1
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Iwata S, Nagahara M, Ido R, Iwamoto T. A Recql5 mutant facilitates complex CRISPR/Cas9-mediated chromosomal engineering in mouse zygotes. Genetics 2024; 227:iyae054. [PMID: 38577877 DOI: 10.1093/genetics/iyae054] [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: 03/07/2024] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024] Open
Abstract
Complex chromosomal rearrangements (CCRs) are often observed in clinical samples from patients with cancer and congenital diseases but are difficult to induce experimentally. Here, we report the first success in establishing animal models for CCRs. Mutation in Recql5, a crucial member of the DNA helicase RecQ family involved in DNA replication, transcription, and repair, enabled CRISPR/Cas9-mediated CCRs, establishing a mouse model containing triple fusion genes and megabase-sized inversions. Some of these structural features of individual chromosomal rearrangements use template switching and microhomology-mediated break-induced replication mechanisms and are reminiscent of the newly described phenomenon "chromoanasynthesis." These data show that Recql5 mutant mice could be a powerful tool to analyze the pathogenesis of CCRs (particularly chromoanasynthesis) whose underlying mechanisms are poorly understood. The Recql5 mutants generated in this study are to be deposited at key animal research facilities, thereby making them accessible for future research on CCRs.
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Affiliation(s)
- Satoru Iwata
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487-8501, Japan
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
- Center for Mathematical Science and Artificial Intelligence, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Miki Nagahara
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Risako Ido
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Takashi Iwamoto
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487-8501, Japan
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2
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Dermawan JK, Slotkin E, Tap WD, Meyers P, Wexler L, Healey J, Vanoli F, Vanderbilt CM, Antonescu CR. Chromoplexy Is a Frequent Early Clonal Event in EWSR1-Rearranged Round Cell Sarcomas That Can Be Detected Using Clinically Validated Targeted Sequencing Panels. Cancer Res 2024; 84:1504-1516. [PMID: 38335254 DOI: 10.1158/0008-5472.can-23-2573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/09/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Chromoplexy is a phenomenon defined by large-scale chromosomal chained rearrangements. A previous study observed chromoplectic events in a subset of Ewing sarcomas (ES), which was linked to an increased relapse rate. Chromoplexy analysis could potentially facilitate patient risk stratification, particularly if it could be detected with clinically applied targeted next-generation sequencing (NGS) panels. Using DELLY, a structural variant (SV) calling algorithm that is part of the MSK-IMPACT pipeline, we characterized the spectrum of SVs in EWSR1-fused round cell sarcomas, including 173 ES and 104 desmoplastic small round cell tumors (DSRCT), to detect chromoplexy and evaluate its association with clinical and genomic features. Chromoplectic events were detected in 31% of the ES cases and 19% of the DSRCT cases. EWSR1 involvement accounted for 76% to 93% of these events, being rearranged with diverse noncanonical gene partners across the genome, involving mainly translocations but also intrachromosomal deletions and inversions. A major breakpoint cluster was located on EWSR1 exons 8-13. In a subset of cases, the SVs disrupted adjacent loci, forming deletion bridges. Longitudinal sequencing and breakpoint allele fraction analysis showed that chromoplexy is an early event that remains detectable throughout disease progression and likely develops simultaneously with the driver fusion. The presence of chromoplexy was validated in an external ES patient cohort with whole exome sequencing. Chromoplexy was significantly more likely to be present in cases that were metastatic at presentation. Together, this study identifies chromoplexy as a frequent genomic alteration in diverse EWSR1-rearranged tumors that can be captured by targeted NGS panels. SIGNIFICANCE Chromoplexy is detectable using targeted NGS in a substantial portion of EWSR1-rearranged round cell sarcomas as an early and persistent clonal event, expanding the genomic complexity of fusion-associated sarcomas.
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Affiliation(s)
- Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John Healey
- Department of Surgery, Orthopedic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fabio Vanoli
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad M Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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3
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Levy B, Kanagal-Shamanna R, Sahajpal NS, Neveling K, Rack K, Dewaele B, Olde Weghuis D, Stevens-Kroef M, Puiggros A, Mallo M, Clifford B, Mantere T, Hoischen A, Espinet B, Kolhe R, Solé F, Raca G, Smith AC. A framework for the clinical implementation of optical genome mapping in hematologic malignancies. Am J Hematol 2024; 99:642-661. [PMID: 38164980 DOI: 10.1002/ajh.27175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/09/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of conventional standard of care cytogenomic clinical testing but it also adds significant new information in certain cases. Since OGM consolidates the diagnostic benefits of multiple costly and laborious tests (e.g., karyotyping, fluorescence in situ hybridization, and chromosomal microarrays) in a single cost-effective assay, many clinical laboratories have started to consider utilizing OGM. In 2021, an international working group of early adopters of OGM who are experienced with routine clinical cytogenomic testing in patients with hematological neoplasms formed a consortium (International Consortium for OGM in Hematologic Malignancies, henceforth "the Consortium") to create a consensus framework for implementation of OGM in a clinical setting. The focus of the Consortium is to provide guidance for laboratories implementing OGM in three specific areas: validation, quality control and analysis and interpretation of variants. Since OGM is a complex technology with many variables, we felt that by consolidating our collective experience, we could provide a practical and useful tool for uniform implementation of OGM in hematologic malignancies with the ultimate goal of achieving globally accepted standards.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katrina Rack
- Laboratory for the Cytogenetic and Molecular Diagnosis of Haematological Malignancies, Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Laboratory for the Cytogenetic and Molecular Diagnosis of Haematological Malignancies, Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Daniel Olde Weghuis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anna Puiggros
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mar Mallo
- MDS Research Group, Microarrays Unit, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | - Tuomo Mantere
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Blanca Espinet
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Francesc Solé
- MDS Research Group, Microarrays Unit, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Adam C Smith
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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4
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Ariffen NA, Ornellas AA, Alves G, Shana'ah AM, Sharma S, Kankel S, Jamali E, Theis B, Liehr T. Amplification of different satellite-DNAs in prostate cancer. Pathol Res Pract 2024; 256:155269. [PMID: 38522124 DOI: 10.1016/j.prp.2024.155269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/11/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
Abstract
In various solid tumors and corresponding cell lines, prior research has identified acquired copy number variations (CNVs) encompassing centromeric satellite-DNA sequences. This observation emerged from the application of centromeric probes (satellite-DNA) as controls in molecular cytogenetic investigations and diagnostics, although these accounts were largely anecdotal. In this study, we conducted a systematic screening for satellite-DNA sequence amplification in 31 prostate cancer (PCa) samples, a prevalent malignancy in men characterized by discernible molecular cytogenetic aberrations. Notably, PCa-typical genetic aberrations, such as TMPRSS2-ERG gene rearrangements and PTEN deletion, were identified in 12 and 6 out of the 31 PCa samples, respectively. Overall, PCa exhibited genomic instability marked by chromosomal gain or loss of signals across nearly all tested satellite-DNA regions, with particular emphasis on the Y-chromosome (18/31 cases). Remarkably, 5/12 PCa samples representing more advanced metastatic cancer displayed amplification of one or two satellite DNA stretches each, being detectable as blocks analogous to homogenously staining regions. Notably, these stretches included α-satellite DNA derived from chromosomes 2, 3, 4, 15, and 20, as well as satellite-III DNAs (D1Z1 and DYZ1). These findings align with recent discoveries indicating that α-satellite DNAs are expressed as long-non-coding RNAs in advanced cancer, particularly in the context of PCa.
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Affiliation(s)
- Nurul Aida Ariffen
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany; Laboratory, Subang Jaya Medical Centre, Subang Jaya, Selangor, Malaysia
| | | | - Gilda Alves
- Circulating Biomarkers Laboratory, Faculty of Medical Sciences, Department of General Pathology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Ahmad Moay Shana'ah
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Samiha Sharma
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Stefanie Kankel
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Elena Jamali
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Bernhard Theis
- Jena University Hospital, Friedrich Schiller University, Institute of Forensic Medicine, Section Pathology, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
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5
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Tuncel T, Ak G, Güneş HV, Metintaş M. Complex Genomic Rearrangement Patterns in Malignant Pleural Mesothelioma due to Environmental Asbestos Exposure. J Environ Pathol Toxicol Oncol 2024; 43:13-27. [PMID: 38505910 DOI: 10.1615/jenvironpatholtoxicoloncol.2023046200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare type of cancer, and its main risk factor is exposure to asbestos. Accordingly, our knowledge of the genomic structure of an MPM tumor is limited when compared to other cancers. In this study, we aimed to characterize complex genomic rearrangement patterns and variations to better understand the genomics of MPM tumors. We comparatively scanned 3 MPM tumor genomes by Whole-Genome Sequencing and High-Resolution SNP array. We also used various computational algorithms to detect both CNAs and complex chromosomal rearrangements. Genomic data obtained from each bioinformatics tool are interpreted comparatively to better understand CNAs and cancer-related Nucleotide variations in MPM tumors. In patients 1 and 2, we found pathogenic nucleotide variants of BAP1, RB1, and TP53. These two MPM genomes exhibited a highly rearranged chromosomal rearrangement pattern resembling Chromomanagesis particularly in the form of Chromoanasynthesis. In patient 3, we found nucleotide variants of important cancer-related genes, including TGFBR1, KMT2C, and PALLD, to have lower chromosomal rearrangement complexity compared with patients 1 and 2. We also detected several actionable nucleotide variants including XRCC1, ERCC2. We also discovered the SKA3-DDX10 fusion in two MPM genomes, which is a novel finding for MPM. We found that MPM genomes are very complex, suggesting that this highly rearranged pattern is strongly related to driver mutational status like BAP1, TP53 and RB1.
