July 15, 2011, was used to detect CRs including abnormal junctions and copy number variations. Potential CR biomarkers with higher incidence in IHRP than in LRP to cancer and having significance in PCa biology were identified. Independent validation was performed by fluorescence in situ hybridization in 152 specimens from 124 patients obtained between February 12, 2002, and July 12, 2008. RESULTS The number of abnormal junctions did not distinguish LRP from IHRP. Loci corresponding to genes implicated in PCa were more frequently altered in IHRP. Integrated analysis of copy number variations and microarray data yielded 6 potential markers that were more frequently detected in Gleason pattern 3 of a Gleason score 7 of PCa than in Gleason pattern 3 of a Gleason score 6 PCa. Five of those were cross-validated in an independent sample set with statistically significant areas under the receiver operating characteristic curves (AUCs) (P≤.01). Probes detecting deletions in PTEN and CHD1 had AUCs of 0.87 (95% CI, 0.77-0.97) and 0.73 (95% CI, 0.60-0.86), respectively, and probes detecting gains in ASAP1, MYC, and HDAC9 had AUCs of 0.71 (95% CI, 0.59-0.84), 0.82 (95% CI, 0.71-0.93), and 0.77 (95% CI, 0.66-0.89), respectively (for expansion of gene symbols, use search tool at www.genenames.org). CONCLUSION Copy number variations in regions encompassing important PCa genes were predictive of cancer significance and have the potential to identify men with LRP PCa by needle biopsy who have IHRP PCa in their prostate gland.
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Affiliation(s)
- George Vasmatzis
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Molecular Medicine, Mayo Clinic, Rochester, MN.
| | - Farhad Kosari
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Molecular Medicine, Mayo Clinic, Rochester, MN
| | - Stephen J Murphy
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Simone Terra
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN; Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
| | - Irina V Kovtun
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN
| | - Faye R Harris
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Shabnam Zarei
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
| | - James B Smadbeck
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Sarah H Johnson
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Athanasios G Gaitatzes
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Terry M Therneau
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | | | | | | | | | | | - John C Cheville
- Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN; Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
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9
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Harris FR, Zhang P, Yang L, Hou X, Leventakos K, Weroha SJ, Vasmatzis G, Kovtun IV. Targeting HER2 in patient-derived xenograft ovarian cancer models sensitizes tumors to chemotherapy. Mol Oncol 2018; 13:132-152. [PMID: 30499260 PMCID: PMC6360362 DOI: 10.1002/1878-0261.12414] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/22/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022] Open
Abstract
Ovarian cancer is the most lethal gynecologic malignancy. About 75% of ovarian cancer patients relapse and/or develop chemo‐resistant disease after initial response to standard‐of‐care treatment with platinum‐based therapies. HER2 amplifications and overexpression in ovarian cancer are reported to vary, and responses to HER2 inhibitors have been poor. Next generation sequencing technologies in conjunction with testing using patient‐derived xenografts (PDX) allow validation of personalized treatments. Using a whole‐genome mate‐pair next generation sequencing (MPseq) protocol, we identified several high grade serous ovarian cancers (HGS‐OC) with DNA alterations in genes encoding members of the ERBB2 pathway. The efficiency of anti‐HER2 therapy was tested in three different PDX lines with the identified alterations and high levels of HER2 protein expression. Treatment responses to pertuzumab or pertuzumab/trastuzumab were compared in each PDX line WITH standard carboplatin and paclitaxel combination treatment. In all three PDX models, HER2‐targeted therapy resulted in significant inhibition of tumor growth compared with untreated controls. However, the responses in each case were inferior to those to chemotherapy, even for chemo‐resistant lines. When chemotherapy and HER2‐targeted therapy were administered together, a significant regression of tumor was observed after 6 weeks of treatment compared with chemotherapy alone. Post‐treatment analysis of these tissues revealed that inhibition of the ERBB2 pathway occurred at the level of phosphorylation and expression of downstream targets. In conclusion, while targeting of presumably activated ERBB2 pathway alone in HGS‐OC results in a modest treatment benefit, a combination therapy including both chemotherapy drugs and HER2 inhibitors provides a far better response. Further studies are needed to address development of recurrence and sensitivity of recurrent disease to HER2‐targeted therapy.
