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Corriveau ML, Korb JC, Michener SL, Owen NM, Wilson EL, Kubala J, Turner A, Takacs DS, Potocki L, Swann JW, Xue M, Dai H, Chao HT. De Novo Chromosomes 3q and 5q Chromothripsis Leads to a 5q14.3 Microdeletion Syndrome Presentation: Case Report and Review of the Literature. Am J Med Genet A 2025; 197:e63975. [PMID: 39887826 DOI: 10.1002/ajmg.a.63975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 11/25/2024] [Accepted: 12/13/2024] [Indexed: 02/01/2025]
Abstract
5q14.3 microdeletion syndrome (MIM#613443) is a neurodevelopmental disorder (NDD) involving copy number loss of multiple genes including Myocyte enhancer factor 2C (MEF2C) gene in the q14.3 region of chromosome 5. Chromosomes 5 and 15 chromothripsis involving 5q14.3 was previously reported in one individual with developmental epileptic encephalopathy (DEE). A complex chromothripsis between chromosomes 3, 5, 7, 9, and 18 that involved 5q14.3 was also reported in a pregnancy complicated by brain and kidney anomalies on fetal ultrasound. Here, we report chromothripsis of chromosomes 3q and 5q involving 5q14.3 in a three-year-old female with Lennox-Gastaut syndrome. The chromosomes 3q and 5q chromothripsis was found by trio genome sequencing (GS) and confirmed by fluorescent in situ hybridization (FISH). Notable clinical findings include medically refractory seizures, global developmental delay, increased fluid-attenuated inversion recovery (FLAIR) signal in the left inferior temporal gyrus, and dysmorphic features. Chromothripsis of chromosomes 3 and 5 was previously recognized in renal cell carcinomas. To the best of our knowledge, this is the first reported case of chromosomes 3q and 5q chromothripsis leading to a developmental epileptic encephalopathy (DEE) due to disruption of 5q14.3. These findings expand chromosomes 3 and 5 chromothripsis as a genomic mechanism underlying 5q14.3 microdeletion syndrome.
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Affiliation(s)
- Melina L Corriveau
- The Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- School of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Joshua C Korb
- The Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- School of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Sydney L Michener
- The Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Nichole M Owen
- Baylor Genetics, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | | | - Alicia Turner
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Danielle S Takacs
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics and Neurology Neurophysiology and Epilepsy, Baylor College of Medicine, Houston, Texas, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - John W Swann
- The Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Mingshan Xue
- The Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Hongzheng Dai
- Baylor Genetics, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Hsiao-Tuan Chao
- The Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- McNair Medical Institute, the Robert and Janice McNair Foundation, Houston, Texas, USA
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2
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Mcneil TR, Sikder S, Dalal Y. Cancer cells' chamber of secrets: the link between micronuclei, chromothripsis and malignancy. Open Biol 2025; 15:240388. [PMID: 40359993 DOI: 10.1098/rsob.240388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 02/19/2025] [Accepted: 04/09/2025] [Indexed: 05/15/2025] Open
Abstract
Micronuclei exhibit defective proteomes rendering their chromatin vulnerable to fragmentation. This fragmentation process, known as chromothripsis, promotes tumorigenesis by catalysing the activation of oncogenes and the silencing of tumor suppressors. With this role in mind, micronuclei serve as promising targets for therapeutic intervention. This review will explore recent discoveries regarding how micronuclei form, their function in catalysing chromothripsis and how chromothripsis provides a selective advantage for cancer cells.
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Affiliation(s)
| | - Sweta Sikder
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yamini Dalal
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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3
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Liu SV, Nagasaka M, Atz J, Solca F, Müllauer L. Oncogenic gene fusions in cancer: from biology to therapy. Signal Transduct Target Ther 2025; 10:111. [PMID: 40223139 PMCID: PMC11994825 DOI: 10.1038/s41392-025-02161-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 12/06/2024] [Accepted: 01/16/2025] [Indexed: 04/15/2025] Open
Abstract
Oncogenic gene fusions occur across a broad range of cancers and are a defining feature of some cancer types. Cancers driven by gene fusion products tend to respond well to targeted therapies, where available; thus, detection of potentially targetable oncogenic fusions is necessary to select optimal treatment. Detection methods include non-sequencing methods, such as fluorescence in situ hybridization and immunohistochemistry, and sequencing methods, such as DNA- and RNA-based next-generation sequencing (NGS). While NGS is an efficient way to analyze multiple genes of interest at once, economic and technical factors may preclude its use in routine care globally, despite several guideline recommendations. The aim of this review is to present a summary of oncogenic gene fusions, with a focus on fusions that affect tyrosine kinase signaling, and to highlight the importance of testing for oncogenic fusions. We present an overview of the identification of oncogenic gene fusions and therapies approved for the treatment of cancers harboring gene fusions, and summarize data regarding treating fusion-positive cancers with no current targeted therapies and clinical studies of fusion-positive cancers. Although treatment options may be limited for patients with rare alterations, healthcare professionals should identify patients most likely to benefit from oncogenic gene fusion testing and initiate the appropriate targeted therapy to achieve optimal treatment outcomes.
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Affiliation(s)
- Stephen V Liu
- Division of Hematology and Oncology, Georgetown University, Washington, DC, USA.