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Affiliation(s)
- Tunç Tuncel
- Health Institutes of Turkey, Turkish Biotechnology Institute, Ankara, Turkey
| | - Güntülü Ak
- Eskisehir Osmangazi University Medical Faculty, Department of Chest Diseases, Lung and Pleural Cancers Research and Clinical Center, Eskisehir, Turkey
| | - Hasan Veysi Güneş
- Eskisehir Osmangazi University Medical Faculty, Department of Medical Biology, Eskisehir, Turkey
| | - Muzaffer Metintaş
- Eskisehir Osmangazi University Medical Faculty, Department of Chest Diseases, Lung and Pleural Cancers Research and Clinical Center, Eskisehir, Turkey
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6
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Ye JC, Heng HH. Tracking Karyotype Changes in Treatment-Induced Drug-Resistant Evolution. Methods Mol Biol 2024; 2825:263-280. [PMID: 38913315 DOI: 10.1007/978-1-0716-3946-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Karyotype coding, which encompasses the complete chromosome sets and their topological genomic relationships within a given species, encodes system-level information that organizes and preserves genes' function, and determines the macroevolution of cancer. This new recognition emphasizes the crucial role of karyotype characterization in cancer research. To advance this cancer cytogenetic/cytogenomic concept and its platforms, this study outlines protocols for monitoring the karyotype landscape during treatment-induced rapid drug resistance in cancer. It emphasizes four key perspectives: combinational analyses of phenotype and karyotype, a focus on the entire evolutionary process through longitudinal analysis, a comparison of whole landscape dynamics by including various types of NCCAs (including genome chaos), and the use of the same process to prioritize different genomic scales. This protocol holds promise for studying numerous evolutionary aspects of cancers, and it further enhances the power of karyotype analysis in cancer research.
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Affiliation(s)
- Jing Christine Ye
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Henry H Heng
- Department of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA.
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7
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Tuncel T, Metintas M, Güntülü AK, Güneş HV. Whole-Genome Comparative Copy Number Alteration Profiling between Malignant Pleural Mesothelioma and Asbestos-Induced Chronic Pleuritis. J Environ Pathol Toxicol Oncol 2024; 43:31-44. [PMID: 37824368 DOI: 10.1615/jenvironpatholtoxicoloncol.2023047755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is rare and aggressive cancer. The most important risk factor for MPM is exposure to asbestos. In this study, we scanned the genomes of individuals MPM and asbestos-induced chronic pleuritis (AICP) to compare and determine copy number alterations (CNAs) between two asbestos-related diseases. We used high-resolution SNP arrays to compare CNA profiles between MPM (n = 55) and AICP (n = 18). DNAs extracted from pleural tissues in both groups. SNP array analysis revealed common losses at 1p, 3p, 6q, 9p, 13q, 14q, 15q, 16q, 22q and frequent gains at chromosomes 1, 3, 5, 7, 8, and 6p, 12q, 15q, 17p, 20q in MPMs (frequencies max 67%-min 30%; these alterations were not detected in AICPs. Besides detecting well-known MPM-associated CNAs, our high -resolution copy number profiling also detected comparatively rare CNAs for MPMs including losses like 9q33.3, 16q and gains of 1p, 1q, 3p, 3q, 6p, 7q, 15q, 12q, 17p, 20q at significant frequencies in the MPM cohort. We also observed Copy Number gains clustered on the NF2 locus in AICPs, whereas this region was commonly deleted in MPMs. According to this distinct genomic profiles between the two groups, AICPs genomes can be clearly distinguished from highly altered MPM genomes. Hence, we can suggest that SNP arrays can be used as a supporting diagnostic tool in terms of discriminating asbestos-related malignant disease such as MPM and benign pleural lesions, which can be challenging in most instances.
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Affiliation(s)
- Tunç Tuncel
- Health Institutes of Turkey, Turkish Biotechnology Institute, Ankara, Turkey
| | - Muzaffer Metintas
- Eskisehir Osmangazi University Medical Faculty, Department of Chest Diseases, Lung and Pleural Cancers Research and Clinical Center, Eskisehir, Turkey
| | - A K Güntülü
- Eskisehir Osmangazi University Medical Faculty, Department of Chest Diseases, Lung and Pleural Cancers Research and Clinical Center, Eskisehir, Turkey
| | - Hasan Veysi Güneş
- Eskisehir Osmangazi University Medical Faculty, Department of Medical Biology, Eskisehir, Turkey
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8
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Barford RG, Whittle E, Weir L, Fong FC, Goodman A, Hartley HE, Allinson LM, Tweddle DA. Use of Optical Genome Mapping to Detect Structural Variants in Neuroblastoma. Cancers (Basel) 2023; 15:5233. [PMID: 37958407 PMCID: PMC10647738 DOI: 10.3390/cancers15215233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Neuroblastoma is the most common extracranial solid tumour in children, accounting for 15% of paediatric cancer deaths. Multiple genetic abnormalities have been identified as prognostically significant in neuroblastoma patients. Optical genome mapping (OGM) is a novel cytogenetic technique used to detect structural variants, which has not previously been tested in neuroblastoma. We used OGM to identify copy number and structural variants (SVs) in neuroblastoma which may have been missed by standard cytogenetic techniques. METHODS Five neuroblastoma cell lines (SH-SY5Y, NBLW, GI-ME-N, NB1691 and SK-N-BE2(C)) and two neuroblastoma tumours were analysed using OGM with the Bionano Saphyr® instrument. The results were analysed using Bionano Access software and compared to previous genetic analyses including G-band karyotyping, FISH (fluorescent in situ hybridisation), single-nucleotide polymorphism (SNP) array and RNA fusion panels for cell lines, and SNP arrays and whole genome sequencing (WGS) for tumours. RESULTS OGM detected copy number abnormalities found using previous methods and provided estimates for absolute copy numbers of amplified genes. OGM identified novel SVs, including fusion genes in two cell lines of potential clinical significance. CONCLUSIONS OGM can reliably detect clinically significant structural and copy number variations in a single test. OGM may prove to be more time- and cost-effective than current standard cytogenetic techniques for neuroblastoma.
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Affiliation(s)
- Ruby G. Barford
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
| | - Emily Whittle
- Newcastle Genetics Laboratory, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK; (E.W.); (L.W.); (A.G.)
| | - Laura Weir
- Newcastle Genetics Laboratory, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK; (E.W.); (L.W.); (A.G.)
| | - Fang Chyi Fong
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
| | - Angharad Goodman
- Newcastle Genetics Laboratory, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK; (E.W.); (L.W.); (A.G.)
| | - Hannah E. Hartley
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
| | - Lisa M. Allinson
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
| | - Deborah A. Tweddle
- Wolfson Childhood Cancer Research Centre, Translational & Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (R.G.B.); (F.C.F.); (H.E.H.); (L.M.A.)
- Great North Children’s Hospital, Newcastle upon Tyne NE1 4LP, UK
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9
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Tamura T, Yamamoto Shimojima K, Okamoto N, Yagasaki H, Morioka I, Kanno H, Minakuchi Y, Toyoda A, Yamamoto T. Long-read sequence analysis for clustered genomic copy number aberrations revealed architectures of intricately intertwined rearrangements. Am J Med Genet A 2023; 191:112-119. [PMID: 36282026 DOI: 10.1002/ajmg.a.62997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/13/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022]
Abstract
Most chromosomal aberrations revealed by chromosomal microarray testing (CMA) are simple; however, very complex chromosomal structural rearrangements can also be found. Although the mechanism of structural rearrangements has been gradually revealed, not all mechanisms have been elucidated. We analyzed the breakpoint-junctions (BJs) of two or more clustered copy number variations (CNVs) in the same chromosome arms to understand their conformation and the mechanism of complex structural rearrangements. Combining CMA with long-read whole-genome sequencing (WGS) analysis, we successfully determined all BJs for the clustered CNVs identified in four patients. Multiple CNVs were intricately intertwined with each other, and clustered CNVs in four patients were involved in global complex chromosomal rearrangements. The BJs of two clustered deletions identified in two patients showed microhomologies, and their characteristics were explained by chromothripsis. In contrast, the BJs in the other two patients, who showed clustered deletions and duplications, consisted of blunt-end and nontemplated insertions. These findings could be explained only by alternative nonhomologous end-joining, a mechanism related to polymerase theta. All the patients had at least one inverted segment. Three patients showed cryptic aberrations involving a disruption and a deletion/duplication, which were not detected by CMA but were first identified by WGS. This result suggested that complex rearrangements should be considered if clustered CNVs are observed in the same chromosome arms. Because CMA has potential limitations in genotype-phenotype correlation analysis, a more detailed analysis by whole genome examination is recommended in cases of suspected complex structural aberrations.