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Affiliation(s)
- Faye R Harris
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Piyan Zhang
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lin Yang
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Xiaonan Hou
- Departments of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | | | - Saravut J Weroha
- Departments of Medical Oncology, Mayo Clinic, Rochester, MN, USA.,Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Irina V Kovtun
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
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10
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Frank S, Nelson P, Vasioukhin V. Recent advances in prostate cancer research: large-scale genomic analyses reveal novel driver mutations and DNA repair defects. F1000Res 2018; 7. [PMID: 30135717 PMCID: PMC6073096 DOI: 10.12688/f1000research.14499.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is a disease of mutated and misregulated genes. However, primary prostate tumors have relatively few mutations, and only three genes (
ERG,
PTEN, and
SPOP) are recurrently mutated in more than 10% of primary tumors. On the other hand, metastatic castration-resistant tumors have more mutations, but, with the exception of the androgen receptor gene (
AR), no single gene is altered in more than half of tumors. Structural genomic rearrangements are common, including
ERG fusions, copy gains involving the
MYC locus, and copy losses containing
PTEN. Overall, instead of being associated with a single dominant driver event, prostate tumors display various combinations of modifications in oncogenes and tumor suppressors. This review takes a broad look at the recent advances in PCa research, including understanding the genetic alterations that drive the disease and how specific mutations can sensitize tumors to potential therapies. We begin with an overview of the genomic landscape of primary and metastatic PCa, enabled by recent large-scale sequencing efforts. Advances in three-dimensional cell culture techniques and mouse models for PCa are also discussed, and particular emphasis is placed on the benefits of patient-derived xenograft models. We also review research into understanding how ETS fusions (in particular,
TMPRSS2-ERG) and
SPOP mutations contribute to tumor initiation. Next, we examine the recent findings on the prevalence of germline DNA repair mutations in about 12% of patients with metastatic disease and their potential benefit from the use of poly(ADP-ribose) polymerase (PARP) inhibitors and immune modulation. Lastly, we discuss the recent increased prevalence of AR-negative tumors (neuroendocrine and double-negative) and the current state of immunotherapy in PCa. AR remains the primary clinical target for PCa therapies; however, it does not act alone, and better understanding of supporting mutations may help guide the development of novel therapeutic strategies.
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Affiliation(s)
- Sander Frank
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Peter Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Departments of Medicine and Urology, University of Washington, Seattle, WA 98195, USA.,Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Valeri Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Pathology, University of Washington, Seattle, WA 98195, USA
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11
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Luijten MNH, Lee JXT, Crasta KC. Mutational game changer: Chromothripsis and its emerging relevance to cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:29-51. [PMID: 30115429 DOI: 10.1016/j.mrrev.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022]
Abstract
In recent years, the paradigm that genomic abnormalities in cancer cells arise through progressive accumulation of mutational events has been challenged by the discovery of single catastrophic events. One such phenomenon termed chromothripsis, involving massive chromosomal rearrangements arising all at once, has emerged as a major mutational game changer. The strong interest in this process stems from its widespread association with a range of cancer types and its potential as a mutational driver. In this review, we first describe chromothripsis detection and incidence in cancers. We then explore recently proposed underlying mechanistic origins, which explain the curious observations of the highly localised nature of the rearrangements on chromothriptic chromosomes. Detection of chromothriptic patterns following incorporation of single chromosomes into micronuclei or following telomere attrition have greatly contributed to our understanding of the reasons behind this chromosomal restriction. These underlying cellular events have been found to be participants in the tumourigenic process, strongly suggesting a potential role for chromothripsis in cancer development. Thus, we discuss potential implications of chromothripsis for cancer progression and therapy.
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Affiliation(s)
| | - Jeannie Xue Ting Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.
| | - Karen Carmelina Crasta
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, 61 Biopolis Drive, 138673, Singapore; Department of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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12
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Smits M, Mehra N, Sedelaar M, Gerritsen W, Schalken JA. Molecular biomarkers to guide precision medicine in localized prostate cancer. Expert Rev Mol Diagn 2018. [PMID: 28635333 DOI: 10.1080/14737159.2017.1345627] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Major advances through tumor profiling technologies, that include next-generation sequencing, epigenetic, proteomic and transcriptomic methods, have been made in primary prostate cancer, providing novel biomarkers that may guide precision medicine in the near future. Areas covered: The authors provided an overview of novel molecular biomarkers in tissue, blood and urine that may be used as clinical tools to assess prognosis, improve selection criteria for active surveillance programs, and detect disease relapse early in localized prostate cancer. Expert commentary: Active surveillance (AS) in localized prostate cancer is an accepted strategy in patients with very low-risk prostate cancer. Many more patients may benefit from watchful waiting, and include patients of higher clinical stage and grade, however selection criteria have to be optimized and early recognition of transformation from localized to lethal disease has to be improved by addition of molecular biomarkers. The role of non-invasive biomarkers is challenging the need for repeat biopsies, commonly performed at 1 and 4 years in men under AS programs.
