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Hu Q, Espejo Valle-Inclán J, Dahiya R, Guyer A, Mazzagatti A, Maurais EG, Engel JL, Lu H, Davis AJ, Cortés-Ciriano I, Ly P. Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors. Nat Commun 2024; 15:5611. [PMID: 38965240 PMCID: PMC11224358 DOI: 10.1038/s41467-024-49985-5] [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: 08/02/2023] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Mitotic errors generate micronuclei entrapping mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates diverse genomic rearrangements associated with human diseases. How specific repair pathways recognize and process these lesions remains poorly understood. Here we use CRISPR/Cas9 to systematically inactivate distinct DSB repair pathways and interrogate the rearrangement landscape of fragmented chromosomes. Deletion of canonical non-homologous end joining (NHEJ) components substantially reduces complex rearrangements and shifts the rearrangement landscape toward simple alterations without the characteristic patterns of chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within sub-nuclear micronuclei bodies (MN bodies) and undergo ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments are rarely engaged by alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics, persistent 53BP1-labeled MN bodies, and cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements from mitotic errors.
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Affiliation(s)
- Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alison Guyer
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth G Maurais
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Justin L Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huiming Lu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anthony J Davis
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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2
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Hu Q, Valle-Inclan JE, Dahiya R, Guyer A, Mazzagatti A, Maurais EG, Engel JL, Cortés-Ciriano I, Ly P. Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552800. [PMID: 37609143 PMCID: PMC10441393 DOI: 10.1101/2023.08.10.552800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Errors in mitosis can generate micronuclei that entrap mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through a process termed chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates a spectrum of simple and complex genomic rearrangements that are associated with human cancers and disorders. How specific DSB repair pathways recognize and process these lesions remains poorly understood. Here we used CRISPR/Cas9 to systematically inactivate distinct DSB processing or repair pathways and interrogated the rearrangement landscape of fragmented chromosomes from micronuclei. Deletion of canonical non-homologous end joining (NHEJ) components, including DNA-PKcs, LIG4, and XLF, substantially reduced the formation of complex rearrangements and shifted the rearrangement landscape toward simple alterations without the characteristic patterns of cancer-associated chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within micronuclei bodies (MN bodies) and undergo successful ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments were rarely engaged by polymerase theta-mediated alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics and persistent 53BP1-labeled MN bodies in the interphase nucleus. Prolonged DNA damage signaling from unrepaired fragments ultimately triggered cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements following chromothripsis from mitotic errors.
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Affiliation(s)
- Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Jose Espejo Valle-Inclan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Alison Guyer
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Present address: Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Elizabeth G. Maurais
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Justin L. Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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3
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PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas. Sci Rep 2022; 12:14083. [PMID: 35982066 PMCID: PMC9388569 DOI: 10.1038/s41598-022-14977-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Oligodendrogliomas are typically associated with the most favorable prognosis among diffuse gliomas. However, many of the tumors progress, eventually leading to patient death. To characterize the changes associated with oligodendroglioma recurrence and progression, we analyzed two recurrent oligodendroglioma tumors upon diagnosis and after tumor relapse based on whole-genome and RNA sequencing. Relapsed tumors were diagnosed as glioblastomas with an oligodendroglioma component before the World Health Organization classification update in 2016. Both patients died within 12 months after relapse. One patient carried an inactivating POLE mutation leading to a clearly hypermutated progressed tumor. Strikingly, both relapsed tumors carried focal chromosomal rearrangements in PTPRD and CNTNAP2 genes with associated decreased gene expression. TP53 mutation was also detected in both patients after tumor relapse. In The Cancer Genome Atlas (TCGA) diffuse glioma cohort, PTPRD and CNTNAP2 expression decreased by tumor grade in oligodendrogliomas and PTPRD expression also in IDH-mutant astrocytomas. Low expression of the genes was associated with poor overall survival. Our analysis provides information about aggressive oligodendrogliomas with worse prognosis and suggests that PTPRD and CNTNAP2 expression could represent an informative marker for their stratification.
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4
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Rokita JL, Rathi KS, Cardenas MF, Upton KA, Jayaseelan J, Cross KL, Pfeil J, Egolf LE, Way GP, Farrel A, Kendsersky NM, Patel K, Gaonkar KS, Modi A, Berko ER, Lopez G, Vaksman Z, Mayoh C, Nance J, McCoy K, Haber M, Evans K, McCalmont H, Bendak K, Böhm JW, Marshall GM, Tyrrell V, Kalletla K, Braun FK, Qi L, Du Y, Zhang H, Lindsay HB, Zhao S, Shu J, Baxter P, Morton C, Kurmashev D, Zheng S, Chen Y, Bowen J, Bryan AC, Leraas KM, Coppens SE, Doddapaneni H, Momin Z, Zhang W, Sacks GI, Hart LS, Krytska K, Mosse YP, Gatto GJ, Sanchez Y, Greene CS, Diskin SJ, Vaske OM, Haussler D, Gastier-Foster JM, Kolb EA, Gorlick R, Li XN, Reynolds CP, Kurmasheva RT, Houghton PJ, Smith MA, Lock RB, Raman P, Wheeler DA, Maris JM. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Rep 2019; 29:1675-1689.e9. [PMID: 31693904 PMCID: PMC6880934 DOI: 10.1016/j.celrep.2019.09.071] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/10/2019] [Accepted: 09/24/2019] [Indexed: 02/08/2023] Open
Abstract
Accelerating cures for children with cancer remains an immediate challenge as a result of extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs)-many of which are refractory to current standard-of-care treatments-from high-risk childhood cancers. Here, we genomically characterize 261 PDX models from 37 unique pediatric cancers; demonstrate faithful recapitulation of histologies and subtypes; and refine our understanding of relapsed disease. In addition, we use expression signatures to classify tumors for TP53 and NF1 pathway inactivation. We anticipate that these data will serve as a resource for pediatric oncology drug development and will guide rational clinical trial design for children with cancer.