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Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Yamamoto Shimojima
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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10
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Ďurovcová I, Kyzek S, Fabová J, Makuková J, Gálová E, Ševčovičová A. Genotoxic potential of bisphenol A: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119346. [PMID: 35489531 DOI: 10.1016/j.envpol.2022.119346] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/05/2022] [Accepted: 04/20/2022] [Indexed: 05/25/2023]
Abstract
Bisphenol A (BPA), as a major component of some plastic products, is abundant environmental pollutant. Due to its ability to bind to several types of estrogen receptors, it can trigger multiple cellular responses, which can contribute to various manifestations at the organism level. The most studied effect of BPA is endocrine disruption, but recently its prooxidative potential has been confirmed. BPA ability to induce oxidative stress through increased ROS production, altered activity of antioxidant enzymes, or accumulation of oxidation products of biomacromolecules is observed in a wide range of organisms - estrogen receptor-positive and -negative. Subsequently, increased intracellular oxidation can lead to DNA damage induction, represented by oxidative damage, single- and double-strand DNA breaks. Importantly, BPA shows several mechanisms of action and can trigger adverse effects on all organisms inhabiting a wide variety of ecosystem types. Therefore, the main aim of this review is to summarize the genotoxic effects of BPA on organisms across all taxa.
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Affiliation(s)
- Ivana Ďurovcová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Stanislav Kyzek
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Jana Fabová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Jana Makuková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Eliška Gálová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Andrea Ševčovičová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
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11
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Ramos-Campoy S, Puiggros A, Kamaso J, Beà S, Bougeon S, Larráyoz MJ, Costa D, Parker H, Rigolin GM, Blanco ML, Collado R, Ancín I, Salgado R, Moro-García MA, Baumann T, Gimeno E, Moreno C, Salido M, Calvo X, Calasanz MJ, Cuneo A, Nguyen-Khac F, Oscier D, Haferlach C, Strefford JC, Schoumans J, Espinet B. TP53 Abnormalities Are Underlying the Poor Outcome Associated with Chromothripsis in Chronic Lymphocytic Leukemia Patients with Complex Karyotype. Cancers (Basel) 2022; 14:3715. [PMID: 35954380 PMCID: PMC9367500 DOI: 10.3390/cancers14153715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Chromothripsis (cth) has been associated with a dismal outcome and poor prognosis factors in patients with chronic lymphocytic leukemia (CLL). Despite being correlated with high genome instability, previous studies have not assessed the role of cth in the context of genomic complexity. Herein, we analyzed a cohort of 33 CLL patients with cth and compared them against a cohort of 129 non-cth cases with complex karyotypes. Nine cth cases were analyzed using optical genome mapping (OGM). Patterns detected by genomic microarrays were compared and the prognostic value of cth was analyzed. Cth was distributed throughout the genome, with chromosomes 3, 6 and 13 being those most frequently affected. OGM detected 88.1% of the previously known copy number alterations and several additional cth-related rearrangements (median: 9, range: 3-26). Two patterns were identified: one with rearrangements clustered in the region with cth (3/9) and the other involving both chromothriptic and non-chromothriptic chromosomes (6/9). Cases with cth showed a shorter time to first treatment (TTFT) than non-cth patients (median TTFT: 2 m vs. 15 m; p = 0.013). However, when stratifying patients based on TP53 status, cth did not affect TTFT. Only TP53 maintained its significance in the multivariate analysis for TTFT, including cth and genome complexity defined by genomic microarrays (HR: 1.60; p = 0.029). Our findings suggest that TP53 abnormalities, rather than cth itself, underlie the poor prognosis observed in this subset.
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Affiliation(s)
- Silvia Ramos-Campoy
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Anna Puiggros
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Joanna Kamaso
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Sílvia Beà
- Hematopathology Section, Department of Pathology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (S.B.); (D.C.); (T.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Sandrine Bougeon
- Oncogenomic Laboratory, Hematology Service, Lausanne University Hospital, 1011 Lausanne, Switzerland; (S.B.); (J.S.)
| | - María José Larráyoz
- Cytogenetics and Hematological Genetics Services, Department of Genetics, University of Navarra, 31008 Pamplona, Spain; (M.J.L.); (M.J.C.)
| | - Dolors Costa
- Hematopathology Section, Department of Pathology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (S.B.); (D.C.); (T.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Helen Parker
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (H.P.); (J.C.S.)
| | - Gian Matteo Rigolin
- Hematology Section, St. Anna University Hospital, 44121 Ferrara, Italy; (G.M.R.); (A.C.)
| | - María Laura Blanco
- Department of Hematology, Hospital de la Santa Creu I Sant Pau, 08041 Barcelona, Spain; (M.L.B.); (C.M.)
| | - Rosa Collado
- Department of Hematology, Consorcio Hospital General Universitario, 46014 Valencia, Spain;
| | - Idoya Ancín
- Department of Hematology and Hemotherapy, Hospital Universitario Cruces, 48903 Bilbao, Spain;
| | - Rocío Salgado
- Cytogenetics Laboratory, Hematology Department, Fundación Jiménez Díaz, 28040 Madrid, Spain;
| | - Marco A. Moro-García
- Laboratory Medicine Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Tycho Baumann
- Hematopathology Section, Department of Pathology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (S.B.); (D.C.); (T.B.)
| | - Eva Gimeno
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Applied Clinical Research in Hematological Malignances, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Carol Moreno
- Department of Hematology, Hospital de la Santa Creu I Sant Pau, 08041 Barcelona, Spain; (M.L.B.); (C.M.)
| | - Marta Salido
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Xavier Calvo
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - María José Calasanz
- Cytogenetics and Hematological Genetics Services, Department of Genetics, University of Navarra, 31008 Pamplona, Spain; (M.J.L.); (M.J.C.)
| | - Antonio Cuneo
- Hematology Section, St. Anna University Hospital, 44121 Ferrara, Italy; (G.M.R.); (A.C.)
| | - Florence Nguyen-Khac
- Sorbonne University, Hematology Department, Hôpital Pitié-Salpêtrière, APHP, INSERM U1138, 75013 Paris, France;
| | - David Oscier
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth BH7 7DW, UK;
| | | | - Jonathan C. Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (H.P.); (J.C.S.)
| | - Jacqueline Schoumans
- Oncogenomic Laboratory, Hematology Service, Lausanne University Hospital, 1011 Lausanne, Switzerland; (S.B.); (J.S.)
| | - Blanca Espinet
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
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12
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Burssed B, Zamariolli M, Bellucco FT, Melaragno MI. Mechanisms of structural chromosomal rearrangement formation. Mol Cytogenet 2022; 15:23. [PMID: 35701783 PMCID: PMC9199198 DOI: 10.1186/s13039-022-00600-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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13
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Cosenza MR, Rodriguez-Martin B, Korbel JO. Structural Variation in Cancer: Role, Prevalence, and Mechanisms. Annu Rev Genomics Hum Genet 2022; 23:123-152. [DOI: 10.1146/annurev-genom-120121-101149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | | | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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14
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Insight into the Molecular Basis Underlying Chromothripsis. Int J Mol Sci 2022; 23:ijms23063318. [PMID: 35328739 PMCID: PMC8948871 DOI: 10.3390/ijms23063318] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
Chromoanagenesis constitutes a group of events that arise from single cellular events during early development. This particular class of complex rearrangements is a newfound occurrence that may lead to chaotic and complex genomic realignments. By that, chromoanagenesis is thought to be a crucial factor regarding macroevolution of the genome, and consequently is affecting the karyotype revolution together with genomic plasticity. One of chromoanagenesis-type of events is chromothripsis. It is characterised by the breakage of the chromosomal structure and its reassembling in random order and orientation which results in the establishment of derivative forms of chromosomes. Molecular mechanisms that underlie this phenomenon are mostly related to chromosomal sequestration throughout the micronuclei formation process. Chromothripsis is linked both to congenital and cancer diseases, moreover, it might be detected in subjects characterised by a normal phenotype. Chromothripsis, as well as the other chromoanagenetic variations, may be confined to one or more chromosomes, which makes up a non-uniform variety of karyotypes among chromothriptic patients. The detection of chromothripsis is enabled via tools like microarray-based comparative genomic hybridisation, next generation sequencing or authorial protocols aimed for the recognition of structural variations.