| | - Misako Nagasaka
- Division of Hematology Oncology, Department of Medicine, University of California Irvine School of Medicine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, Orange, CA, USA
| | - Judith Atz
- Boehringer Ingelheim International GmbH, Ingelheim am Rhein, Germany
| | - Flavio Solca
- Boehringer Ingelheim RCV GmbH & Co.KG, Vienna, Austria
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
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4
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Ejaz U, Dou Z, Yao PY, Wang Z, Liu X, Yao X. Chromothripsis: an emerging crossroad from aberrant mitosis to therapeutic opportunities. J Mol Cell Biol 2024; 16:mjae016. [PMID: 38710586 PMCID: PMC11487160 DOI: 10.1093/jmcb/mjae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/23/2024] [Accepted: 05/04/2024] [Indexed: 05/08/2024] Open
Abstract
Chromothripsis, a type of complex chromosomal rearrangement originally known as chromoanagenesis, has been a subject of extensive investigation due to its potential role in various diseases, particularly cancer. Chromothripsis involves the rapid acquisition of tens to hundreds of structural rearrangements within a short period, leading to complex alterations in one or a few chromosomes. This phenomenon is triggered by chromosome mis-segregation during mitosis. Errors in accurate chromosome segregation lead to formation of aberrant structural entities such as micronuclei or chromatin bridges. The association between chromothripsis and cancer has attracted significant interest, with potential implications for tumorigenesis and disease prognosis. This review aims to explore the intricate mechanisms and consequences of chromothripsis, with a specific focus on its association with mitotic perturbations. Herein, we discuss a comprehensive analysis of crucial molecular entities and pathways, exploring the intricate roles of the CIP2A-TOPBP1 complex, micronuclei formation, chromatin bridge processing, DNA damage repair, and mitotic checkpoints. Moreover, the review will highlight recent advancements in identifying potential therapeutic targets and the underlying molecular mechanisms associated with chromothripsis, paving the way for future therapeutic interventions in various diseases.
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Affiliation(s)
- Umer Ejaz
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
- Anhui Key Laboratory for Chemical Biology, Hefei National Science Center for Inter-disciplinary Sciences, Hefei 230027, China
| | - Zhen Dou
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
- Anhui Key Laboratory for Chemical Biology, Hefei National Science Center for Inter-disciplinary Sciences, Hefei 230027, China
| | - Phil Y Yao
- University of California San Diego School of Medicine, San Diego, CA 92103, USA
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
- Anhui Key Laboratory for Chemical Biology, Hefei National Science Center for Inter-disciplinary Sciences, Hefei 230027, China
| | - Xing Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
- Anhui Key Laboratory for Chemical Biology, Hefei National Science Center for Inter-disciplinary Sciences, Hefei 230027, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
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Han K, Liu X, Sun G, Wang Z, Shi C, Liu W, Huang M, Liu S, Guo Q. Enhancing subcellular protein localization mapping analysis using Sc2promap utilizing attention mechanisms. Biochim Biophys Acta Gen Subj 2024; 1868:130601. [PMID: 38522679 DOI: 10.1016/j.bbagen.2024.130601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Aberrant protein localization is a prominent feature in many human diseases and can have detrimental effects on the function of specific tissues and organs. High-throughput technologies, which continue to advance with iterations of automated equipment and the development of bioinformatics, enable the acquisition of large-scale data that are more pattern-rich, allowing for the use of a wider range of methods to extract useful patterns and knowledge from them. METHODS The proposed sc2promap (Spatial and Channel for SubCellular Protein Localization Mapping) model, designed to proficiently extract meaningful features from a vast repository of single-channel grayscale protein images for the purposes of protein localization analysis and clustering. Sc2promap incorporates a prediction head component enriched with supplementary protein annotations, along with the integration of a spatial-channel attention mechanism within the encoder to enables the generation of high-resolution protein localization maps that encapsulate the fundamental characteristics of cells, including elemental cellular localizations such as nuclear and non-nuclear domains. RESULTS Qualitative and quantitative comparisons were conducted across internal and external clustering evaluation metrics, as well as various facets of the clustering results. The study also explored different components of the model. The research outcomes conclusively indicate that, in comparison to previous methods, Sc2promap exhibits superior performance. CONCLUSIONS The amalgamation of the attention mechanism and prediction head components has led the model to excel in protein localization clustering and analysis tasks. GENERAL SIGNIFICANCE The model effectively enhances the capability to extract features and knowledge from protein fluorescence images.
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Affiliation(s)
- Kaitai Han
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Xi Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Guocheng Sun
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Zijun Wang
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Chaojing Shi
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Wu Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Mengyuan Huang
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Shitou Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Qianjin Guo
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
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6
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Terrazzan A, Vanini R, Ancona P, Bianchi N, Taccioli C, Aguiari G. State-of-the-art in transposable element modulation affected by drugs in malignant prostatic cancer cells. J Cell Biochem 2024; 125:e30557. [PMID: 38501160 DOI: 10.1002/jcb.30557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Over recent years, the investigation of transposable elements (TEs) has granted researchers a deeper comprehension of their characteristics and functions, particularly regarding their significance in the mechanisms contributing to cancer development. This manuscript focuses on prostate carcinoma cell lines and offers a comprehensive review intended to scrutinize the associations and interactions between TEs and genes, as well as their response to treatment using various chemical drugs, emphasizing their involvement in cancer progression. We assembled a compendium of articles retrieved from the PubMed database to construct networks demonstrating correlations with genes and pharmaceuticals. In doing so, we linked the transposition of certain TE types to the expression of specific transcripts directly implicated in carcinogenesis. Additionally, we underline that treatment employing different drugs revealed unique patterns of TE reactivation. Our hypothesis gathers the current understanding and guides research toward evidence-based investigations, emphasizing the association between antiviral drugs, chemotherapy, and the reduced expression of TEs in patients affected by prostate cancer.