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Affiliation(s)
- Jo Lynne Rokita
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Komal S Rathi
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Maria F Cardenas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristen A Upton
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Joy Jayaseelan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Jacob Pfeil
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Laura E Egolf
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory P Way
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alvin Farrel
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan M Kendsersky
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khushbu Patel
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Krutika S Gaonkar
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Apexa Modi
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Esther R Berko
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Gonzalo Lopez
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zalman Vaksman
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chelsea Mayoh
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Jonas Nance
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX 79430, USA
| | - Kristyn McCoy
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX 79430, USA
| | - Michelle Haber
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kathryn Evans
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Hannah McCalmont
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Katerina Bendak
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Julia W Böhm
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia; Sydney Children's Hospital, Sydney, NSW, Australia
| | | | - Karthik Kalletla
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Frank K Braun
- Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lin Qi
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yunchen Du
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huiyuan Zhang
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Holly B Lindsay
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sibo Zhao
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jack Shu
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Patricia Baxter
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Morton
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dias Kurmashev
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Jay Bowen
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Anthony C Bryan
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Kristen M Leraas
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Sara E Coppens
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | | | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wendong Zhang
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gregory I Sacks
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Lori S Hart
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Kateryna Krytska
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Yael P Mosse
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Gregory J Gatto
- Department of Global Health Technologies, RTI International, Research Triangle Park, NC 27709, USA
| | - Yolanda Sanchez
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - Casey S Greene
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA 19102, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sharon J Diskin
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Julie M Gastier-Foster
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; The Ohio State University College of Medicine, Departments of Pathology and Pediatrics, Columbus, OH 43210, USA
| | - E Anders Kolb
- Department of Pediatrics, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA; Nemours Center for Cancer and Blood Disorders, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Richard Gorlick
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiao-Nan Li
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Division of Hematology, Oncology, Neuro-oncology and Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - C Patrick Reynolds
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX 79430, USA
| | - Raushan T Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | | | | | - Pichai Raman
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA.
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5
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Schimmel J, van Schendel R, den Dunnen JT, Tijsterman M. Templated Insertions: A Smoking Gun for Polymerase Theta-Mediated End Joining. Trends Genet 2019; 35:632-644. [PMID: 31296341 DOI: 10.1016/j.tig.2019.06.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/23/2023]
Abstract
A recognized source of disease-causing genome alterations is erroneous repair of broken chromosomes, which can be executed by two distinct mechanisms: non-homologous end joining (NHEJ) and the recently discovered polymerase theta-mediated end joining (TMEJ) pathway. While TMEJ has previously been considered to act as an alternative mechanism backing up NHEJ, recent work points to a role for TMEJ in the repair of replication-associated DNA breaks that are excluded from repair through homologous recombination. Because of its mode of action, TMEJ is intrinsically mutagenic and sometimes leaves behind a recognizable genomic scar when joining chromosome break ends (i.e., 'templated insertions'). This review article focuses on the intriguing observation that this polymerase theta signature is frequently observed in disease alleles, arguing for a prominent role of this double-strand break repair pathway in genome diversification and disease-causing spontaneous mutagenesis in humans.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
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6
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Tessarin GWL, Michalec OM, Torres-da-Silva KR, Da Silva AV, Cruz-Rizzolo RJ, Gonçalves A, Gasparini DC, Horta-Júnior JAC, Ervolino E, Bittencourt JC, Lovejoy DA, Casatti CA. A Putative Role of Teneurin-2 and Its Related Proteins in Astrocytes. Front Neurosci 2019; 13:655. [PMID: 31316338 PMCID: PMC6609321 DOI: 10.3389/fnins.2019.00655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Teneurins are type II transmembrane proteins comprised of four phylogenetically conserved homologs (Ten-1-4) that are highly expressed during neurogenesis. An additional bioactive peptide named teneurin C-terminal-associated peptide (TCAP-1-4) is present at the carboxyl terminal of teneurins. The possible correlation between the Ten/TCAP system and brain injuries has not been explored yet. Thus, this study examined the expression of these proteins in the cerebral cortex after mechanical brain injury. Adult rats were subjected to cerebral cortex injury by needle-insertion lesion and sacrificed at various time points. This was followed by analysis of the lesion area by immunohistochemistry and conventional RT-PCR techniques. Control animals (no brain injury) showed only discrete Ten-2-like immunoreactive pyramidal neurons in the cerebral cortex. In contrast, Ten-2 immunoreactivity was significantly up-regulated in the reactive astrocytes in all brain-injured groups (p < 0.0001) when compared to the control group. Interestingly, reactive astrocytes also showed intense immunoreactivity to LPHN-1, an endogenous receptor for the Ten-2 splice variant named Lasso. Semi-quantitative analysis of Ten-2 and TCAP-2 expression revealed significant increases of both at 48 h, 3 days and 5 days (p < 0.0001) after brain injury compared to the remaining groups. Immortalized cerebellar astrocytes were also evaluated for Ten/TCAP expression and intracellular calcium signaling by fluorescence microscopy after TCAP-1 treatment. Immortalized astrocytes expressed additional Ten/TCAP homologs and exhibited significant increases in intracellular calcium concentrations after TCAP-1 treatment. This study is the first to demonstrate that Ten-2/TCAP-2 and LPHN-1 are upregulated in reactive astrocytes after a mechanical brain injury. Immortalized cerebellar astrocytes expressed Ten/TCAP homologs and TCAP-1 treatment stimulated intracellular calcium signaling. These findings disclose a new functional role of the Ten/TCAP system in astrocytes during tissue repair of the CNS.
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Affiliation(s)
- Gestter W L Tessarin
- Department of Basic Sciences, School of Dentistry of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil.,Department of Anatomy, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Ola M Michalec
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Kelly R Torres-da-Silva
- Department of Basic Sciences, School of Dentistry of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil.,Department of Anatomy, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - André V Da Silva
- Department of Anatomy, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil.,School of Medicine, Federal University of Mato Grosso do Sul (UFMS), Três Lagoas, Brazil
| | - Roelf J Cruz-Rizzolo
- Department of Basic Sciences, School of Dentistry of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Alaide Gonçalves
- Department of Basic Sciences, School of Dentistry of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Daniele C Gasparini
- Department of Basic Sciences, School of Dentistry of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil
| | - José A C Horta-Júnior
- Department of Anatomy, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Edilson Ervolino
- Department of Basic Sciences, School of Dentistry of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Jackson C Bittencourt
- Department of Anatomy, Institute of Biomedical Sciences, São Paulo University (USP), São Paulo, Brazil
| | - David A Lovejoy
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Cláudio A Casatti
- Department of Basic Sciences, School of Dentistry of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil.,Department of Anatomy, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
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7
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Hynst J, Plevova K, Radova L, Bystry V, Pal K, Pospisilova S. Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants. PeerJ 2019; 7:e7071. [PMID: 31223530 PMCID: PMC6571010 DOI: 10.7717/peerj.7071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 05/06/2019] [Indexed: 11/21/2022] Open
Abstract
Background Extensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical course. The functional impact of cSVs can be studied at the RNA level using whole transcriptome sequencing (total RNA-Seq). It represents a powerful tool for discovering, profiling, and quantifying changes of gene expression in the overall genomic context. However, bioinformatic analysis of transcriptomic data, especially in cases with cSVs, is a complex and challenging task, and the development of proper bioinformatic tools for transcriptome studies is necessary. Methods We designed a bioinformatic workflow for the analysis of total RNA-Seq data consisting of two separate parts (pipelines): The first pipeline incorporates a statistical solution for differential gene expression analysis in a biologically heterogeneous sample set. We utilized results from transcriptomic arrays which were carried out in parallel to increase the precision of the analysis. The second pipeline is used for the identification of de novo fusion genes. Special attention was given to the filtering of false positives (FPs), which was achieved through consensus fusion calling with several fusion gene callers. We applied the workflow to the data obtained from ten patients with chronic lymphocytic leukemia (CLL) to describe the consequences of their cSVs in detail. The fusion genes identified by our pipeline were correlated with genomic break-points detected by genomic arrays. Results We set up a novel solution for differential gene expression analysis of individual samples and de novo fusion gene detection from total RNA-Seq data. The results of the differential gene expression analysis were concordant with results obtained by transcriptomic arrays, which demonstrates the analytical capabilities of our method. We also showed that the consensus fusion gene detection approach was able to identify true positives (TPs) efficiently. Detected coordinates of fusion gene junctions were in concordance with genomic breakpoints assessed using genomic arrays. Discussion Byapplying our methods to real clinical samples, we proved that our approach for total RNA-Seq data analysis generates results consistent with other genomic analytical techniques. The data obtained by our analyses provided clues for the study of the biological consequences of cSVs with far-reaching implications for clinical outcome and management of cancer patients. The bioinformatic workflow is also widely applicable for addressing other research questions in different contexts, for which transcriptomic data are generated.