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15
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Kosari F, Disselhorst M, Yin J, Peikert T, Udell J, Johnson S, Smadbeck J, Murphy S, McCune A, Karagouga G, Desai A, Schaefer-Klein J, Borad MJ, Cheville J, Vasmatzis G, Baas P, Mansfield AS. Tumor Junction Burden and Antigen Presentation as Predictors of Survival in Mesothelioma Treated With Immune Checkpoint Inhibitors. J Thorac Oncol 2022; 17:446-454. [PMID: 34800701 PMCID: PMC8882146 DOI: 10.1016/j.jtho.2021.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The favorable outcomes with immunotherapy for mesothelioma were somewhat unexpected because this tumor has a low tumor mutation burden which has been associated with benefit in other cancers. Because chromosomal rearrangements are common in mesothelioma and have neoantigenic potential, we sought to determine whether they are associated with survival in patients treated with immunotherapy. METHODS Pleural biopsies of mesothelioma after at least one line of therapy were obtained from patients (n = 44) before treatment with nivolumab alone (NCT29908324) or in combination with ipilimumab (NCT30660511). RNA and whole-genome sequencing were performed to identify the junctions resulting from chromosomal rearrangements and antigen processing and presentation gene set expression. Associations with overall survival (OS) were estimated using Cox models. An OS cutoff of 1.5 years was used to distinguish patients with and without durable benefit for use in receiving operating characteristic curves. RESULTS Although tumor junction burdens were not predictive of OS, we identified significant interactions between the junction burdens and multiple antigen processing and presentation gene sets. The "regulation of antigen processing and presentation of peptide antigen" gene set revealed an interaction with tumor junction burden and was predictive of OS. This interaction also predicted 1.5-year or greater survival with an area under the receiving operating characteristic curve of 0.83. This interaction was not predictive of survival in a separate cohort of patients with mesothelioma who did not receive immune checkpoint inhibitors. CONCLUSIONS Analysis of structural variants and antigen presentation gene set expression may facilitate patient selection for immune checkpoint inhibitors.
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Affiliation(s)
- Farhad Kosari
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Maria Disselhorst
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jun Yin
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Tobias Peikert
- Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Julia Udell
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Sarah Johnson
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - James Smadbeck
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Stephen Murphy
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Alexa McCune
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Giannoula Karagouga
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Aakash Desai
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | - Janet Schaefer-Klein
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Mitesh J. Borad
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ,Department of Medical Oncology, Mayo Clinic, Phoenix, Arizona
| | - John Cheville
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - George Vasmatzis
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Paul Baas
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aaron S. Mansfield
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ,Division of Medical Oncology, Mayo Clinic, Rochester, MN
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16
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Genome-wide identification and expression profiling analysis of Wnt family genes affecting adipocyte differentiation in cattle. Sci Rep 2022; 12:489. [PMID: 35017603 PMCID: PMC8752766 DOI: 10.1038/s41598-021-04468-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022] Open
Abstract
The Wnt family features conserved glycoproteins that play roles in tissue regeneration, animal development and cell proliferation and differentiation. For its functional diversity and importance, this family has been studied in several species, but not in the Bovinae. Herein we identified 19 Wnt genes in cattle, and seven other species of Bovinae, and described their corresponding protein properties. Phylogenetic analysis clustered the 149 Wnt proteins in Bovinae, and 38 Wnt proteins from the human and mouse into 12 major clades. Wnt genes from the same subfamilies shared similar protein motif compositions and exon–intron patterns. Chromosomal distribution and collinearity analysis revealed that they were conservative in cattle and five species of Bovinae. RNA-seq data analysis indicated that Wnt genes exhibited tissue-specific expression in cattle. qPCR analysis revealed a unique expression pattern of each gene during bovine adipocytes differentiation. Finally, the comprehensive analysis indicated that Wnt2B may regulate adipose differentiation by activating FZD5, which is worthy of further study. Our study presents the first genome-wide study of the Wnt gene family in Bovinae, and lays the foundation for further functional characterization of this family in bovine adipocytes differentiation.
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17
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Bolzán AD. Mutagen-induced telomere instability in human cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2021; 868-869:503387. [PMID: 34454696 DOI: 10.1016/j.mrgentox.2021.503387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 11/27/2022]
Abstract
Telomere instability is one of the main sources of genome instability and may result from chromosome end loss (due to chromosome breakage at one or both ends) or, more frequently, telomere dysfunction. Dysfunctional telomeres arise when they lose their end-capping function or become critically short, which causes chromosomal termini to behave like a DNA double-strand break. Telomere instability may occur at the chromosomal or at the molecular level, giving rise, respectively, to telomere-related chromosomal aberrations or the loss or modification of any of the components of the telomere (telomere DNA, telomere-associated proteins, or telomere RNA). Since telomeres play a fundamental role in maintaining genome stability, the study of telomere instability in cells exposed to mutagens is of great importance to understand the telomere-driven genomic instability present in those cells. In the present review, we will focus on the current knowledge about telomere instability induced by physical, chemical, and biological mutagens in human cells.
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Affiliation(s)
- Alejandro D Bolzán
- Laboratorio de Citogenética y Mutagénesis, Instituto Multidisciplinario de Biología Celular (IMBICE, CONICET-CICPBA-UNLP), calle 526 y Camino General Belgrano, B1906APO La Plata, Buenos Aires, Argentina; Universidad Nacional de La Plata, Facultad de Ciencias Naturales y Museo, calle 60 y 122, La Plata, Buenos Aires, Argentina.
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18
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Guo W, Comai L, Henry IM. Chromoanagenesis from radiation-induced genome damage in Populus. PLoS Genet 2021; 17:e1009735. [PMID: 34432802 PMCID: PMC8423247 DOI: 10.1371/journal.pgen.1009735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/07/2021] [Accepted: 07/22/2021] [Indexed: 11/18/2022] Open
Abstract
Chromoanagenesis is a genomic catastrophe that results in chromosomal shattering and reassembly. These extreme single chromosome events were first identified in cancer, and have since been observed in other systems, but have so far only been formally documented in plants in the context of haploid induction crosses. The frequency, origins, consequences, and evolutionary impact of such major chromosomal remodeling in other situations remain obscure. Here, we demonstrate the occurrence of chromoanagenesis in poplar (Populus sp.) trees produced from gamma-irradiated pollen. Specifically, in this population of siblings carrying indel mutations, two individuals exhibited highly frequent copy number variation (CNV) clustered on a single chromosome, one of the hallmarks of chromoanagenesis. Using short-read sequencing, we confirmed the presence of clustered segmental rearrangement. Independently, we identified and validated novel DNA junctions and confirmed that they were clustered and corresponded to these rearrangements. Our reconstruction of the novel sequences suggests that the chromosomal segments have reorganized randomly to produce a novel rearranged chromosome but that two different mechanisms might be at play. Our results indicate that gamma irradiation can trigger chromoanagenesis, suggesting that this may also occur when natural or induced mutagens cause DNA breaks. We further demonstrate that such events can be tolerated in poplar, and even replicated clonally, providing an attractive system for more in-depth investigations of their consequences. Plant breeders often use radiation treatment to produce variation, with the goal of identifying new varieties with superior traits. We studied a population of poplar trees produced by gamma irradiation of pollen, and asked what kind of DNA changes were associated with this variation. We found many changes, most often in the form of added (insertions) or removed (deletions) pieces of DNA. We also found two lines with much more drastic changes. In those lines, we observed massive reorganization. We characterized these two lines in detail and found that catastrophic pulverization and random reassembly only occurred on a single chromosome. Looking closely at how the pieces were put back together suggest that the rearrangements in these two lines may have resulted from two slightly different mechanisms. This type of rearrangement is commonly observed in human cancer cells, but has rarely been observed in plants. We demonstrated here that they can be induced by gamma irradiation, indicating this type of event might be more widespread than we expected. Characterizing such genome restructuring instances helps to understand how genome instability can remodel chromosomes and affect genome function.