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Affiliation(s)
- Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, Ferrara, Italy
| | - Riccardo Vanini
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Pietro Ancona
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Gianluca Aguiari
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
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Trivedi P, Steele CD, Au FKC, Alexandrov LB, Cleveland DW. Mitotic tethering enables inheritance of shattered micronuclear chromosomes. Nature 2023; 618:1049-1056. [PMID: 37316668 PMCID: PMC10424572 DOI: 10.1038/s41586-023-06216-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
Chromothripsis, the shattering and imperfect reassembly of one (or a few) chromosome(s)1, is an ubiquitous2 mutational process generating localized and complex chromosomal rearrangements that drive genome evolution in cancer. Chromothripsis can be initiated by mis-segregation errors in mitosis3,4 or DNA metabolism5-7 that lead to entrapment of chromosomes within micronuclei and their subsequent fragmentation in the next interphase or following mitotic entry6,8-10. Here we use inducible degrons to demonstrate that chromothriptically produced pieces of a micronucleated chromosome are tethered together in mitosis by a protein complex consisting of mediator of DNA damage checkpoint 1 (MDC1), DNA topoisomerase II-binding protein 1 (TOPBP1) and cellular inhibitor of PP2A (CIP2A), thereby enabling en masse segregation to the same daughter cell. Such tethering is shown to be crucial for the viability of cells undergoing chromosome mis-segregation and shattering after transient inactivation of the spindle assembly checkpoint. Transient, degron-induced reduction in CIP2A following chromosome micronucleation-dependent chromosome shattering is shown to drive acquisition of segmental deletions and inversions. Analyses of pancancer tumour genomes showed that expression of CIP2A and TOPBP1 was increased overall in cancers with genomic rearrangements, including copy number-neutral chromothripsis with minimal deletions, but comparatively reduced in cancers with canonical chromothripsis in which deletions were frequent. Thus, chromatin-bound tethers maintain the proximity of fragments of a shattered chromosome enabling their re-encapsulation into, and religation within, a daughter cell nucleus to form heritable, chromothriptically rearranged chromosomes found in the majority of human cancers.
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Affiliation(s)
- Prasad Trivedi
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Christopher D Steele
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Franco K C Au
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
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Johnson TA, Maekawa S, Fujita M, An J, Ju YS, Maejima K, Kanazashi Y, Jikuya R, Okawa Y, Sasagawa S, Yagi K, Okazaki Y, Kuroda N, Takata R, Obara W, Nakagawa H. Genomic features of renal cell carcinoma developed during end-stage renal disease and dialysis. Hum Mol Genet 2023; 32:290-303. [PMID: 35981075 DOI: 10.1093/hmg/ddac180] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 07/28/2022] [Indexed: 01/18/2023] Open
Abstract
Patients with end-stage renal disease (ESRD) or receiving dialysis have a much higher risk for renal cell carcinoma (RCC), but carcinogenic mechanisms and genomic features remain little explored and undefined. This study's goal was to identify the genomic features of ESRD RCC and characterize them for associations with tumor histology and dialysis exposure. In this study, we obtained 33 RCCs, with various histological subtypes, that developed in ESRD patients receiving dialysis and performed whole-genome sequencing and transcriptome analyses. Driver events, copy-number alteration (CNA) analysis and mutational signature profiling were performed using an analysis pipeline that integrated data from germline and somatic SNVs, Indels and structural variants as well as CNAs, while transcriptome data were analyzed for differentially expressed genes and through gene set enrichment analysis. ESRD related clear cell RCCs' driver genes and mutations mirrored those in sporadic ccRCCs. Longer dialysis periods significantly correlated with a rare mutational signature SBS23, whose etiology is unknown, and increased mitochondrial copy number. All acquired cystic disease (ACD)-RCCs, which developed specifically in ESRD patients, showed chromosome 16q amplification. Gene expression analysis suggests similarity between certain ACD-RCCs and papillary RCCs and in TCGA papillary RCCs with chromosome 16 gain identified enrichment for genes related to DNA repair, as well as pathways related to reactive oxygen species, oxidative phosphorylation and targets of Myc. This analysis suggests that ESRD or dialysis could induce types of cellular stress that impact some specific types of genomic damage leading to oncogenesis.
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Affiliation(s)
- Todd A Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Shigekatsu Maekawa
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Iwate, 028-3694, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Jisong An
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Young-Seok Ju
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yuki Kanazashi
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ryosuke Jikuya
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Urology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yuki Okawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ken Yagi
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yasushi Okazaki
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Naoto Kuroda
- Department of Diagnostic Pathology, Kochi Red Cross Hospital, Kochi 780-8562, Japan
| | - Ryo Takata
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Iwate, 028-3694, Japan
| | - Wataru Obara
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Iwate, 028-3694, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
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Sienkiewicz K, Yang C, Paschal BM, Ratan A. Genomic analyses of the metastasis-derived prostate cancer cell lines LNCaP, VCaP, and PC3-AR. Prostate 2022; 82:442-451. [PMID: 34951700 PMCID: PMC8792310 DOI: 10.1002/pros.24290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND The lymph node metastasis-derived LNCaP, the bone metastasis-derived PC3 (skull), and VCaP (vertebral) cell lines are widely used as preclinical models of human prostate cancer (CaP) and have been described in more than 19,000 publications. Here, we report on short-read whole-genome sequencing and genomic analyses of LNCaP, VCaP, and PC3 cells stably transduced with WT AR (PC3-AR). METHODS LNCaP, VCaP, and PC3-AR cell lines were sequenced to an average depth of more than 30-fold using Illumina short-read sequencing. Using various computational methods, we identified and compared the single-nucleotide variants, copy-number profiles, and the structural variants observed in the three cell lines. RESULTS LNCaP cells are composed of multiple subpopulations, which results in nonintegral copy number states and a high mutational load when the data is analyzed in bulk. All three cell lines contain pathogenic mutations and homozygous deletions in genes involved in DNA mismatch repair, along with deleterious mutations in cell-cycle, Wnt signaling, and other critical cellular processes. PC3-AR cells have a truncating mutation in TP53 and do not express the p53 protein. The VCaP cells contain a homozygous gain-of-function mutation in TP53 (p.R248W) that promotes cancer invasion, metastasis, and progression and has also been observed in prostate adenocarcinomas. In addition, we detect the signatures of chromothripsis of the q arms of chromosome 5 in both PC3-AR and VCaP cells, strengthening the association of TP53 inactivation with chromothripsis reported in other systems. CONCLUSIONS Our work provides a resource for genetic, genomic, and biological studies employing these commonly-used prostate cancer cell lines.