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Affiliation(s)
- Minke Smits
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
| | - Niven Mehra
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
| | - Michiel Sedelaar
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
| | - Winald Gerritsen
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
| | - Jack A Schalken
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
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13
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Chromothripsis in acute myeloid leukemia: biological features and impact on survival. Leukemia 2018; 32:1609-1620. [PMID: 29472722 PMCID: PMC6035145 DOI: 10.1038/s41375-018-0035-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/31/2017] [Accepted: 11/21/2017] [Indexed: 12/12/2022]
Abstract
Chromothripsis is a one-step genome-shattering catastrophe resulting from disruption of one or few chromosomes in multiple fragments and consequent random rejoining and repair. This study defines incidence of chromothripsis in 395 newly diagnosed adult acute myeloid leukemia (AML) patients from three institutions, its impact on survival and its genomic background. SNP 6.0 or CytoscanHD Array (Affymetrix®) were performed on all samples. We detected chromothripsis with a custom algorithm in 26/395 patients. Patients harboring chromothripsis had higher age (p = 0.002), ELN high risk (HR) (p < 0.001), lower white blood cell (WBC) count (p = 0.040), TP53 loss, and/or mutations (p < 0.001) while FLT3 (p = 0.025), and NPM1 (p = 0.032) mutations were mutually exclusive with chromothripsis. Chromothripsis-positive patients showed a worse overall survival (OS) (p < 0.001) compared with HR patients (p = 0.011) and a poor prognosis in a COX-HR optimal regression model. Chromothripsis presented the hallmarks of chromosome instability [i.e., TP53 alteration, 5q deletion, higher mean of copy number alteration (CNA), complex karyotype, alterations in DNA repair, and cell cycle] and focal deletions on chromosomes 4, 7, 12, 16, and 17. CBA. FISH showed that chromothripsis is associated with marker, derivative, and ring chromosomes. In conclusion, chromothripsis frequently occurs in AML (6.6%) and influences patient prognosis and disease biology.
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14
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Fontana MC, Marconi G, Milosevic Feenstra JD, Fonzi E, Papayannidis C, Ghelli Luserna di Rorá A, Padella A, Solli V, Franchini E, Ottaviani E, Ferrari A, Baldazzi C, Testoni N, Iacobucci I, Soverini S, Haferlach T, Guadagnuolo V, Semerad L, Doubek M, Steurer M, Racil Z, Paolini S, Manfrini M, Cavo M, Simonetti G, Kralovics R, Martinelli G. Chromothripsis in Acute Myeloid Leukemia: biological features and
impact on survival. Leukemia 2017:10.1038/leu.2017.351. [PMCID: PMC5892717 DOI: 10.1038/leu.2017.351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Chromothripsis is a one-step genome-shattering catastrophe resulting from
disruption of one or few chromosomes in multiple fragments and consequent random
rejoining and repair. This study define incidence of chromothripsis in 395
newly-diagnosed adult acute myeloid leukemia (AML) patients from three
institutions, its impact on survival and its genomic background. SNP 6.0 or
CytoscanHD Array (Affymetrix®) were performed on all samples. We detected
chromothripsis with a custom algorithm in 26/395 patients. Patients harboring
chromothripsis had higher age (p=.002), ELN high risk (HR) (p<.001),
lower white blood cell (WBC) count (p=.040), TP53 loss and/or
mutations (p<.001) while FLT3 (p=.025) and
NPM1 (p=.032) mutations were mutually exclusive with
chromothripsis. Chromothripsis-positive patients showed a worse overall survival
(OS) (p<.001) compared with HR patients (p=.011) and a poor prognosis in
a COX-HR optimal regression model. Chromothripsis presented the hallmarks of
chromosome instability [i.e. TP53 alteration, 5q deletion,
higher mean of copy number alteration (CNA), complex karyotype, alterations in
DNA repair and cell cycle] and focal deletions on chromosomes 4, 7, 12, 16, 17.