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Affiliation(s)
- Jakub Hynst
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vojtech Bystry
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
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8
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Trigg RM, Shaw JA, Turner SD. Opportunities and challenges of circulating biomarkers in neuroblastoma. Open Biol 2019; 9:190056. [PMID: 31088252 PMCID: PMC6544987 DOI: 10.1098/rsob.190056] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Molecular analysis of nucleic acid and protein biomarkers is becoming increasingly common in paediatric oncology for diagnosis, risk stratification and molecularly targeted therapeutics. However, many current and emerging biomarkers are based on analysis of tumour tissue, which is obtained through invasive surgical procedures and in some cases may not be accessible. Over the past decade, there has been growing interest in the utility of circulating biomarkers such as cell-free nucleic acids, circulating tumour cells and extracellular vesicles as a so-called liquid biopsy of cancer. Here, we review the potential of emerging circulating biomarkers in the management of neuroblastoma and highlight challenges to their implementation in the clinic.
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Affiliation(s)
- Ricky M. Trigg
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Jacqui A. Shaw
- Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, Leicester LE2 7LX, UK
| | - Suzanne D. Turner
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB2 0QQ, UK
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9
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Rebolledo-Jaramillo B, Ziegler A. Teneurins: An Integrative Molecular, Functional, and Biomedical Overview of Their Role in Cancer. Front Neurosci 2018; 12:937. [PMID: 30618566 PMCID: PMC6297388 DOI: 10.3389/fnins.2018.00937] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/28/2018] [Indexed: 12/16/2022] Open
Abstract
Teneurins are large transmembrane proteins originally identified in Drosophila. Their essential role in development of the central nervous system is conserved throughout species, and evidence supports their involvement in organogenesis of additional tissues. Homophilic and heterophilic interactions between Teneurin paralogues mediate cellular adhesion in crucial processes such as neuronal pathfinding and synaptic organization. At the molecular level, Teneurins are proteolytically processed into distinct subdomains that have been implicated in extracellular and intracellular signaling, and in transcriptional regulation. Phylogenetic studies have shown a high degree of intra- and interspecies conservation of Teneurin genes. Accordingly, the occurrence of genetic variants has been associated with functional and phenotypic alterations in experimental systems, and with some inherited or sporadic conditions. Recently, tumor-related variations in Teneurin gene expression have been associated with patient survival in different cancers. Although these findings were incidental and molecular mechanisms were not addressed, they suggested a potential utility of Teneurin transcript levels as biomarkers for disease prognosis. Mutations and chromosomal alterations affecting Teneurin genes have been found occasionally in tumors, but literature remains scarce. The analysis of open-access molecular and clinical datasets derived from large oncologic cohorts provides an invaluable resource for the identification of additional somatic mutations. However, Teneurin variants have not been classified in terms of pathogenic risk and their phenotypic impact remains unknown. On this basis, is it plausible to hypothesize that Teneurins play a role in carcinogenesis? Does current evidence support a tumor suppressive or rather oncogenic function for these proteins? Here, we comprehensively discuss available literature with integration of molecular evidence retrieved from open-access databases. We show that Teneurins undergo somatic changes comparable to those of well-established cancer genes, and discuss their involvement in cancer-related signaling pathways. Current data strongly suggest a functional contribution of Teneurins to human carcinogenesis.
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Affiliation(s)
| | - Annemarie Ziegler
- Center for Genetics and Genomics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
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10
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Nazaryan-Petersen L, Eisfeldt J, Pettersson M, Lundin J, Nilsson D, Wincent J, Lieden A, Lovmar L, Ottosson J, Gacic J, Mäkitie O, Nordgren A, Vezzi F, Wirta V, Käller M, Hjortshøj TD, Jespersgaard C, Houssari R, Pignata L, Bak M, Tommerup N, Lundberg ES, Tümer Z, Lindstrand A. Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization. PLoS Genet 2018; 14:e1007780. [PMID: 30419018 PMCID: PMC6258378 DOI: 10.1371/journal.pgen.1007780] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/26/2018] [Accepted: 10/23/2018] [Indexed: 01/25/2023] Open
Abstract
Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs). The rearrangements were further sub-classified depending on the patterns observed: I) Cases with only deletions (n = 8) often had additional structural rearrangements, such as insertions and inversions typical to chromothripsis; II) cases with only duplications (n = 7) or III) combinations of deletions and duplications (n = 6) demonstrated mostly interspersed duplications and BPJs enriched with microhomology. In two cases the rearrangement mutational signatures indicated both a breakage-fusion-bridge cycle process and haltered formation of a ring chromosome. Finally, we observed two cases with Alu- and LINE-mediated rearrangements as well as two unrelated individuals with seemingly identical clustered CNVs on 2p25.3, possibly a rare European founder rearrangement. In conclusion, through detailed characterization of the derivative chromosomes we show that multiple mechanisms are likely involved in the formation of clustered CNVs and add further evidence for chromoanagenesis mechanisms in both “simple” and highly complex chromosomal rearrangements. Finally, WGS characterization adds positional information, important for a correct clinical interpretation and deciphering mechanisms involved in the formation of these rearrangements. Clustered copy number variants (CNVs) as detected by chromosomal microarray are often reported as germline chromoanagenesis. However, such cases might need further investigation by whole genome sequencing (WGS) to accurately resolve the complexity of the structural rearrangement and predict underlying mutational mechanisms. Here, we used WGS to characterize 83 breakpoint-junctions (BPJs) from 21 clustered CNVs, and outlined the rearrangement connectivity pictures. Cases with only deletions often had additional structural rearrangements, such as insertions and inversions, which could be a result of multiple double-strand DNA breaks followed by non-homologous repair, typical to chromothripsis. In contrast, cases with only duplications or combinations of deletions and duplications, demonstrated mostly interspersed duplications and BPJs enriched with microhomology, consistent with serial template switching during DNA replication (chromoanasynthesis). Only two rearrangements were repeat mediated. In aggregate, our results suggest that multiple CNVs clustered on a single chromosome may arise through either chromothripsis or chromoanasynthesis.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Johanna Lundin
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agne Lieden
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Lovisa Lovmar
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jesper Ottosson
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jelena Gacic
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Valtteri Wirta
- SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Max Käller
- SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Tina Duelund Hjortshøj
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Cathrine Jespersgaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Rayan Houssari
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Laura Pignata
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- * E-mail: (AL); (ZT)
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (AL); (ZT)
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11
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Abstract
Chromosomal rearrangements, including translocations, are early and essential events in the formation of many tumors. Previous studies that defined the genetic requirements for rearrangement formation have identified differences between murine and human cells, most notably in the role of classic and alternative nonhomologous end-joining (NHEJ) factors. We reported that poly(ADP)ribose polymerase 3 (PARP3) promotes chromosomal rearrangements induced by endonucleases in multiple human cell types. We show here that in contrast to classic (c-NHEJ) factors, Parp3 also promotes rearrangements in murine cells, including translocations in murine embryonic stem cells (mESCs), class-switch recombination in primary B cells, and inversions in tail fibroblasts that generate Eml4-Alk fusions. In mESCs, Parp3-deficient cells had shorter deletion lengths at translocation junctions. This was corroborated using next-generation sequencing of Eml4-Alk junctions in tail fibroblasts and is consistent with a role for Parp3 in promoting the processing of DNA double-strand breaks. We confirmed a previous report that Parp1 also promotes rearrangement formation. In contrast with Parp3, rearrangement junctions in the absence of Parp1 had longer deletion lengths, suggesting that Parp1 may suppress double-strand break processing. Together, these data indicate that Parp3 and Parp1 promote rearrangements with distinct phenotypes.