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Affiliation(s)
| | - Chunsong Yang
- Center for Cell Signaling, University of Virginia, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Virginia, USA
| | - Bryce M. Paschal
- Center for Cell Signaling, University of Virginia, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Virginia, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Virginia, USA
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10
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Hoogstrate Y, Komor MA, Böttcher R, van Riet J, van de Werken HJG, van Lieshout S, Hoffmann R, van den Broek E, Bolijn AS, Dits N, Sie D, van der Meer D, Pepers F, Bangma CH, van Leenders GJLH, Smid M, French PJ, Martens JWM, van Workum W, van der Spek PJ, Janssen B, Caldenhoven E, Rausch C, de Jong M, Stubbs AP, Meijer GA, Fijneman RJA, Jenster GW. Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data. Gigascience 2021; 10:giab080. [PMID: 34891161 PMCID: PMC8673554 DOI: 10.1093/gigascience/giab080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/08/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However, non-poly(A)-enriched RNA-seq contains large proportions of intronic reads that also span genomic breakpoints. RESULTS We have developed an algorithm, Dr. Disco, that searches for fusion transcripts by taking an entire reference genome into account as search space. This includes exons but also introns, intergenic regions, and sequences that do not meet splice junction motifs. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)-enriched and ribosomal RNA-minus RNA-seq data. Comparison with whole-genome sequencing data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG-positive tumours were present at RNA level. We also revealed tumours in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and messenger RNA that incorporated intergenic cryptic exons. In breast cancer we identified rearrangement hot spots near CCND1 and in glioma near CDK4 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. CONCLUSION By using the full potential of non-poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects.
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Affiliation(s)
- Youri Hoogstrate
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
- Department of Neurology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - Malgorzata A Komor
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - René Böttcher
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain
| | - Job van Riet
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Harmen J G van de Werken
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
- Cancer Computational Biology Center, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | | | - Evert van den Broek
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen 9713GZ, The Netherlands
| | - Anne S Bolijn
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Natasja Dits
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - Daoud Sie
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | | | | | - Chris H Bangma
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | | | - Marcel Smid
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Pim J French
- Department of Neurology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | - Peter J van der Spek
- Department of Pathology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | | | | | | | - Andrew P Stubbs
- Department of Pathology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Guido W Jenster
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
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11
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Pederzoli F, Bandini M, Marandino L, Ali SM, Madison R, Chung J, Ross JS, Necchi A. Targetable gene fusions and aberrations in genitourinary oncology. Nat Rev Urol 2020; 17:613-625. [PMID: 33046892 DOI: 10.1038/s41585-020-00379-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2020] [Indexed: 12/14/2022]
Abstract
Gene fusions result from either structural chromosomal rearrangement or aberrations caused by splicing or transcriptional readthrough. The precise and distinctive presence of fusion genes in neoplastic tissues and their involvement in multiple pathways central to cancer development, growth and survival make them promising targets for personalized therapy. In genitourinary malignancies, rearrangements involving the E26 transformation-specific family of transcription factors have emerged as very frequent alterations in prostate cancer, especially the TMPRSS2-ERG fusion. In renal malignancies, Xp11 and t(6;11) translocations are hallmarks of a distinct pathological group of tumours described as microphthalmia-associated transcription factor family translocation-associated renal cell carcinomas. Novel druggable fusion events have been recognized in genitourinary malignancies, leading to the activation of several clinical trials. For instance, ALK-rearranged renal cell carcinomas have shown responses to alectinib and crizotinib. Erdafitinib has been tested for the treatment of FGFR-rearranged bladder cancer. Other anti-fibroblast growth factor receptor 3 (FGFR3) compounds are showing promising results in the treatment of bladder cancer, including infigratinib and pemigatinib, and all are currently in clinical trials.
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Affiliation(s)
- Filippo Pederzoli
- Urological Research Institute (URI), Unit of Urology, IRCCS Ospedale San Raffaele, Vita-Salute San Raffaele University, Milan, Italy.
| | - Marco Bandini
- Urological Research Institute (URI), Unit of Urology, IRCCS Ospedale San Raffaele, Vita-Salute San Raffaele University, Milan, Italy
| | - Laura Marandino
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Siraj M Ali
- Foundation Medicine Inc., Cambridge, MA, USA
| | | | - Jon Chung
- Foundation Medicine Inc., Cambridge, MA, USA
| | - Jeffrey S Ross
- Foundation Medicine Inc., Cambridge, MA, USA.,Upstate Medical University, Syracuse, NY, USA
| | - Andrea Necchi
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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12
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Rasche H, Hiltemann S. Galactic Circos: User-friendly Circos plots within the Galaxy platform. Gigascience 2020; 9:giaa065. [PMID: 32530465 PMCID: PMC7291503 DOI: 10.1093/gigascience/giaa065] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/30/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Circos is a popular, highly flexible software package for the circular visualization of complex datasets. While especially popular in the field of genomic analysis, Circos enables interactive graphing of any analytical data, including alternative scientific domain data and non-scientific data. This high degree of flexibility also comes with a high degree of complexity, which may present an obstacle for researchers not trained in programming or the UNIX command line. The Galaxy platform provides a user-friendly browser-based graphical interface incorporating a broad range of "wrapped" command line tools to facilitate accessibility. FINDINGS We have developed a Galaxy wrapper for Circos, thus combining the power of Circos with the accessibility and ease of use of the Galaxy platform. The combination substantially simplifies the specification and configuration of Circos plots for end users while retaining the power to produce publication-quality visualizations of complex multidimensional datasets. CONCLUSIONS Galactic Circos enables the creation of publication-ready Circos plots using only a web browser, via the Galaxy platform. Users may download the full set of Circos configuration files of their plots for further manual customization. This version of Circos is available as an open-source installable application from the Galaxy ToolShed, with its use clarified in a training manual hosted by the Galaxy Training Network.