CBA. FISH showed that chromothripsis is associated with marker, derivative and
ring chromosomes. In conclusion, chromothripsis frequently occurs in AML (6.6%)
and influences patient prognosis and disease biology.
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Affiliation(s)
| | - Giovanni Marconi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | - Eugenio Fonzi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | | | - Antonella Padella
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Vincenza Solli
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Eugenia Franchini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Emanuela Ottaviani
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Anna Ferrari
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Carmen Baldazzi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Nicoletta Testoni
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Ilaria Iacobucci
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Simona Soverini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | | | - Lukas Semerad
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Michael Steurer
- Division of Hematology and Oncology, Medical University of
Innsbruck, Innsbruck, Austria
| | - Zdenek Racil
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Stefania Paolini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Marco Manfrini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Michele Cavo
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Giorgia Simonetti
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences, Wien, Austria
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15
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Abstract
Genetic abnormalities are present in all tumor types, although the frequency and type can vary. Chromosome abnormalities include highly aberrant structures, particularly chromothriptic chromosomes. The generation of massive sequencing data has illuminated the scope of the mutational burden in cancer genomes, identifying patterns of mutations (mutation signatures), which have the potential to shed light on the relatedness and etiologies of cancers and impact therapy response. Some mutation patterns are clearly attributable to disruptions in pathways that maintain genomic integrity. Here we review recent advances in our understanding of genetic changes occurring in cancers and the roles of genome maintenance pathways.
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Affiliation(s)
- Elizabeth M Kass
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mary Ellen Moynahan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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16
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Abstract
Aberrations in telomere biology are among the earliest events in prostate cancer tumorigenesis and continue during tumour progression. Substantial telomere shortening occurs in prostate cancer cells and high-grade prostatic intraepithelial neoplasia. Not all mechanisms of telomere shortening are understood, but oxidative stress from local inflammation might accelerate prostatic telomere loss. Critically short telomeres can drive the accumulation of tumour-promoting genomic alterations; however, continued telomere erosion is unsustainable and must be mitigated to ensure cancer cell survival and unlimited replication potential. Prostate cancers predominantly maintain telomeres by activating telomerase, but alternative mechanisms of telomere extension can occur in metastatic disease. Telomerase activity and telomere length assessment might be useful in prostate cancer diagnosis and prognosis. Telomere shortening in normal stromal cells has been associated with prostate cancer, whereas variable telomere lengths in prostate cancer cells and telomere shortening in cancer-associated stromal cells correlated with lethal disease. Single-agent telomerase-targeted treatments for solid cancers were ineffective in clinical trials but have not been investigated in prostate cancer and might be useful in combination with established regimens. Telomere-directed strategies have not been explored as extensively. Telomere deprotection strategies have the advantage of being effective in both telomerase-dependent and telomerase-independent cancers. Disruption of androgen receptor function in prostate cancer cells results in telomere dysfunction, indicating telomeres and telomerase as potential therapeutic targets in prostate cancer.