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12
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Duffy DJ, Konietzny A, Krstic A, Mehta JP, Halasz M, Kolch W. Identification of a MYCN and Wnt-related VANGL2-ITLN1 fusion gene in neuroblastoma. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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13
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Abstract
RNA-Seq approach enables the detection and characterization of fusion or chimeric transcript associated to complex genome rearrangement. Until now, these events are classically identified at DNA level.Here we describe a complete procedure including a novel way of analyzing reads that combines genomic locations and local coverage to directly infer chimeric junctions with a high sensitivity and specificity, allowing identification of different classes of chimeric RNA events. We also recommend the best practices for the bioinformatics analysis and describe the experimental process for RNA validation using real-time PCR and sequencing.
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14
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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: 76] [Impact Index Per Article: 12.7] [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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15
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Chen L, Humphreys A, Turnbull L, Bellini A, Schleiermacher G, Salwen H, Cohn SL, Bown N, Tweddle DA. Identification of different ALK mutations in a pair of neuroblastoma cell lines established at diagnosis and relapse. Oncotarget 2018; 7:87301-87311. [PMID: 27888620 PMCID: PMC5349989 DOI: 10.18632/oncotarget.13541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 11/06/2016] [Indexed: 11/25/2022] Open
Abstract
Anaplastic Lymphoma Kinase (ALK) is a transmembrane receptor kinase that belongs to the insulin receptor superfamily and has previously been shown to play a role in cell proliferation, migration and invasion in neuroblastoma. Activating ALK mutations are reported in both hereditary and sporadic neuroblastoma tumours, and several ALK inhibitors are currently under clinical evaluation as novel treatments for neuroblastoma. Overall, mutations at codons F1174, R1275 and F1245 together account for ~85% of reported ALK mutations in neuroblastoma. NBLW and NBLW-R are paired cell lines originally derived from an infant with metastatic MYCN amplified Stage IVS (Evans Criteria) neuroblastoma, at diagnosis and relapse, respectively. Using both Sanger and targeted deep sequencing, this study describes the identification of distinct ALK mutations in these paired cell lines, including the rare R1275L mutation, which has not previously been reported in a neuroblastoma cell line. Analysis of the sensitivity of NBLW and NBLW-R cells to a panel of ALK inhibitors (TAE-684, Crizotinib, Alectinib and Lorlatinib) revealed differences between the paired cell lines, and overall NBLW-R cells with the F1174L mutation were more resistant to ALK inhibitor induced apoptosis compared with NBLW cells. This pair of cell lines represents a valuable pre-clinical model of clonal evolution of ALK mutations associated with neuroblastoma progression.
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Affiliation(s)
- Lindi Chen
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Angharad Humphreys
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Lisa Turnbull
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | | | | | - Helen Salwen
- Department of Pediatrics, University of Chicago, Chicago, Illinois 60637, USA
| | - Susan L Cohn
- Department of Pediatrics, University of Chicago, Chicago, Illinois 60637, USA
| | - Nick Bown
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Deborah A Tweddle
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
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16
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De Wilde B, Beckers A, Lindner S, Kristina A, De Preter K, Depuydt P, Mestdagh P, Sante T, Lefever S, Hertwig F, Peng Z, Shi LM, Lee S, Vandermarliere E, Martens L, Menten B, Schramm A, Fischer M, Schulte J, Vandesompele J, Speleman F. The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease. Oncotarget 2017; 9:8334-8349. [PMID: 29492199 PMCID: PMC5823580 DOI: 10.18632/oncotarget.23614] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/28/2017] [Indexed: 12/27/2022] Open
Abstract
Genetically engineered mouse models have proven to be essential tools for unraveling fundamental aspects of cancer biology and for testing novel therapeutic strategies. To optimally serve these goals, it is essential that the mouse model faithfully recapitulates the human disease. Recently, novel mouse models for neuroblastoma have been developed. Here, we report on the further genomic characterization through exome sequencing and DNA copy number analysis of four of the currently available murine neuroblastoma model systems (ALK, Th-MYCN, Dbh-MYCN and Lin28b). The murine tumors revealed a low number of genomic alterations – in keeping with human neuroblastoma - and a positive correlation of the number of genetic lesions with the time to onset of tumor formation was observed. Gene copy number alterations are the hallmark of both murine and human disease and frequently affect syntenic genomic regions. Despite low mutational load, the genes mutated in murine disease were found to be enriched for genes mutated in human disease. Taken together, our study further supports the validity of the tested mouse models for mechanistic and preclinical studies of human neuroblastoma.