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Affiliation(s)
- Helena Rasche
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg im Breisgau, Germany
| | - Saskia Hiltemann
- Erasmus Medical Center, Clinical Bioinformatics Group, Department of Pathology, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
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13
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Tuna M, Amos CI, Mills GB. Molecular mechanisms and pathobiology of oncogenic fusion transcripts in epithelial tumors. Oncotarget 2019; 10:2095-2111. [PMID: 31007851 PMCID: PMC6459343 DOI: 10.18632/oncotarget.26777] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Recurrent fusion transcripts, which are one of the characteristic hallmarks of cancer, arise either from chromosomal rearrangements or from transcriptional errors in splicing. DNA rearrangements include intrachromosomal or interchromosomal translocation, tandem duplication, deletion, inversion, or result from chromothripsis, which causes complex rearrangements. In addition, fusion proteins can be created through transcriptional read-through. Fusion genes can be transcribed to fusion transcripts and translated to chimeric proteins, with many having demonstrated transforming activities through multiple mechanisms in cells. Fusion proteins represent novel therapeutic targets and diagnostic biomarkers of diagnosis, disease status, or progression. This review focuses on the mechanisms underlying the formation of oncogenic fusion genes and transcripts and their impact on the pathobiology of epithelial tumors.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I. Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Gordon B. Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR, USA
- Precision Oncology, Knight Cancer Institute, Portland, OR, USA
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14
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15
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Böttcher R, Dulla K, van Strijp D, Dits N, Verhoef EI, Baillie GS, van Leenders GJLH, Houslay MD, Jenster G, Hoffmann R. Human PDE4D isoform composition is deregulated in primary prostate cancer and indicative for disease progression and development of distant metastases. Oncotarget 2018; 7:70669-70684. [PMID: 27683107 PMCID: PMC5342582 DOI: 10.18632/oncotarget.12204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/12/2016] [Indexed: 02/07/2023] Open
Abstract
Phosphodiesterase 4D7 was recently shown to be specifically over-expressed in localized prostate cancer, raising the question as to which regulatory mechanisms are involved and whether other isoforms of this gene family (PDE4D) are affected under the same conditions.We investigated PDE4D isoform composition in prostatic tissues using a total of seven independent expression datasets and also included data on DNA methylation, copy number and AR and ERG binding in PDE4D promoters to gain insight into their effect on PDE4D transcription.We show that expression of PDE4D isoforms is consistently altered in primary human prostate cancer compared to benign tissue, with PDE4D7 being up-regulated while PDE4D5 and PDE4D9 are down-regulated. Disease progression is marked by an overall down-regulation of long PDE4D isoforms, while short isoforms (PDE4D1/2) appear to be relatively unaffected. While these alterations seem to be independent of copy number alterations in the PDE4D locus and driven by AR and ERG binding, we also observed increased DNA methylation in the promoter region of PDE4D5, indicating a long lasting alteration of the isoform composition in prostate cancer tissues.We propose two independent metrics that may serve as diagnostic and prognostic markers for prostate disease: (PDE4D7 - PDE4D5) provides an effective means for distinguishing PCa from normal adjacent prostate, whereas PDE4D1/2 - (PDE4D5 + PDE4D7 + PDE4D9) offers strong prognostic potential to detect aggressive forms of PCa and is associated with metastasis free survival. Overall, our findings highlight the relevance of PDE4D as prostate cancer biomarker and potential drug target.
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Affiliation(s)
- René Böttcher
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Bioinformatics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Kalyan Dulla
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands
| | - Dianne van Strijp
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands
| | - Natasja Dits
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Esther I Verhoef
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - George S Baillie
- Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, Scotland, UK
| | | | - Miles D Houslay
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Guido Jenster
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ralf Hoffmann
- Department of Oncology Solutions and Precision Diagnostics, Philips Research Europe, Eindhoven, The Netherlands.,Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, Scotland, UK
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16
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van Riet J, Krol NMG, Atmodimedjo PN, Brosens E, van IJcken WFJ, Jansen MPHM, Martens JWM, Looijenga LH, Jenster G, Dubbink HJ, Dinjens WNM, van de Werken HJG. SNPitty: An Intuitive Web Application for Interactive B-Allele Frequency and Copy Number Visualization of Next-Generation Sequencing Data. J Mol Diagn 2018; 20:166-176. [PMID: 29305224 DOI: 10.1016/j.jmoldx.2017.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 11/16/2017] [Accepted: 11/27/2017] [Indexed: 01/19/2023] Open
Abstract
Exploration and visualization of next-generation sequencing data are crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions of interest coupled with dynamic heuristic filtering of genetic aberrations is, however, lacking. Therefore, the authors developed the web application SNPitty that allows interactive visualization and interrogation of variant call format files by using B-allele frequencies of single-nucleotide polymorphisms and single-nucleotide variants, coverage metrics, and copy numbers analysis results. SNPitty displays variant alleles and allelic imbalances with a focus on loss of heterozygosity and copy number variation using genome-wide heterozygous markers and somatic mutations. In addition, SNPitty is capable of generating predefined reports that summarize and highlight disease-specific targets of interest. SNPitty was validated for diagnostic interpretation of somatic events by showcasing a serial dilution series of glioma tissue. Additionally, SNPitty is demonstrated in four cancer-related scenarios encountered in daily clinical practice and on whole-exome sequencing data of peripheral blood from a Down syndrome patient. SNPitty allows detection of loss of heterozygosity, chromosomal and gene amplifications, homozygous or heterozygous deletions, somatic mutations, or any combination thereof in regions or genes of interest. Furthermore, SNPitty can be used to distinguish molecular relationships between multiple tumors from a single patient. On the basis of these data, the authors demonstrate that SNPitty is robust and user friendly in a wide range of diagnostic scenarios.
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Affiliation(s)
- Job van Riet
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Niels M G Krol
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | | | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Leendert H Looijenga
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.