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Affiliation(s)
- Weier Guo
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
| | - Luca Comai
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
| | - Isabelle M. Henry
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Rasnic R, Linial M. Chromoanagenesis Landscape in 10,000 TCGA Patients. Cancers (Basel) 2021; 13:4197. [PMID: 34439350 PMCID: PMC8392194 DOI: 10.3390/cancers13164197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022] Open
Abstract
During the past decade, whole-genome sequencing of tumor biopsies and individuals with congenital disorders highlighted the phenomenon of chromoanagenesis, a single chaotic event of chromosomal rearrangement. Chromoanagenesis was shown to be frequent in many types of cancers, to occur in early stages of cancer development, and significantly impact the tumor's nature. However, an in-depth, cancer-type dependent analysis has been somewhat incomplete due to the shortage in whole genome sequencing of cancerous samples. In this study, we extracted data from The Pan-Cancer Analysis of Whole Genome (PCAWG) and The Cancer Genome Atlas (TCGA) to construct and test a machine learning algorithm that can detect chromoanagenesis with high accuracy (86%). The algorithm was applied to ~10,000 unlabeled TCGA cancer patients. We utilize the chromoanagenesis assignment results, to analyze cancer-type specific chromoanagenesis characteristics in 20 TCGA cancer types. Our results unveil prominent genes affected in either chromoanagenesis or non-chromoanagenesis tumorigenesis. The analysis reveals a mutual exclusivity relationship between the genes impaired in chromoanagenesis versus non-chromoanagenesis cases. We offer the discovered characteristics as possible targets for cancer diagnostic and therapeutic purposes.
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Affiliation(s)
- Roni Rasnic
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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20
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Mechanisms Underlying the Suppression of Chromosome Rearrangements by Ataxia-Telangiectasia Mutated. Genes (Basel) 2021; 12:genes12081232. [PMID: 34440406 PMCID: PMC8392746 DOI: 10.3390/genes12081232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosome rearrangements are structural variations in chromosomes, such as inversions and translocations. Chromosome rearrangements have been implicated in a variety of human diseases. Ataxia-telangiectasia (A-T) is an autosomal recessive disorder characterized by a broad range of clinical and cellular phenotypes. At the cellular level, one of the most prominent features of A-T cells is chromosome rearrangement, especially that in T lymphocytes. The gene that is defective in A-T is ataxia-telangiectasia mutated (ATM). The ATM protein is a serine/threonine kinase and plays a central role in the cellular response to DNA damage, particularly DNA double-strand breaks. In this review, the mechanisms by which ATM suppresses chromosome rearrangements are discussed.
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21
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Thondehaalmath T, Kulaar DS, Bondada R, Maruthachalam R. Understanding and exploiting uniparental genome elimination in plants: insights from Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4646-4662. [PMID: 33851980 DOI: 10.1093/jxb/erab161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Uniparental genome elimination (UGE) refers to the preferential exclusion of one set of the parental chromosome complement during embryogenesis following successful fertilization, giving rise to uniparental haploid progeny. This artificially induced phenomenon was documented as one of the consequences of distant (wide) hybridization in plants. Ten decades since its discovery, attempts to unravel the molecular mechanism behind this process remained elusive due to a lack of genetic tools and genomic resources in the species exhibiting UGE. Hence, its successful adoption in agronomic crops for in planta (in vivo) haploid production remains implausible. Recently, Arabidopsis thaliana has emerged as a model system to unravel the molecular basis of UGE. It is now possible to simulate the genetic consequences of distant crosses in an A. thaliana intraspecific cross by a simple modification of centromeres, via the manipulation of the centromere-specific histone H3 variant gene, CENH3. Thus, the experimental advantages conferred by A. thaliana have been used to elucidate and exploit the benefits of UGE in crop breeding. In this review, we discuss developments and prospects of CENH3 gene-mediated UGE and other in planta haploid induction strategies to illustrate its potential in expediting plant breeding and genetics in A. thaliana and other model plants.
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Affiliation(s)
- Tejas Thondehaalmath
- School of Biology, Indian Institute of Science Education and Research (IISER)- Thiruvananthapuram, Vithura, Kerala, India
| | - Dilsher Singh Kulaar
- School of Biology, Indian Institute of Science Education and Research (IISER)- Thiruvananthapuram, Vithura, Kerala, India
| | - Ramesh Bondada
- School of Biology, Indian Institute of Science Education and Research (IISER)- Thiruvananthapuram, Vithura, Kerala, India
| | - Ravi Maruthachalam
- School of Biology, Indian Institute of Science Education and Research (IISER)- Thiruvananthapuram, Vithura, Kerala, India
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22
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Villela D, Mazzonetto PC, Migliavacca MP, Perrone E, Guida G, Milanezi MFG, Jorge AAL, Ribeiro-Bicudo LA, Kok F, Campagnari F, de Rosso-Giuliani L, da Costa SS, Vianna-Morgante AM, Pearson PL, Krepischi ACV, Rosenberg C. Congenital chromoanagenesis in the routine postnatal chromosomal microarray analyses. Am J Med Genet A 2021; 185:2335-2344. [PMID: 33988290 DOI: 10.1002/ajmg.a.62237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 11/07/2022]
Abstract
Chromosomal microarray analyses (CMA) have greatly increased both the yield and diagnostic accuracy of postnatal analysis; it has been used as a first-tier cytogenetic test in patients with intellectual disability, autism spectrum disorder, and multiple congenital abnormalities. During the last 15 years, we performed CMA in approximately 8,000 patients with neurodevelopmental and/or congenital disorders, of which 13 (0.16%) genetically catastrophic complex chromosomal rearrangements were identified. These ultrarare rearrangements showed clustering of breakpoints, characteristic of chromoanagenesis events. Al1 13 complex events display underlying formation mechanisms, originating either by a synchronization of the shattering of clustered chromosome regions in which regional asynchrony of DNA replication may be one of the main causes of disruption. We provide an overview of the copy number profiling in these patients. Although several previous studies have suggested that chromoanagenesis is often a genetic disease source in postnatal diagnostic screening, due to either the challenge of clinical interpretation of these complex rearrangements or the limitation of microarray resolution relative to the small size and complexity of chromogenic induced chromosome abnormalities, bringing further attention and to study its occurrence in the clinical setting is extremely important.
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Affiliation(s)
- Darine Villela
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,GeneOne, DASA, Brazil
| | | | | | - Eduardo Perrone
- GeneOne, DASA, Brazil.,Department of Clinical Genetics, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | | | | | - Alexander A L Jorge
- Genetic Endocrinology Unit, Laboratory of Cellular and Molecular Endocrinology LIM25, Division of Endocrinology and Metabology, Clinical Hospital of University of São Paulo Medical School (FMUSP), São Paulo, Brazil
| | | | | | | | - Liane de Rosso-Giuliani
- University Hospital Maria Aparecida Pedrossian, Federal University of Mato Grosso Do Sul (HUMAP-UFMS), Campo Grande, Brazil
| | - Silvia Souza da Costa
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Angela M Vianna-Morgante
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Peter L Pearson
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,GeneOne, DASA, Brazil
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23
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Zhao J, Li H, Chen G, Du L, Xu P, Zhang X, Xie M, Cao T, Li H. Aneuploid abortion correlates positively with MAD1 overexpression and miR-125b down-regulation. Mol Cytogenet 2021; 14:22. [PMID: 33902659 PMCID: PMC8074413 DOI: 10.1186/s13039-021-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aneuploidy is the most frequent cause of early-embryo abortion. Any defect in chromosome segregation would fail to satisfy the spindle assembly checkpoint (SAC) during mitosis, halting metaphase and causing aneuploidy. The mitotic checkpoint complex (MCC), comprising MAD1, MAD2, Cdc20, BUBR1 and BUB3, plays a vital role in SAC activation. Studies have confirmed that overexpression of MAD2 and BUBR1 can facilitate correct chromosome segregation and embryo stability. Research also proves that miR-125b negatively regulates MAD1 expression by binding to its 3'UTR. However, miR-125b, Mad1 and Bub3 gene expression in aneuploid embryos of spontaneous abortion has not been reported to date. METHODS In this study, embryonic villi from miscarried pregnancies were collected and divided into two groups (aneuploidy and euploidy) based on High-throughput ligation-dependent probe amplification (HLPA) and Fluorescence in situ hybridization (FISH) analyses. RNA levels of miR-125b, MAD1 and BUB3 were detected by Quantitative real-time PCR (qRT-PCR); protein levels of MAD1 and BUB3 were analysed by Western blotting. RESULTS statistical analysis (p < 0.05) showed that miR-125b and BUB3 were significantly down-regulated in the aneuploidy group compared to the control group and that MAD1 was significantly up-regulated. Additionally, the MAD1 protein level was significantly higher in aneuploidy abortion villus, but BUB3 protein was only mildly increased. Correlation analysis revealed that expression of MAD1 correlated negatively with miR-125b. CONCLUSION These results suggest that aneuploid abortion correlates positively with MAD1 overexpression, which might be caused by insufficient levels of miR-125b. Taken together, our findings first confirmed the negative regulatory mode between MAD1 and miR-125b, providing a basis for further mechanism researches in aneuploid abortion.