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Affiliation(s)
- Bram De Wilde
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | | | - Sven Lindner
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Althoff Kristina
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pauline Depuydt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Zhiyu Peng
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Le-Ming Shi
- Center for Pharmacogenomics and Fudan-Zhangjiang Center for Clinical Genomics, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Sangkyun Lee
- Department of Computer Science, Artificial Intelligence Group, TU Dortmund, Dortmund, Germany
| | - Elien Vandermarliere
- Medical Biotechnology Center, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- Medical Biotechnology Center, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Schramm
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Johannes Schulte
- Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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17
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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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18
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Li Y, Ohira M, Zhou Y, Xiong T, Luo W, Yang C, Li X, Gao Z, Zhou R, Nakamura Y, Kamijo T, Kaneko Y, Taketani T, Ueyama J, Tajiri T, Zhang H, Wang J, Yang H, Yin Y, Nakagawara A. Genomic analysis-integrated whole-exome sequencing of neuroblastomas identifies genetic mutations in axon guidance pathway. Oncotarget 2017; 8:56684-56697. [PMID: 28915622 PMCID: PMC5593593 DOI: 10.18632/oncotarget.18079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/27/2017] [Indexed: 12/12/2022] Open
Abstract
Neuroblastoma (NB) is a childhood solid malignant tumor originating from precursor cells of the peripheral nervous system. We have previously established a risk classification system based on DNA copy number profiles. To further explore the pathogenesis of NBs in distinct risk groups, we performed whole-exome sequencing analysis of 57 primary and 7 recurrent/metastatic tumors with unique chromosomal aberration profiles as categorized by our genomic sub-grouping system. Overall, a low frequency of somatic mutations was found. Besides ALK (4/64, 6.3%), SEMA6C, SLIT1 and NRAS, genes involved in the axon guidance pathway, were identified as recurrently mutated in 6 of 64 tumors (9.4%). Pathway enrichment analysis revealed enrichment of 25 mutated genes in the mitogen-activated protein kinase (MAPK) pathway, 13 genes in the Wnt pathway, and 12 genes in the axon guidance pathway. Genomic analyses demonstrated that primary and matched recurrent or metastatic tumors obtained from sporadic and monozygotic twin NBs were clonally related with variable extents of genetic heterogeneity. Monozygotic twin NBs displayed different evolutionary trajectories. These results indicate the involvement of the axon guidance, MAPK and Wnt pathways in NB and demonstrate genomic diversity with NB progression.
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Affiliation(s)
- Yuanyuan Li
- Life Science Research Institute, Saga Medical Center Koseikan, Saga, Japan.,Division of Biochemistry and Innovative Cancer Therapy, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Miki Ohira
- Division of Cancer Genomics, Chiba Cancer Center Research Institute, Chiba, Japan.,Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | | | | | - Wen Luo
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | | | - Yohko Nakamura
- Division of Biochemistry and Innovative Cancer Therapy, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Yasuhiko Kaneko
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Takeshi Taketani
- Department of Pediatrics, Shimane University School of Medicine, Shimane, Japan
| | - Junichi Ueyama
- Division of Pediatrics and Perinatology, Tottori University School of Medicine, Tottori, Japan
| | - Tatsuro Tajiri
- Department of Pediatric Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Science, Hangzhou, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Science, Hangzhou, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, China
| | - Akira Nakagawara
- Life Science Research Institute, Saga Medical Center Koseikan, Saga, Japan.,Division of Biochemistry and Innovative Cancer Therapy, Chiba Cancer Center Research Institute, Chiba, Japan
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19
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Graumann R, Di Capua GA, Oyarzún JE, Vásquez MA, Liao C, Brañes JA, Roa I, Casanello P, Corvalán AH, Owen GI, Delgado I, Zangemeister-Wittke U, Ziegler A. Expression of teneurins is associated with tumor differentiation and patient survival in ovarian cancer. PLoS One 2017; 12:e0177244. [PMID: 28472127 PMCID: PMC5417686 DOI: 10.1371/journal.pone.0177244] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/24/2017] [Indexed: 11/29/2022] Open
Abstract
Teneurins are a family of highly conserved pair-rule proteins involved in morphogenesis and development of the central nervous system. Their function in adult tissues and in disease is largely unknown. Recent evidence suggests a role for dysregulated expression of Teneurins in human tumors, but systematic investigations are missing. Here, we investigated Teneurin-2 and Teneurin-4 expression in various cancer cell lines and in ovarian tumor tissues. Teneurin-2 and Teneurin-4 were expressed in most of the breast cancer cell lines tested. Teneurin-4 was also detected in ovarian cancer cell lines, and throughout ovarian tumors and normal ovary tissue. Ovarian tumors with low Teneurin-4 expression showed less differentiated phenotypes and these patients had shorter mean overall survival. Similarly, Teneurin-2 expression correlated with overall survival as well, especially in patients with serous tumors. In the various cell lines, 5-Aza-cytidine-induced changes in DNA methylation did not alter expression of Teneurin-2 and Teneurin-4, despite the existence of predicted CpG islands in both genes. Interestingly, however, we found evidence for the control of Teneurin-2 expression by the oncogenic growth factor FGF8. Furthermore, we identified multiple transcript splicing variants for Teneurin-2 and Teneurin-4, indicating complex gene expression patterns in malignant cells. Finally, downregulation of Teneurin-4 expression using siRNA caused a cell-type dependent increase in proliferation and resistance to cisplatin. Altogether, our data suggest that low Teneurin-4 expression provides a growth advantage to cancer cells and marks an undifferentiated state characterized by increased drug resistance and clinical aggressiveness. We conclude that Teneurin-2 and Teneurin-4 expression levels could be of prognostic value in ovarian cancer.
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Affiliation(s)
- Rebecca Graumann
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Gabriella A. Di Capua
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Juan E. Oyarzún
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Marcos A. Vásquez
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Christine Liao
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Jorge A. Brañes
- Division of Obstetrics and Gynecology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Iván Roa
- Division of Pathology, Clínica Alemana de Santiago, Santiago, Chile
| | - Paola Casanello
- Perinatology Research Laboratory, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro H. Corvalán
- Advanced Center for Chronic Diseases (ACCDiS), and UC-Center for Investigational Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gareth I. Owen
- Advanced Center for Chronic Diseases (ACCDiS), and UC-Center for Investigational Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Iris Delgado
- Center for Epidemiology and Health Policies, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | | | - Annemarie Ziegler
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
- * E-mail:
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20
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Abáigar M, Robledo C, Benito R, Ramos F, Díez-Campelo M, Hermosín L, Sánchez-del-Real J, Alonso JM, Cuello R, Megido M, Rodríguez JN, Martín-Núñez G, Aguilar C, Vargas M, Martín AA, García JL, Kohlmann A, del Cañizo MC, Hernández-Rivas JM. Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes. PLoS One 2016; 11:e0164370. [PMID: 27741277 PMCID: PMC5065168 DOI: 10.1371/journal.pone.0164370] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022] Open
Abstract
To explore novel genetic abnormalities occurring in myelodysplastic syndromes (MDS) through an integrative study combining array-based comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.