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17
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Mani RS, Amin MA, Li X, Kalyana-Sundaram S, Veeneman BA, Wang L, Ghosh A, Aslam A, Ramanand SG, Rabquer BJ, Kimura W, Tran M, Cao X, Roychowdhury S, Dhanasekaran SM, Palanisamy N, Sadek HA, Kapur P, Koch AE, Chinnaiyan AM. Inflammation-Induced Oxidative Stress Mediates Gene Fusion Formation in Prostate Cancer. Cell Rep 2017; 17:2620-2631. [PMID: 27926866 DOI: 10.1016/j.celrep.2016.11.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/09/2016] [Accepted: 11/02/2016] [Indexed: 12/25/2022] Open
Abstract
Approximately 50% of prostate cancers are associated with gene fusions of the androgen-regulated gene TMPRSS2 to the oncogenic erythroblast transformation-specific (ETS) transcription factor ERG. The three-dimensional proximity of TMPRSS2 and ERG genes, in combination with DNA breaks, facilitates the formation of TMPRSS2-ERG gene fusions. However, the origins of DNA breaks that underlie gene fusion formation in prostate cancers are far from clear. We demonstrate a role for inflammation-induced oxidative stress in the formation of DNA breaks leading to recurrent TMPRSS2-ERG gene fusions. The transcriptional status and epigenetic features of the target genes influence this effect. Importantly, inflammation-induced de novo genomic rearrangements are blocked by homologous recombination (HR) and promoted by non-homologous end-joining (NHEJ) pathways. In conjunction with the association of proliferative inflammatory atrophy (PIA) with human prostate cancer, our results support a working model in which recurrent genomic rearrangements induced by inflammatory stimuli lead to the development of prostate cancer.
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Affiliation(s)
- Ram S Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75235, USA; Department of Urology, UT Southwestern Medical Center, Dallas, TX 75235, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75235, USA.
| | - Mohammad A Amin
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Xiangyi Li
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Shanker Kalyana-Sundaram
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brendan A Veeneman
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lei Wang
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Aparna Ghosh
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Adam Aslam
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Susmita G Ramanand
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Bradley J Rabquer
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Wataru Kimura
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75235, USA; Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki 305-8577, Japan
| | - Maxwell Tran
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sameek Roychowdhury
- Department of Internal Medicine, The James Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Hesham A Sadek
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Payal Kapur
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75235, USA; Department of Urology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Alisa E Koch
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; VA Ann Arbor, Ann Arbor, MI 48105, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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18
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Hovelson DH, Liu CJ, Wang Y, Kang Q, Henderson J, Gursky A, Brockman S, Ramnath N, Krauss JC, Talpaz M, Kandarpa M, Chugh R, Tuck M, Herman K, Grasso CS, Quist MJ, Feng FY, Haakenson C, Langmore J, Kamberov E, Tesmer T, Husain H, Lonigro RJ, Robinson D, Smith DC, Alva AS, Hussain MH, Chinnaiyan AM, Tewari M, Mills RE, Morgan TM, Tomlins SA. Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy. Oncotarget 2017; 8:89848-89866. [PMID: 29163793 PMCID: PMC5685714 DOI: 10.18632/oncotarget.21163] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/08/2017] [Indexed: 12/11/2022] Open
Abstract
Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~0.01x) tumor content determination through genome-wide copy number alteration (CNA) profiling. We applied PRINCe to a retrospective cohort of 124 cfDNA samples from 100 patients with advanced cancers, including 76 men with metastatic castration-resistant prostate cancer (mCRPC), enabling cfDNA tumor content approximation and actionable focal CNA detection, while facilitating concordance analyses between cfDNA and tissue-based NGS profiles and assessment of cfDNA alteration associations with mCRPC treatment outcomes. Therapeutically relevant focal CNAs were present in 42 (34%) cfDNA samples, including 36 of 93 (39%) mCRPC patient samples harboring AR amplification. PRINCe identified pre-treatment cfDNA CNA profiles facilitating disease monitoring. Combining PRINCe with routine targeted NGS of cfDNA enabled mutation and CNA assessment with coverages tuned to cfDNA tumor content. In mCRPC, genome-wide PRINCe cfDNA and matched tissue CNA profiles showed high concordance (median Pearson correlation = 0.87), and PRINCe detectable AR amplifications predicted reduced time on therapy, independent of therapy type (Kaplan-Meier log-rank test, chi-square = 24.9, p < 0.0001). Our screening approach enables robust, broadly applicable cfDNA-based precision oncology for patients with advanced cancer through scalable identification of therapeutically relevant CNAs and pre-/post-treatment genomic profiles, enabling cfDNA- or tissue-based precision oncology workflow optimization.
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Affiliation(s)
- Daniel H. Hovelson
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yugang Wang
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Qing Kang
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
| | - James Henderson
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Amy Gursky
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Scott Brockman
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nithya Ramnath
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
| | - John C. Krauss
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
| | - Moshe Talpaz
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
| | - Malathi Kandarpa
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rashmi Chugh
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
| | - Missy Tuck
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kirk Herman
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
| | - Catherine S. Grasso
- Division of Hematology-Oncology, University of California, Los Angeles and the Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
- The Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Michael J. Quist
- Division of Hematology-Oncology, University of California, Los Angeles and the Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
- The Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Felix Y. Feng
- Departments of Radiation Oncology, Urology, and Medicine, University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Hatim Husain
- Medical Oncology, University of California, San Diego Moore's Cancer Center, San Diego, CA, USA
| | - Robert J. Lonigro
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David C. Smith
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ajjai S. Alva
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Maha H. Hussain
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Present address: Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Hematology-Oncology, University of California, Los Angeles and the Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Muneesh Tewari
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biointerfaces Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ryan E. Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Todd M. Morgan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Scott A. Tomlins
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
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19
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Hoogstrate Y, Zhang C, Senf A, Bijlard J, Hiltemann S, van Enckevort D, Repo S, Heringa J, Jenster G, J A Fijneman R, Boiten JW, A Meijer G, Stubbs A, Rambla J, Spalding D, Abeln S. Integration of EGA secure data access into Galaxy. F1000Res 2017; 5. [PMID: 28232859 PMCID: PMC5302147 DOI: 10.12688/f1000research.10221.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/30/2016] [Indexed: 12/31/2022] Open
Abstract
High-throughput molecular profiling techniques are routinely generating vast amounts of data for translational medicine studies. Secure access controlled systems are needed to manage, store, transfer and distribute these data due to its personally identifiable nature. The European Genome-phenome Archive (EGA) was created to facilitate access and management to long-term archival of bio-molecular data. Each data provider is responsible for ensuring a Data Access Committee is in place to grant access to data stored in the EGA. Moreover, the transfer of data during upload and download is encrypted. ELIXIR, a European research infrastructure for life-science data, initiated a project (2016 Human Data Implementation Study) to understand and document the ELIXIR requirements for secure management of controlled-access data. As part of this project, a full ecosystem was designed to connect archived raw experimental molecular profiling data with interpreted data and the computational workflows, using the CTMM Translational Research IT (CTMM-TraIT) infrastructure
http://www.ctmm-trait.nl as an example. Here we present the first outcomes of this project, a framework to enable the download of EGA data to a Galaxy server in a secure way. Galaxy provides an intuitive user interface for molecular biologists and bioinformaticians to run and design data analysis workflows. More specifically, we developed a tool -- ega_download_streamer - that can download data securely from EGA into a Galaxy server, which can subsequently be further processed. This tool will allow a user within the browser to run an entire analysis containing sensitive data from EGA, and to make this analysis available for other researchers in a reproducible manner, as shown with a proof of concept study. The tool ega_download_streamer is available in the Galaxy tool shed:
https://toolshed.g2.bx.psu.edu/view/yhoogstrate/ega_download_streamer.