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Affiliation(s)
- Juan Zhao
- Department of the Clinical Laboratory, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangdong, 510800, China
| | - Hui Li
- Department of Internal Medicine, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangdong, 510800, China
| | - Guangxin Chen
- Department of the Clinical Laboratory, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangdong, 510800, China
| | - Lijun Du
- Department of the Clinical Laboratory, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangdong, 510800, China
| | - Peiyan Xu
- Department of Internal Medicine, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangdong, 510800, China
| | - Xiaoli Zhang
- Department of Obstetrics and Gynaecology, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangdong, 510800, China
| | - Min Xie
- Central Laboratory of Birth Defects Prevention and Control, Ningbo Women & Children's Hospital, Ningbo, 315000, Zhejiang, China
| | - Tiansheng Cao
- Surgical Department, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangdong, 510800, China.
| | - Haibo Li
- Central Laboratory of Birth Defects Prevention and Control, Ningbo Women & Children's Hospital, Ningbo, 315000, Zhejiang, China.
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24
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Arya P, Hodge JC, Matlock PA, Vance GH, Breman AM. Two Patients with Complex Rearrangements Suggestive of Germline Chromoanagenesis. Cytogenet Genome Res 2021; 160:671-679. [PMID: 33535208 DOI: 10.1159/000512898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/09/2020] [Indexed: 11/19/2022] Open
Abstract
Chromoanagenesis, a phenomenon characterized by complex chromosomal rearrangement and reorganization events localized to a limited number of genomic regions, includes the subcategories chromothripsis, chromoanasynthesis, and chromoplexy. Although definitions of these terms are evolving, constitutional chromoanagenesis events have been reported in a limited number of patients with variable phenotypes. We report on 2 cases with complex genomic events characterized by multiple copy number gains and losses confined to a single chromosome region, which are suggestive of constitutional chromoanagenesis. Case 1 is a 43-year-old male with intellectual disability and recently developed generalized tonic-clonic seizures. Chromosomal microarray analysis identified a complex rearrangement involving chromosome region 14q31.1q32.2, consisting of 16 breakpoints ranging in size from 0.2 to 6.2 Mb, with 5 segments of normal copy number present between these alterations. Interestingly, this case represents the oldest known patient with a complex rearrangement indicative of constitutional chromoanagenesis. Case 2 is a 2-year-old female with developmental delay, speech delay, low muscle tone, and seizures. Chromosomal microarray analysis identified a complex rearrangement consisting of 28 breakpoints localized to 18q21.32q23. The size of the copy number alterations ranged from 0.042 to 5.1 Mb, flanked by 12 small segments of normal copy number. These cases add to a growing body of literature demonstrating complex chromosomal rearrangements as a disease mechanism for congenital anomalies.
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Affiliation(s)
- Priyanka Arya
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jennelle C Hodge
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Peggy A Matlock
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Gail H Vance
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amy M Breman
- IU Genetic Testing Laboratories, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA,
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25
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Abstract
Bladder cancer has been successfully treated with immunotherapy, whereas prostate cancer is a cold tumor with inadequate immune-related treatment response. A greater understanding of the tumor microenvironment and methods for harnessing the immune system to address tumor growth will be needed to improve immunotherapies for both prostate and bladder cancer. Here, we provide an overview of prostate and bladder cancer, including fundamental aspects of the disease and treatment, the elaborate cellular makeup of the tumor microenvironment, and methods for exploiting relevant pathways to develop more effective treatments.
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26
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Eisfeldt J, Pettersson M, Petri A, Nilsson D, Feuk L, Lindstrand A. Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier. Hum Genet 2020; 140:775-790. [PMID: 33315133 PMCID: PMC8052244 DOI: 10.1007/s00439-020-02242-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
Chromoanagenesis is a genomic event responsible for the formation of complex structural chromosomal rearrangements (CCRs). Germline chromoanagenesis is rare and the majority of reported cases are associated with an affected phenotype. Here, we report a healthy female carrying two de novo CCRs involving chromosomes 4, 19, 21 and X and chromosomes 7 and 11, respectively, with a total of 137 breakpoint junctions (BPJs). We characterized the CCRs using a hybrid-sequencing approach, combining short-read sequencing, nanopore sequencing, and optical mapping. The results were validated using multiple cytogenetic methods, including fluorescence in situ hybridization, spectral karyotyping, and Sanger sequencing. We identified 137 BPJs, which to our knowledge is the highest number of reported breakpoint junctions in germline chromoanagenesis. We also performed a statistical assessment of the positioning of the breakpoints, revealing a significant enrichment of BPJ-affecting genes (96 intragenic BPJs, 26 genes, p < 0.0001), indicating that the CCRs formed during active transcription of these genes. In addition, we find that the DNA fragments are unevenly and non-randomly distributed across the derivative chromosomes indicating a multistep process of scattering and re-joining of DNA fragments. In summary, we report a new maximum number of BPJs (137) in germline chromoanagenesis. We also show that a hybrid sequencing approach is necessary for the correct characterization of complex CCRs. Through in-depth statistical assessment, it was found that the CCRs most likely was formed through an event resembling chromoplexy—a catastrophic event caused by erroneous transcription factor binding.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Petri
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Lars Feuk
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden. .,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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27
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Sessa M, Cavazzini F, Cavallari M, Rigolin GM, Cuneo A. A Tangle of Genomic Aberrations Drives Multiple Myeloma and Correlates with Clinical Aggressiveness of the Disease: A Comprehensive Review from a Biological Perspective to Clinical Trial Results. Genes (Basel) 2020; 11:E1453. [PMID: 33287156 PMCID: PMC7761770 DOI: 10.3390/genes11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Multiple myeloma (MM) is a genetically heterogeneous disease, in which the process of tumorigenesis begins and progresses through the appearance and accumulation of a tangle of genomic aberrations. Several are the mechanisms of DNA damage in MM, varying from single nucleotide substitutions to complex genomic events. The timing of appearance of aberrations is well studied due to the natural history of the disease, that usually progress from pre-malignant to malignant phase. Different kinds of aberrations carry different prognostic significance and have been associated with drug resistance in some studies. Certain genetic events are well known to be associated with prognosis and are incorporated in risk evaluation in MM at diagnosis in the revised International Scoring System (R-ISS). The significance of some other aberrations needs to be further explained. Since now, few phase 3 randomized trials included analysis on patient's outcomes according to genetic risk, and further studies are needed to obtain useful data to stratify the choice of initial and subsequent treatment in MM.
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Affiliation(s)
- Mariarosaria Sessa
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
| | - Francesco Cavazzini
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
| | - Maurizio Cavallari
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
| | - Gian Matteo Rigolin
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
| | - Antonio Cuneo
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S.Anna, University of Ferrara, 44121 Ferrara, Italy
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28
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The Cytogenomic "Theory of Everything": Chromohelkosis May Underlie Chromosomal Instability and Mosaicism in Disease and Aging. Int J Mol Sci 2020; 21:ijms21218328. [PMID: 33171981 PMCID: PMC7664247 DOI: 10.3390/ijms21218328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/28/2023] Open
Abstract
Mechanisms for somatic chromosomal mosaicism (SCM) and chromosomal instability (CIN) are not completely understood. During molecular karyotyping and bioinformatic analyses of children with neurodevelopmental disorders and congenital malformations (n = 612), we observed colocalization of regular chromosomal imbalances or copy number variations (CNV) with mosaic ones (n = 47 or 7.7%). Analyzing molecular karyotyping data and pathways affected by CNV burdens, we proposed a mechanism for SCM/CIN, which had been designated as “chromohelkosis” (from the Greek words chromosome ulceration/open wound). Briefly, structural chromosomal imbalances are likely to cause local instability (“wreckage”) at the breakpoints, which results either in partial/whole chromosome loss (e.g., aneuploidy) or elongation of duplicated regions. Accordingly, a function for classical/alpha satellite DNA (protection from the wreckage towards the centromere) has been hypothesized. Since SCM and CIN are ubiquitously involved in development, homeostasis and disease (e.g., prenatal development, cancer, brain diseases, aging), we have metaphorically (ironically) designate the system explaining chromohelkosis contribution to SCM/CIN as the cytogenomic “theory of everything”, similar to the homonymous theory in physics inasmuch as it might explain numerous phenomena in chromosome biology. Recognizing possible empirical and theoretical weaknesses of this “theory”, we nevertheless believe that studies of chromohelkosis-like processes are required to understand structural variability and flexibility of the genome.