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Affiliation(s)
- María Abáigar
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Cristina Robledo
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Rocío Benito
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fernando Ramos
- IBIOMED, Instituto de Biomedicina, Universidad de León, León, Spain
- Servicio de Hematología, Hospital Universitario de León, León, Spain
| | - María Díez-Campelo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Servicio de Hematología, Hospital Jerez de la Frontera, Cádiz, Spain
| | | | - Jose M. Alonso
- Servicio de Hematología, Hospital Río Carrión, Palencia, Spain
| | - Rebeca Cuello
- Servicio de Hematología, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Marta Megido
- Servicio de Hematología, Hospital del Bierzo, Ponferrada, Spain
| | | | | | - Carlos Aguilar
- Servicio de Hematología, Hospital General de Soria, Soria, Spain
| | - Manuel Vargas
- Servicio de Hematología, Hospital Comarcal de Jarrio, Jarrio-Coaña, Spain
| | - Ana A. Martín
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Juan L. García
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Alexander Kohlmann
- AstraZeneca, Personalized Healthcare and Biomarkers, Innovative Medicines and Early Development, Cambridge, United Kingdom
| | - M. Consuelo del Cañizo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
| | - Jesús M. Hernández-Rivas
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- * E-mail:
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21
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Iakovishina D, Janoueix-Lerosey I, Barillot E, Regnier M, Boeva V. SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. Bioinformatics 2016; 32:984-92. [PMID: 26740523 PMCID: PMC4896370 DOI: 10.1093/bioinformatics/btv751] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 12/20/2016] [Indexed: 12/13/2022] Open
Abstract
Motivation: Whole genome sequencing of paired-end reads can be applied to characterize the landscape of large somatic rearrangements of cancer genomes. Several methods for detecting structural variants with whole genome sequencing data have been developed. So far, none of these methods has combined information about abnormally mapped read pairs connecting rearranged regions and associated global copy number changes automatically inferred from the same sequencing data file. Our aim was to create a computational method that could use both types of information, i.e. normal and abnormal reads, and demonstrate that by doing so we can highly improve both sensitivity and specificity rates of structural variant prediction. Results: We developed a computational method, SV-Bay, to detect structural variants from whole genome sequencing mate-pair or paired-end data using a probabilistic Bayesian approach. This approach takes into account depth of coverage by normal reads and abnormalities in read pair mappings. To estimate the model likelihood, SV-Bay considers GC-content and read mappability of the genome, thus making important corrections to the expected read count. For the detection of somatic variants, SV-Bay makes use of a matched normal sample when it is available. We validated SV-Bay on simulated datasets and an experimental mate-pair dataset for the CLB-GA neuroblastoma cell line. The comparison of SV-Bay with several other methods for structural variant detection demonstrated that SV-Bay has better prediction accuracy both in terms of sensitivity and false-positive detection rate. Availability and implementation:https://github.com/InstitutCurie/SV-Bay Contact:valentina.boeva@inserm.fr Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Isabelle Janoueix-Lerosey
- Institut Curie, Centre De Recherche, Paris Inserm, U830, Department Genetics and Biology of Cancers, Paris, France
| | - Emmanuel Barillot
- Institut Curie, Centre De Recherche, Paris Inserm, Department of Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, U900, Paris, France Mines ParisTech, Centre for Computational Biology, Fontainebleau, France PSL Research University, Paris, France
| | | | - Valentina Boeva
- Institut Curie, Centre De Recherche, Paris Inserm, Department of Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, U900, Paris, France Mines ParisTech, Centre for Computational Biology, Fontainebleau, France PSL Research University, Paris, France
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22
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Bosse KR, Maris JM. Advances in the translational genomics of neuroblastoma: From improving risk stratification and revealing novel biology to identifying actionable genomic alterations. Cancer 2015; 122:20-33. [PMID: 26539795 DOI: 10.1002/cncr.29706] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/13/2015] [Accepted: 08/31/2015] [Indexed: 12/21/2022]
Abstract
Neuroblastoma is an embryonal malignancy that commonly affects young children and is remarkably heterogenous in its malignant potential. Recently, the genetic basis of neuroblastoma has come into focus and not only has catalyzed a more comprehensive understanding of neuroblastoma tumorigenesis but also has revealed novel oncogenic vulnerabilities that are being therapeutically leveraged. Neuroblastoma is a model pediatric solid tumor in its use of recurrent genomic alterations, such as high-level MYCN (v-myc avian myelocytomatosis viral oncogene neuroblastoma-derived homolog) amplification, for risk stratification. Given the relative paucity of recurrent, activating, somatic point mutations or gene fusions in primary neuroblastoma tumors studied at initial diagnosis, innovative treatment approaches beyond small molecules targeting mutated or dysregulated kinases will be required moving forward to achieve noticeable improvements in overall patient survival. However, the clonally acquired, oncogenic aberrations in relapsed neuroblastomas are currently being defined and may offer an opportunity to improve patient outcomes with molecularly targeted therapy directed toward aberrantly regulated pathways in relapsed disease. This review summarizes the current state of knowledge about neuroblastoma genetics and genomics, highlighting the improved prognostication and potential therapeutic opportunities that have arisen from recent advances in understanding germline predisposition, recurrent segmental chromosomal alterations, somatic point mutations and translocations, and clonal evolution in relapsed neuroblastoma.
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Affiliation(s)
- Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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23
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Weckselblatt B, Rudd MK. Human Structural Variation: Mechanisms of Chromosome Rearrangements. Trends Genet 2015; 31:587-599. [PMID: 26209074 PMCID: PMC4600437 DOI: 10.1016/j.tig.2015.05.010] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 01/05/2023]
Abstract
Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation.
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Affiliation(s)
- Brooke Weckselblatt
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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24
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van Schendel R, Roerink SF, Portegijs V, van den Heuvel S, Tijsterman M. Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis. Nat Commun 2015; 6:7394. [PMID: 26077599 PMCID: PMC4490562 DOI: 10.1038/ncomms8394] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/04/2015] [Indexed: 12/22/2022] Open
Abstract
Cells are protected from toxic DNA double-stranded breaks (DSBs) by a number of DNA repair mechanisms, including some that are intrinsically error prone, thus resulting in mutations. To what extent these mechanisms contribute to evolutionary diversification remains unknown. Here, we demonstrate that the A-family polymerase theta (POLQ) is a major driver of inheritable genomic alterations in Caenorhabditis elegans. Unlike somatic cells, which use non-homologous end joining (NHEJ) to repair DNA transposon-induced DSBs, germ cells use polymerase theta-mediated end joining, a conceptually simple repair mechanism requiring only one nucleotide as a template for repair. Also CRISPR/Cas9-induced genomic changes are exclusively generated through polymerase theta-mediated end joining, refuting a previously assumed requirement for NHEJ in their formation. Finally, through whole-genome sequencing of propagated populations, we show that only POLQ-proficient animals accumulate genomic scars that are abundantly present in genomes of wild C. elegans, pointing towards POLQ as a major driver of genome diversification.