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Affiliation(s)
- Youri Hoogstrate
- Department of Bioinformatics, ErasmusMC Rotterdam, Rotterdam, Netherlands
| | - Chao Zhang
- Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands
| | - Alexander Senf
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Saskia Hiltemann
- Department of Bioinformatics, ErasmusMC Rotterdam, Rotterdam, Netherlands
| | | | | | - Jaap Heringa
- Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands
| | - Guido Jenster
- Department of Urology, ErasmusMC Rotterdam, Rotterdam, Netherlands
| | | | | | - Gerrit A Meijer
- Diagnostic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Andrew Stubbs
- Department of Bioinformatics, ErasmusMC Rotterdam, Rotterdam, Netherlands
| | - Jordi Rambla
- Centre for Genomic Regulation, Parc de Recerca Biomédica de Barcelona, Barcelona, Spain
| | - Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sanne Abeln
- Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands
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20
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Leibowitz ML, Zhang CZ, Pellman D. Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annu Rev Genet 2015; 49:183-211. [DOI: 10.1146/annurev-genet-120213-092228] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mitchell L. Leibowitz
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
| | - Cheng-Zhong Zhang
- Department of Pediatric Oncology,
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| | - David Pellman
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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21
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de Pagter MS, Kloosterman WP. The Diverse Effects of Complex Chromosome Rearrangements and Chromothripsis in Cancer Development. Recent Results Cancer Res 2015; 200:165-193. [PMID: 26376877 DOI: 10.1007/978-3-319-20291-4_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In recent years, enormous progress has been made with respect to the identification of somatic mutations that contribute to cancer development. Mutation types range from small substitutions to large structural genomic rearrangements, including complex reshuffling of the genome. Sets of mutations in individual cancer genomes may show specific signatures, which can be provoked by both exogenous and endogenous forces. One of the most remarkable mutation patterns observed in human cancers involve massive rearrangement of just a few chromosomal regions. This phenomenon has been termed chromothripsis and appears widespread in a multitude of cancer types. Chromothripsis provides a way for cancer to rapidly evolve through a one-off massive change in genome structure as opposed to a gradual process of mutation and selection. This chapter focuses on the origin, prevalence and impact of chromothripsis and related complex genomic rearrangements during cancer development.
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Affiliation(s)
- Mirjam S de Pagter
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands.
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22
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Pellestor F, Gatinois V, Puechberty J, Geneviève D, Lefort G. Chromothripsis: potential origin in gametogenesis and preimplantation cell divisions. A review. Fertil Steril 2014; 102:1785-96. [PMID: 25439810 DOI: 10.1016/j.fertnstert.2014.09.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/04/2014] [Accepted: 09/04/2014] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To review the discovery of chromothripsis and analyze its impact on human reproduction. DESIGN Database and literature analysis. SETTING University hospital. PATIENT(S) Carriers of massive and complex chromosomal rearrangements. INTERVENTION(S) Cytogenetic analysis and molecular testing (fluorescence in situ hybridization, microarray, whole-genome sequencing). MAIN OUTCOME MEASURE(S) Chromothripsis occurrence in human gametes and preimplantation embryos, with regard to the potential causative mechanisms described in literature. RESULT(S) Databases were searched for the literature published up to March 2014. Chromothripsis is characterized by the shattering of one (or a few) chromosome segments followed by a haphazard reassembly of the fragments generated, arising through a single initial catastrophic event. Several mechanisms involving abortive apoptosis, telomere erosion, mitotic errors, micronuclei formation, and p53 inactivation might cause chromothripsis. The remarkable point is that all these plausible mechanisms have been identified in the field of human reproduction as causal factors for reproductive failures and the genesis of chromosomal abnormalities. Specific features of gametogenesis and early embryonic development such as the weakness of cell cycle and mitosis checkpoints and the rapid kinetics of division in germ cells and early cleavage embryos may contribute to the emergence of chromothripsis. CONCLUSION(S) The discovery of this new class of massive chromosomal rearrangement has deeply modified our understanding on the genesis of complex genomic rearrangements. Data presented in this review support the assumption that chromothripsis could operate in human germlines and during early embryonic development. Chromothripsis might arise more frequently than previously thought in both gametogenesis and early human embryogenesis.