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29
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Anzick S, Thurm A, Burkett S, Velez D, Cho E, Chlebowski C, Virtaneva K, Bruno D, Martin CB, Lang DM, Brooks B, Martens C, McDermott DH, Murphy PM. Chromoanasynthesis as a cause of Jacobsen syndrome. Am J Med Genet A 2020; 182:2533-2539. [PMID: 32841469 PMCID: PMC11007684 DOI: 10.1002/ajmg.a.61824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 01/02/2023]
Abstract
Jacobsen syndrome (MIM #147791) is a rare multisystem genomic disorder involving craniofacial abnormalities, intellectual disability, other neurodevelopmental defects, and terminal truncation of chromosome 11q, typically deleting ~170 to >340 genes. We describe the first case of Jacobsen syndrome caused by congenital chromoanasynthesis, an extreme form of complex chromosomal rearrangement. Six duplications and five deletions occurred on one copy of chromosome 11q with microhomology signatures in the breakpoint junctions, indicating an all-at-once replication-based rearrangement mechanism in a gametocyte or early post-zygotic cell. Eighteen genes were deleted from the Jacobsen region, including KIRREL3, which is associated with intellectual disability.
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Affiliation(s)
- Sarah Anzick
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Audrey Thurm
- National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | | | - Daniel Velez
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Elena Cho
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Colby Chlebowski
- National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Kimmo Virtaneva
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Daniel Bruno
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Clare B. Martin
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - David M. Lang
- Warren Grant Magnuson Clinical Center, NIH, Bethesda, MD 20892, USA
| | - Brian Brooks
- National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Craig Martens
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - David H. McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Philip M. Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
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30
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Mayrose I, Lysak MA. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biol Evol 2020; 13:5923296. [PMID: 33566095 PMCID: PMC7875004 DOI: 10.1093/gbe/evaa220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
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Affiliation(s)
- Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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31
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Lemaire J, Larrue R, Perrais M, Cauffiez C, Pottier N. [Fundamental aspects of oncogenesis]. Bull Cancer 2020; 107:1148-1160. [PMID: 33039132 DOI: 10.1016/j.bulcan.2020.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/13/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Tumorigenesis has traditionally been considered as a multi-step process involving the activation of oncogenes as well as the inactivation of tumor suppressor genes. However, the mechanisms driving cancer initiation and progression are not restricted to molecular alterations and instead should be viewed as a complex process that interfaces with the entire organism. This didactic review provides an integrated and global view of the key fundamental principles of cancer development.
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Affiliation(s)
- Julie Lemaire
- CHU de Lille, université Lille, CNRS, Inserm, UMR9020-UMR-S 1277, 59000 Lille, France
| | - Romain Larrue
- CHU de Lille, service de toxicologie et génopathies, 59000 Lille, France
| | - Michael Perrais
- CHU de Lille, université Lille, CNRS, Inserm, UMR9020-UMR-S 1277, 59000 Lille, France
| | - Christelle Cauffiez
- CHU de Lille, université Lille, CNRS, Inserm, UMR9020-UMR-S 1277, 59000 Lille, France
| | - Nicolas Pottier
- CHU de Lille, université Lille, CNRS, Inserm, UMR9020-UMR-S 1277, 59000 Lille, France; CHU de Lille, service de toxicologie et génopathies, 59000 Lille, France.
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32
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Using telomeric chromosomal aberrations to evaluate clastogen-induced genomic instability in mammalian cells. Chromosome Res 2020; 28:259-276. [DOI: 10.1007/s10577-020-09641-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/06/2020] [Accepted: 09/06/2020] [Indexed: 12/13/2022]
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33
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Kirsch-Volders M, Bolognesi C, Ceppi M, Bruzzone M, Fenech M. Micronuclei, inflammation and auto-immune disease. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108335. [PMID: 33339583 DOI: 10.1016/j.mrrev.2020.108335] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 12/16/2022]
Abstract
Auto-immune diseases (AUD) are characterized by an immune response to antigenic components of the host itself. The etiology of AUD is not well understood. The available evidence points to an interaction between genetic, epigenetic, environmental, infectious and life-style factors. AUD are more prevalent in women than in men; sex hormones play a crucial role in this sex bias. Micronuclei (MN) emerged as a new player in the induction of AUD, based on the capacity of DNA-sensors to detect self-DNA that leaks into the cytoplasm from disrupted MN and induce the cGAS-STING pathway triggering an innate auto-immune response and chronic inflammation. It was found that inflammation can induce MN and MN can induce inflammation, leading to a vicious inflammation-oxidative-DNA damage-MN-formation-chromothripsis cycle. MN originating from sex chromosome-loss may induce inflammation and AUD. We performed a systematic review of studies reporting MN in patients with systemic or organ-specific AUD. A meta-analysis was performed on lymphocyte MN in diabetes mellitus (10 studies, 457 patients/290 controls) and Behcet's disease (3 studies, 100 patients/70 controls) and for buccal MN in diabetes mellitus (11 studies, 507 patients/427 controls). A statistically significant increase in patients compared to controls was found in the meta-analyses providing an indication of an association between MN and AUD. A 36%-higher mean-MRi in buccal cells (3.8+/-0.7) was found compared to lymphocytes (2.8+/-0.7)(P = 0.01). The meta-MRi in lymphocytes and buccal cells (1.7 and 3.0 respectively) suggest that buccal cells may be more sensitive. To assess their relative sensitivity, studies with measurements from the same subjects would be desirable. It is important that future studies (i) investigate, in well-designed powered studies, the prospective association of MN-formation with AUD and (ii) explore the molecular mechanisms by which chromosome shattering in MN and the release of chromatin fragments from MN lead to the formation of auto-antibodies.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Claudia Bolognesi
- Environmental Carcinogenesis Unit, Ospedale Policlinico San Martino, 16132 Genoa, Italy.
| | - Marcello Ceppi
- Unit of Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Marco Bruzzone
- Unit of Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Michael Fenech
- Genome Health Foundation, North Brighton, 5048, Australia; Clinical and Health Sciences, University of South Australia, SA 5000, Australia
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Di Pietro P, D'Auria R, Viggiano A, Ciaglia E, Meccariello R, Russo RD, Puca AA, Vecchione C, Nori SL, Santoro A. Bisphenol A induces DNA damage in cells exerting immune surveillance functions at peripheral and central level. CHEMOSPHERE 2020; 254:126819. [PMID: 32334263 DOI: 10.1016/j.chemosphere.2020.126819] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 05/25/2023]
Abstract
Bisphenol A (BPA) is a synthetic xenoestrogen diffused worldwide. Humans are chronically exposed to low doses of BPA from food and drinks, thus BPA accumulates in tissues posing human health risk. In this study, we investigated the effects of BPA on peripheral blood mononuclear cells (PBMC) from human healthy donors, and in glia and microglia of rat offspring at postnatal day 17 (17PND) from pregnant females who received BPA soon after coupling and during lactation and weaning. Results indicated that BPA affected Phytoemagglutinin (PHA) stimulated PBMC proliferation causing an S-phase cell cycle accumulation at nanomolar concentrations while BPA was almost ineffective in resting PBMC. Furthermore, BPA induced chromosome aberrations and the appearance of shattered cells characterized by high number of fragmented and pulverized chromosomes, suggesting that the compound could cause a massive genomic rearrangement by inducing catastrophic events. The BPA-induced DNA damage was observed mainly in TCD4+ and TCD8+ subsets of T lymphocytes and was mediated by the increase of ERK1/2 phosphorylation, p21/Waf1 and PARP1 protein expression. Intriguingly, we observed for the first time that BPA-induced effects were associated to a sex specific modulation of ERα and ERβ in human PBMC. Immunofluorescence analysis of rat hippocampus corroborated in vitro findings showing that BPA induced ɣH2AX phosphorylation in microglia and astrocytosis by decreasing ERα expression within the dentate gyrus. Overall these results suggest that BPA can alter immune surveillance functions at both peripheral and central level with a potential risk for cancer, neuroinflammation and neurodegeneration.
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Affiliation(s)
- Paola Di Pietro
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Raffaella D'Auria
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Andrea Viggiano
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Elena Ciaglia
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Rosaria Meccariello
- Department of Movement Sciences and Wellbeing, Parthenope University of Naples, 80133, Naples, Italy
| | - Rossana Dello Russo
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Annibale Alessandro Puca
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy; Cardiovascular Research Unit, IRCCS MultiMedica, 20138, Milan, Italy
| | - Carmine Vecchione
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy; IRCCS Neuromed, Department of Vascular Physiopathology, 86077, Pozzilli, IS, Italy
| | | | - Antonietta Santoro
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy.