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Affiliation(s)
- Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Sophie F. Roerink
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Vincent Portegijs
- Department of Biology, Division of Developmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sander van den Heuvel
- Department of Biology, Division of Developmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
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25
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Ortiz B, White JR, Wu WH, Chan TA. Deletion of Ptprd and Cdkn2a cooperate to accelerate tumorigenesis. Oncotarget 2015; 5:6976-82. [PMID: 25138050 PMCID: PMC4196177 DOI: 10.18632/oncotarget.2106] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PTPRD encodes the protein tyrosine phosphatase receptor type D and is frequently inactivated across many human cancers. Despite its frequent inactivation, it is unknown whether loss of PTPRD promotes tumorigenesis in vivo. PTPRD is located on chromosome 9p, as is CDKN2A, and the two loci are frequently deleted together. Here, we show that co-deletion of Ptprd and Cdkn2a cooperate to accelerate tumorigenesis. Interestingly, heterozygous loss of Ptprd was sufficient to promote tumorigenesis in our model, suggesting that Ptprd may be a haploinsufficient tumor suppressor. The loss of Ptprd resulted in changes to the tumor spectrum in mice and increased the frequency of lymphomas. In total, we reveal that Ptprd is a tumor suppressor that can promote tumorigenesis in concert with Cdkn2a loss.
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Affiliation(s)
- Berenice Ortiz
- Gerstner Sloan-Kettering Graduate School, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Julie R White
- The Tri-Institutional Laboratory of Comparative Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Wei H Wu
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Dept. of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
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26
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Berbegall AP, Villamón E, Tadeo I, Martinsson T, Cañete A, Castel V, Navarro S, Noguera R. Neuroblastoma after childhood: prognostic relevance of segmental chromosome aberrations, ATRX protein status, and immune cell infiltration. Neoplasia 2015; 16:471-80. [PMID: 25077701 PMCID: PMC4198743 DOI: 10.1016/j.neo.2014.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma (NB) is a common malignancy in children but rarely occurs during adolescence or adulthood. This subgroup is characterized by an indolent disease course, almost uniformly fatal, yet little is known about the biologic characteristics. The aim of this study was to identify differential features regarding DNA copy number alterations, α-thalassemia/mental retardation syndrome X-linked (ATRX) protein expression, and the presence of tumor-associated inflammatory cells. Thirty-one NB patients older than 10 years who were included in the Spanish NB Registry were considered for the current study; seven young and middle-aged adult patients (range 18-60 years) formed part of the cohort. We performed single nucleotide polymorphism arrays, immunohistochemistry for immune markers (CD4, CD8, CD20, CD11b, CD11c, and CD68), and ATRX protein expression. Assorted genetic profiles were found with a predominant presence of a segmental chromosome aberration (SCA) profile. Preadolescent and adolescent NB tumors showed a higher number of SCA, including 17q gain and 11q deletion. There was also a marked infiltration of immune cells, mainly high and heterogeneous, in young and middle-aged adult tumors. ATRX negative expression was present in the tumors. The characteristics of preadolescent, adolescent, young adult, and middle-aged adult NB tumors are different, not only from childhood NB tumors but also from each other. Similar examinations of a larger number of such tumor tissues from cooperative groups should lead to a better older age–dependent tumor pattern and to innovative, individual risk-adapted therapeutic approaches for these patients.
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Affiliation(s)
- Ana P Berbegall
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain; Medical Research Foundation INCLIVA, Hospital Clínico, INCLIVA, Valencia, Spain
| | - Eva Villamón
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Irene Tadeo
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain; Medical Research Foundation INCLIVA, Hospital Clínico, INCLIVA, Valencia, Spain
| | - Tommy Martinsson
- Department of Clinical Genetics, Göteborg University, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adela Cañete
- Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Victoria Castel
- Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Samuel Navarro
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Rosa Noguera
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain.
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Kuhlen M, Borkhardt A. Cancer susceptibility syndromes in children in the area of broad clinical use of massive parallel sequencing. Eur J Pediatr 2015; 174:987-97. [PMID: 25982339 PMCID: PMC4516864 DOI: 10.1007/s00431-015-2565-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 01/23/2023]
Abstract
UNLABELLED Children diagnosed with cancer are considered for inherited cancer susceptibility testing according to well-established clinical criteria. With increasing efforts to personalize cancer medicine, comprehensive genome analyses will find its way into daily clinical routine in pediatric oncology. Whole genome and exome sequencing unavoidably generates incidental findings. The somatic "molecular make-up" of a tumor genome may suggest a germline mutation in a cancer susceptibility syndrome. At least two mechanisms are well-known, (a) chromothripsis (Li-Fraumeni syndrome) and (b) a high total number of mutational events which exceeds that of other samples of the same tumor type (defective DNA mismatch repair). Hence, pediatricians are faced with the fact that genetic events within the tumor genome itself can point toward underlying germline cancer susceptibility. Whenever genetic testing including next-generation sequencing (NGS) is initiated, the pediatrician has to inform about the benefits, risks, and alternatives, discuss the possibility of incidental findings and its disclosure, and to obtain informed consent prior to testing. CONCLUSIONS Genetic testing and translational research in pediatric oncology can incidentally uncover an underlying cancer susceptibility syndrome with implications for the entire family. Pediatricians should therefore increase their awareness of chances and risks that accompany the increasingly wide clinical implementation of NGS platforms.
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Affiliation(s)
- Michaela Kuhlen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225, Duesseldorf, Germany,
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children’s Hospital, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Duesseldorf, Germany
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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: 5.2] [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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The mutational pattern of primary lymphoma of the central nervous system determined by whole-exome sequencing. Leukemia 2014; 29:677-85. [PMID: 25189415 DOI: 10.1038/leu.2014.264] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/05/2014] [Accepted: 08/29/2014] [Indexed: 01/15/2023]
Abstract
To decipher the mutational pattern of primary CNS lymphoma (PCNSL), we performed whole-exome sequencing to a median coverage of 103 × followed by mutation verification in 9 PCNSL and validation using Sanger sequencing in 22 PCNSL. We identified a median of 202 (range: 139-251) potentially somatic single nucleotide variants (SNV) and 14 small indels (range: 7-22) with potentially protein-changing features per PCNSL. Mutations affected the B-cell receptor, toll-like receptor, and NF-κB and genes involved in chromatin structure and modifications, cell-cycle regulation, and immune recognition. A median of 22.2% (range: 20.0-24.7%) of somatic SNVs in 9 PCNSL overlaps with the RGYW motif targeted by somatic hypermutation (SHM); a median of 7.9% (range: 6.2-12.6%) affects its hotspot position suggesting a major impact of SHM on PCNSL pathogenesis. In addition to the well-known targets of aberrant SHM (aSHM) (PIM1), our data suggest new targets of aSHM (KLHL14, OSBPL10, and SUSD2). Among the four most frequently mutated genes was ODZ4 showing protein-changing mutations in 4/9 PCNSL. Together with mutations affecting CSMD2, CSMD3, and PTPRD, these findings may suggest that alterations in genes having a role in CNS development may facilitate diffuse large B-cell lymphoma manifestation in the CNS. This may point to intriguing mechanisms of CNS tropism in PCNSL.