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Affiliation(s)
- Franck Pellestor
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France; INSERM Unit Plasticity of the Genome and Aging, Institute of Functional Genomics, Montpellier, France.
| | - Vincent Gatinois
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France; INSERM Unit Plasticity of the Genome and Aging, Institute of Functional Genomics, Montpellier, France
| | - Jacques Puechberty
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France
| | - David Geneviève
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France
| | - Geneviève Lefort
- Laboratory of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, Montpellier, France
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23
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Kloosterman WP, Koster J, Molenaar JJ. Prevalence and clinical implications of chromothripsis in cancer genomes. Curr Opin Oncol 2014; 26:64-72. [PMID: 24305569 DOI: 10.1097/cco.0000000000000038] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW A variety of mutational mechanisms shape the landscape of somatic mutations in cancer genomes. Although the contribution of single nucleotide mutations is well studied, getting a hold of structural genomic rearrangements is more difficult due to their complexity and diversity in sizes and classes. Here, we discuss the incidence of complex genomic rearrangements and their impact on cancer development and progression. RECENT FINDINGS Catastrophic genome rearrangements have recently been described in various cancer genomes. Such complex genomic rearrangements may be a result of local shattering of chromosomes followed by reassembly of DNA fragments, a process termed chromothripsis. In addition, DNA replication errors may lead to complex genomic rearrangements in cancer. Complex reshuffling of chromosomes can cause formation of gene fusions, disruption of tumor suppressors, and amplification of oncogenes. Furthermore, the occurrence of chromothripsis has been associated with poor prognosis in neuroblastoma, melanoma, and multiple myeloma. SUMMARY Complex genomic rearrangements, such as chromothripsis, may affect cancer gene function and thereby have a major impact on cancer progression, prognosis, and therapy response.
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Affiliation(s)
- Wigard P Kloosterman
- aDepartment of Medical Genetics, University Medical Center Utrecht, Utrecht bDepartment of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
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24
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Long Noncoding RNA in Prostate, Bladder, and Kidney Cancer. Eur Urol 2014; 65:1140-51. [DOI: 10.1016/j.eururo.2013.12.003] [Citation(s) in RCA: 493] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/04/2013] [Indexed: 02/07/2023]
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25
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Pellestor F, Gatinois V, Puechberty J, Geneviève D, Lefort G. [Chromothripsis, an unexpected novel form of complexity for chromosomal rearrangements]. Med Sci (Paris) 2014; 30:266-73. [PMID: 24685217 DOI: 10.1051/medsci/20143003014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The recent discovery of a new kind of massive chromosomal rearrangement in different cancers, named "chromothripsis" (chromo for chromosome, thripsis for shattering) has questioned the established models for a progressive development of tumors. Indeed, this phenomenon, which is characterized by the shattering of one (or a few) chromosome segments followed by a random reassembly of the fragments generated, occurs during one unique cellular event. The same phenomenon was identified in constitutional genetics in patients with various developmental pathologies, indicating that chromothripsis also occurs at the germ cell level. Diverse situations can cause chromothripsis (radiations, telomere erosion, abortive apoptosis, etc.), and two express "repair routes" are used by the cell to chaotically reorganise the chromosomal regions concerned: non-homologous end-joining and repair by replicative stress. The in-depth analysis of the DNA sequences involved in the regions of chromothripsis leads to a better understanding of the molecular basis of chromothripsis and also helps to better apprehend its unexpected role in the development of constitutional pathologies and the progression of cancers.
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Affiliation(s)
- Franck Pellestor
- Laboratoire de génétique chromosomique, hôpital Arnaud de Villeneuve, CHRU de Montpellier, 371, avenue du doyen Gaston Giraud, 34295 Montpellier, France
| | - Vincent Gatinois
- Laboratoire de génétique chromosomique, hôpital Arnaud de Villeneuve, CHRU de Montpellier, 371, avenue du doyen Gaston Giraud, 34295 Montpellier, France
| | - Jacques Puechberty
- Laboratoire de génétique chromosomique, hôpital Arnaud de Villeneuve, CHRU de Montpellier, 371, avenue du doyen Gaston Giraud, 34295 Montpellier, France
| | - David Geneviève
- Laboratoire de génétique chromosomique, hôpital Arnaud de Villeneuve, CHRU de Montpellier, 371, avenue du doyen Gaston Giraud, 34295 Montpellier, France
| | - Geneviève Lefort
- Laboratoire de génétique chromosomique, hôpital Arnaud de Villeneuve, CHRU de Montpellier, 371, avenue du doyen Gaston Giraud, 34295 Montpellier, France
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26
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Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer. Proc Natl Acad Sci U S A 2014; 111:E672-81. [PMID: 24469795 DOI: 10.1073/pnas.1313580111] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using complete genome analysis, we sequenced five bladder tumors accrued from patients with muscle-invasive transitional cell carcinoma of the urinary bladder (TCC-UB) and identified a spectrum of genomic aberrations. In three tumors, complex genotype changes were noted. All three had tumor protein p53 mutations and a relatively large number of single-nucleotide variants (SNVs; average of 11.2 per megabase), structural variants (SVs; average of 46), or both. This group was best characterized by chromothripsis and the presence of subclonal populations of neoplastic cells or intratumoral mutational heterogeneity. Here, we provide evidence that the process of chromothripsis in TCC-UB is mediated by nonhomologous end-joining using kilobase, rather than megabase, fragments of DNA, which we refer to as "stitchers," to repair this process. We postulate that a potential unifying theme among tumors with the more complex genotype group is a defective replication-licensing complex. A second group (two bladder tumors) had no chromothripsis, and a simpler genotype, WT tumor protein p53, had relatively few SNVs (average of 5.9 per megabase) and only a single SV. There was no evidence of a subclonal population of neoplastic cells. In this group, we used a preclinical model of bladder carcinoma cell lines to study a unique SV (translocation and amplification) of the gene glutamate receptor ionotropic N-methyl D-aspertate as a potential new therapeutic target in bladder cancer.
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27
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Zhang CZ, Leibowitz ML, Pellman D. Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements. Genes Dev 2013; 27:2513-30. [PMID: 24298051 PMCID: PMC3861665 DOI: 10.1101/gad.229559.113] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent genome sequencing studies have identified several classes of complex genomic rearrangements that appear to be derived from a single catastrophic event. These discoveries identify ways that genomes can be altered in single large jumps rather than by many incremental steps. Here we compare and contrast these phenomena and examine the evidence that they arise "all at once." We consider the impact of massive chromosomal change for the development of diseases such as cancer and for evolution more generally. Finally, we summarize current models for underlying mechanisms and discuss strategies for testing these models.
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Affiliation(s)
- Cheng-Zhong Zhang
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Mitchell L. Leibowitz
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Pellman
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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