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17
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Chen H, Singh RR, Lu X, Huo L, Yao H, Aldape K, Abraham R, Virani S, Mehrotra M, Mishra BM, Bousamra A, Albarracin C, Wu Y, Roy-Chowdhuri S, Shamanna RK, Routbort MJ, Medeiros LJ, Patel KP, Broaddus R, Sahin A, Luthra R. Genome-wide copy number aberrations and HER2 and FGFR1 alterations in primary breast cancer by molecular inversion probe microarray. Oncotarget 2017; 8:10845-10857. [PMID: 28125801 PMCID: PMC5355228 DOI: 10.18632/oncotarget.14802] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/10/2017] [Indexed: 11/25/2022] Open
Abstract
Breast cancer remains the second leading cause of cancer-related death in women despite stratification based on standard hormonal receptor (HR) and HER2 testing. Additional prognostic markers are needed to improve breast cancer treatment. Chromothripsis, a catastrophic genome rearrangement, has been described recently in various cancer genomes and affects cancer progression and prognosis. However, little is known about chromothripsis in breast cancer. To identify novel prognostic biomarkers in breast cancer, we used molecular inversion probe (MIP) microarray to explore genome-wide copy number aberrations (CNA) and breast cancer-related gene alterations in DNA extracted from formalin-fixed paraffin-embedded tissue. We examined 42 primary breast cancers with known HR and HER2 status assessed via immunohistochemistry and FISH and analyzed MIP microarray results for correlation with standard tests and survival outcomes. Global genome-wide CNA ranged from 0.2% to 65.7%. Chromothripsis-like patterns were observed in 23/38 (61%) cases and were more prevalent in cases with ≥10% CNA (20/26, 77%) than in cases with <10% CNA (3/12, 25%; p<0.01). Most frequently involved chromosomal segment was 17q12-q21, the HER2 locus. Chromothripsis-like patterns involving 17q12 were observed in 8/19 (42%) of HER2-amplified tumors but not in any of the tumors without HER2 amplification (0/19; p<0.01). HER2 amplification detected by MIP microarray was 95% concordant with conventional testing (39/41). Interestingly, 21% of patients (9/42) had fibroblast growth factor receptor 1 (FGFR1)amplification and had a 460% higher risk for mortality than those without FGFR1 amplification (p<0.01). In summary, MIP microarray provided a robust assessment of genomic CNA of breast cancer.
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MESH Headings
- Adult
- Aged
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Breast Neoplasms, Male/genetics
- Breast Neoplasms, Male/metabolism
- Breast Neoplasms, Male/pathology
- Chromosomes, Human, Pair 17/genetics
- Chromothripsis
- DNA Copy Number Variations
- Female
- Gene Amplification
- Genome-Wide Association Study/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunohistochemistry
- In Situ Hybridization, Fluorescence
- Male
- Microarray Analysis/methods
- Middle Aged
- Molecular Probes/genetics
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Survival Analysis
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Affiliation(s)
- Hui Chen
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajesh R. Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinyan Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lei Huo
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth Aldape
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Ronald Abraham
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumaila Virani
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bal Mukund Mishra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alex Bousamra
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Allegheny Health Network, Pittsburgh, PA, USA
| | - Constance Albarracin
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yun Wu
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sinchita Roy-Chowdhuri
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark J. Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Russell Broaddus
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aysegul Sahin
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Integrated analysis of the genomic instability of PTEN in clinically insignificant and significant prostate cancer. Mod Pathol 2016; 29:143-56. [PMID: 26612463 DOI: 10.1038/modpathol.2015.136] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/08/2022]
Abstract
Patients with clinically insignificant prostate cancer remain a major over-treated population. PTEN loss is one of the most recurrent alterations in prostate cancer associated with an aggressive phenotype, however, the occurrence of PTEN loss in insignificant prostate cancer has not been reported and its role in the separation of insignificant from significant prostate cancer is unclear. An integrated analysis of PTEN loss was, therefore, performed for structural variations, point mutations and protein expression in clinically insignificant (48 cases) and significant (76 cases) prostate cancers treated by radical prostatectomy. Whole-genome mate pair sequencing was performed on tumor cells isolated by laser capture microdissection to characterize PTEN structural alterations. Fluorescence in situ hybridization probes were constructed from the sequencing data to detect the spectrum of these PTEN alterations. PTEN loss by mate pair sequencing and fluorescence in situ hybridization occurred in 2% of insignificant, 13% of large volume Gleason score 6, and 46% of Gleason score 7 and higher cancers. In Gleason score 7 cancers with PTEN loss, PTEN alterations were detected in both Gleason pattern 3 and 4 in 57% of cases by mate pair sequencing, 75% by in situ hybridization and 86% by immunohistochemistry. PTEN loss by sequencing was strongly associated with TMPRSS2-ERG fusion, biochemical recurrence, PTEN loss by in situ hybridization and protein loss by immunohistochemistry. The complex nature of PTEN rearrangements was unveiled by sequencing, detailing the heterogeneous events leading to homozygous loss of PTEN. PTEN point mutation was present in 5% of clinically significant tumors and not in insignificant cancer or high-grade prostatic intraepithelial neoplasia. PTEN loss is infrequent in clinically insignificant prostate cancer, and is associated with higher grade tumors. Detection of PTEN loss in Gleason score 6 cancer in a needle biopsy specimen indicates a higher likelihood of clinically significant prostate cancer.
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