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The teneurins: new players in the generation of visual topography. Semin Cell Dev Biol 2014; 35:173-9. [PMID: 25152333 DOI: 10.1016/j.semcdb.2014.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/08/2014] [Accepted: 08/15/2014] [Indexed: 01/03/2023]
Abstract
A functionally critical feature of the nervous system is the precision of its connectivity. An emerging molecular mediator of this process is the teneurin/ten-m/odz family of transmembrane proteins. A number of recent studies have provided compelling evidence that teneurins have homophilic adhesive properties which, together with their corresponding expression patterns in interconnected groups of neurons, enables them to promote appropriate patterns of connectivity. Particularly important roles have been demonstrated in the visual, olfactory and motor systems. This review attempts to relate new insights into the complex biology of these molecules to their roles in the establishment of functional neural circuits.
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Schleiermacher G, Janoueix-Lerosey I, Delattre O. Recent insights into the biology of neuroblastoma. Int J Cancer 2014; 135:2249-61. [PMID: 25124476 DOI: 10.1002/ijc.29077] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/08/2014] [Indexed: 01/24/2023]
Abstract
Neuroblastoma (NB) is an embryonal tumor of the sympathetic nervous system which accounts for 8-10% of pediatric cancers. It is characterized by a broad spectrum of clinical behaviors from spontaneous regression to fatal outcome despite aggressive therapies. Considerable progress has been made recently in the germline and somatic genetic characterization of patients and tumors. Indeed, predisposition genes that account for a significant proportion of familial and syndromic cases have been identified and genome-wide association studies have retrieved a number of susceptibility loci. In addition, genome-wide sequencing, copy-number and expression studies have been conducted on tumors and have detected important gene modifications, profiles and signatures that have strong implications for the therapeutic stratification of patients. The identification of major players in NB oncogenesis, including MYCN, ALK, PHOX2B and LIN28B, has enabled the development of new animal models. Our review focuses on these recent advances, on the insights they provide on the mechanisms involved in NB development and their applications for the clinical management of patients.
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Affiliation(s)
- Gudrun Schleiermacher
- Equipe SIRIC Recherche Translationnelle en Oncologie Pédiatrique, Département de Recherche Translationnelle et Inserm U830, Centre de Recherche, Paris Cedex, 05, France; Département de pédiatrie, Institut Curie, Paris Cedex, 05, France; Unité Génétique et Biologie des Cancers, Inserm U830, Centre de Recherche, Institut Curie, Paris Cedex, 05, France
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Plaisancié J, Kleinfinger P, Cances C, Bazin A, Julia S, Trost D, Lohmann L, Vigouroux A. Constitutional chromoanasynthesis: description of a rare chromosomal event in a patient. Eur J Med Genet 2014; 57:567-70. [PMID: 25128687 DOI: 10.1016/j.ejmg.2014.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/30/2014] [Indexed: 11/24/2022]
Abstract
Structural alterations in chromosomes are a frequent cause of cancers and congenital diseases. Recently, the phenomenon of chromosome crisis, consisting of a set of tens to hundreds of clustered genomic rearrangements, localized in one or a few chromosomes, was described in cancer cells under the term chromothripsis. Better knowledge and recognition of this catastrophic chromosome event has brought to light two distinct entities, chromothripsis and chromoanasynthesis. The complexity of these rearrangements and the original descriptions in tumor cells initially led to the thought that it was an acquired anomaly. In fact, a few patients have been reported with constitutional chromothripsis or chromoanasynthesis. Using microarray we identified a very complex chromosomal rearrangement in a patient who had a cytogenetically visible rearrangement of chromosome 18. The rearrangement contained more than 15 breakpoints localized on a single chromosome. Our patient displayed intellectual disability, behavioral troubles and craniofacial dysmorphism. Interestingly, the succession of duplications and triplications identified in our patient was not clustered on a single chromosomal region but spread over the entire chromosome 18. In the light of this new spectrum of chromosomal rearrangements, this report outlines the main features of these catastrophic events and discusses the underlying mechanism of the complex chromosomal rearrangement identified in our patient, which is strongly evocative of a chromoanasynthesis.
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Affiliation(s)
- Julie Plaisancié
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, France.
| | - Pascale Kleinfinger
- Laboratoire Cerba, Département de Génétique Humaine, Saint-Ouen l'Aumône, France
| | - Claude Cances
- Service de Neuropédiatrie, Hôpital des Enfants, CHU Toulouse, France
| | - Anne Bazin
- Laboratoire Cerba, Département de Génétique Humaine, Saint-Ouen l'Aumône, France
| | - Sophie Julia
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, France
| | - Detlef Trost
- Laboratoire Cerba, Département de Génétique Humaine, Saint-Ouen l'Aumône, France
| | - Laurence Lohmann
- Laboratoire Cerba, Département de Génétique Humaine, Saint-Ouen l'Aumône, France
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Loss of the tyrosine phosphatase PTPRD leads to aberrant STAT3 activation and promotes gliomagenesis. Proc Natl Acad Sci U S A 2014; 111:8149-54. [PMID: 24843164 DOI: 10.1073/pnas.1401952111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PTPRD, which encodes the protein tyrosine phosphatase receptor-δ, is one of the most frequently inactivated genes across human cancers, including glioblastoma multiforme (GBM). PTPRD undergoes both deletion and mutation in cancers, with copy number loss comprising the primary mode of inactivation in GBM. However, it is unknown whether loss of PTPRD promotes tumorigenesis in vivo, and the mechanistic basis of PTPRD function in tumors is unclear. Here, using genomic analysis and a glioma mouse model, we demonstrate that loss of Ptprd accelerates tumor formation and define the oncogenic context in which Ptprd loss acts. Specifically, we show that in human GBMs, heterozygous loss of PTPRD is the predominant type of lesion and that loss of PTPRD and the CDKN2A/p16(INK4A) tumor suppressor frequently co-occur. Accordingly, heterozygous loss of Ptprd cooperates with p16 deletion to drive gliomagenesis in mice. Moreover, loss of the Ptprd phosphatase resulted in phospho-Stat3 accumulation and constitutive activation of Stat3-driven genetic programs. Surprisingly, the consequences of Ptprd loss are maximal in the heterozygous state, demonstrating a tight dependence on gene dosage. Ptprd loss did not increase cell proliferation but rather altered pathways governing the macrophage response. In total, we reveal that PTPRD is a bona fide tumor suppressor, pinpoint PTPRD loss as a cause of aberrant STAT3 activation in gliomas, and establish PTPRD loss, in the setting of CDKN2A/p16(INK4A) deletion, as a driver of glioma progression.
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