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Imaizumi T, Yamamoto-Shimojima K, Yanagishita T, Ondo Y, Nishi E, Okamoto N, Yamamoto T. Complex chromosomal rearrangements of human chromosome 21 in a patient manifesting clinical features partially overlapped with that of Down syndrome. Hum Genet 2020; 139:1555-1563. [PMID: 32535809 DOI: 10.1007/s00439-020-02196-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/06/2020] [Indexed: 01/16/2023]
Abstract
The chromosomal region critical in Down syndrome has long been analyzed through genotype-phenotype correlation studies using data from many patients with partial trisomy 21. Owing to that, a relatively small region of human chromosome 21 (35.9 ~ 38.0 Mb) has been considered as Down syndrome critical region (DSCR). In this study, microarray-based comparative genomic hybridization analysis identified complex rearrangements of chromosome 21 in a patient manifesting clinical features partially overlapped with that of Down syndrome. Although the patient did not show up-slanting palpebral fissures and single transverse palmar creases, other symptoms were consistent with Down syndrome. Rearrangements were analyzed by whole-genome sequencing using Nanopore long-read sequencing. The analysis revealed that chromosome 21 was fragmented into seven segments and reassembled by six connected points. Among 12 breakpoints, 5 are located within the short region and overlapped with repeated segments. The rearrangement resulted in a maximum gain of five copies, but no region showed loss of genomic copy numbers. Breakpoint-junctions showed no homologous region. Based on these findings, chromoanasynthesis was considered as the mechanism. Although the distal 21q22.13 region was not included in the aberrant regions, some of the genes located on the duplicated regions, SOD1, SON, ITSN1, RCAN1, and RUNX1, were considered as possible candidate genes for clinical features of the patient. We discussed the critical region for Down syndrome, with the literature review.
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Affiliation(s)
- Taichi Imaizumi
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Keiko Yamamoto-Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan
- Japan Society for the Promotion of Science (RPD), Tokyo, Japan
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
| | - Tomoe Yanagishita
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yumiko Ondo
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan
| | - Eriko Nishi
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan.
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan.
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan.
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.
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Analyses of breakpoint junctions of complex genomic rearrangements comprising multiple consecutive microdeletions by nanopore sequencing. J Hum Genet 2020; 65:735-741. [PMID: 32355308 DOI: 10.1038/s10038-020-0762-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 12/19/2022]
Abstract
The widespread use of genomic copy number analysis has revealed many previously unknown genomic structural variations, including some which are more complex. In this study, three consecutive microdeletions were identified in the same chromosome by microarray-based comparative genomic hybridization (aCGH) analysis for a patient with a neurodevelopmental disorder. Subsequent fluorescence in situ hybridization (FISH) analyses unexpectedly suggested complicated translocations and inversions. For better understanding of the mechanism, breakpoint junctions were analyzed by nanopore sequencing, as a new long-read whole-genome sequencing (WGS) tool. The results revealed a new chromosomal disruption, giving rise to four junctions in chromosome 7. According the sequencing results of breakpoint junctions, all junctions were considered as the consequence of multiple double-strand breaks and the reassembly of DNA fragments by nonhomologous end-joining, indicating chromothripsis. KMT2E, located within the deletion region, was considered as the gene responsible for the clinical features of the patient. Combinatory usage of aCGH and FISH analyses would be recommended for interpretation of structural variations analyzed through WGS.
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Centromere scission drives chromosome shuffling and reproductive isolation. Proc Natl Acad Sci U S A 2020; 117:7917-7928. [PMID: 32193338 DOI: 10.1073/pnas.1918659117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A fundamental characteristic of eukaryotic organisms is the generation of genetic variation via sexual reproduction. Conversely, significant large-scale genome structure variations could hamper sexual reproduction, causing reproductive isolation and promoting speciation. The underlying processes behind large-scale genome rearrangements are not well understood and include chromosome translocations involving centromeres. Recent genomic studies in the Cryptococcus species complex revealed that chromosome translocations generated via centromere recombination have reshaped the genomes of different species. In this study, multiple DNA double-strand breaks (DSBs) were generated via the CRISPR/Cas9 system at centromere-specific retrotransposons in the human fungal pathogen Cryptococcus neoformans The resulting DSBs were repaired in a complex manner, leading to the formation of multiple interchromosomal rearrangements and new telomeres, similar to chromothripsis-like events. The newly generated strains harboring chromosome translocations exhibited normal vegetative growth but failed to undergo successful sexual reproduction with the parental wild-type strain. One of these strains failed to produce any spores, while another produced ∼3% viable progeny. The germinated progeny exhibited aneuploidy for multiple chromosomes and showed improved fertility with both parents. All chromosome translocation events were accompanied without any detectable change in gene sequences and thus suggest that chromosomal translocations alone may play an underappreciated role in the onset of reproductive isolation and speciation.
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Plesser Duvdevani M, Pettersson M, Eisfeldt J, Avraham O, Dagan J, Frumkin A, Lupski JR, Lindstrand A, Harel T. Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome. Am J Med Genet A 2020; 182:1143-1151. [PMID: 32125084 DOI: 10.1002/ajmg.a.61539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 02/05/2023]
Abstract
Clinical laboratory diagnostic evaluation of the genomes of children with suspected genetic disorders, including chromosomal microarray and exome sequencing, cannot detect copy number neutral genomic rearrangements such as inversions, balanced translocations, and complex chromosomal rearrangements (CCRs). We describe an infant with a clinical diagnosis of Cornelia de Lange syndrome (CdLS) in whom chromosome analysis revealed a de novo complex balanced translocation, 46,XY,t(5;7;6)(q11.2;q32;q13)dn. Subsequent molecular characterization by whole-genome sequencing (WGS) identified 23 breakpoints, delineating segments derived from four chromosomes (5;6;7;21) in ancestral or inverted orientation. One of the breakpoints disrupted a known CdLS gene, NIPBL. Further investigation revealed paternal origin of the CCR allele, clustering of the breakpoint junctions, and molecular repair signatures suggestive of a single catastrophic event. Notably, very short DNA segments (25 and 41 bp) were included in the reassembled chromosomes, lending additional support that the DNA repair machinery can detect and repair such segments. Interestingly, there was an independent paternally derived miniscule complex rearrangement, possibly predisposing to subsequent genomic instability. In conclusion, we report a CCR causing a monogenic Mendelian disorder, urging WGS analysis of similar unsolved cases with suspected Mendelian disorders. Breakpoint analysis allowed for identification of the underlying molecular diagnosis and implicated chromoanagenesis in CCR formation.
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Affiliation(s)
- Morasha Plesser Duvdevani
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - 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
| | - Ortal Avraham
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Judith Dagan
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ayala Frumkin
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - 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
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Balachandran P, Beck CR. Structural variant identification and characterization. Chromosome Res 2020; 28:31-47. [PMID: 31907725 PMCID: PMC7131885 DOI: 10.1007/s10577-019-09623-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/15/2019] [Accepted: 11/24/2019] [Indexed: 01/06/2023]
Abstract
Structural variant (SV) differences between human genomes can cause germline and mosaic disease as well as inter-individual variation. De-regulation of accurate DNA repair and genomic surveillance mechanisms results in a large number of SVs in cancer. Analysis of the DNA sequences at SV breakpoints can help identify pathways of mutagenesis and regions of the genome that are more susceptible to rearrangement. Large-scale SV analyses have been enabled by high-throughput genome-level sequencing on humans in the past decade. These studies have shed light on the mechanisms and prevalence of complex genomic rearrangements. Recent advancements in both sequencing and other mapping technologies as well as calling algorithms for detection of genomic rearrangements have helped propel SV detection into population-scale studies, and have begun to elucidate previously inaccessible regions of the genome. Here, we discuss the genomic organization of simple and complex SVs, the molecular mechanisms of their formation, and various ways to detect them. We also introduce methods for characterizing SVs and their consequences on human genomes.
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Affiliation(s)
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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Zhang Y, Zeng L, Zhou C, Li Y, Wu L, Xia C, Jiang W, Hu Y, Liao D, Xiao L, Liu L, Yang H, Xiong Y, Guan R, Lizaso A, Mansfield AS, Yang N. Detection of Nonreciprocal/Reciprocal ALK Translocation as Poor Predictive Marker in Patients With First-Line Crizotinib-Treated ALK-Rearranged NSCLC. J Thorac Oncol 2020; 15:1027-1036. [PMID: 32112982 DOI: 10.1016/j.jtho.2020.02.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
Abstract
INTRODUCTION During nonreciprocal/reciprocal translocation process, 5'-anaplastic lymphoma kinase (ALK) sometimes gets retained in the genome and is detectable by next-generation sequencing; however, no study has investigated its clinical significance. Our study aimed to assess the impact of harboring 5'-ALK on the efficacy of crizotinib. METHODS A total of 150 patients with next-generation sequencing-identified ALK-rearranged NSCLC from March 2014 to July 2018 at the Hunan Cancer Hospital were enrolled in this study. The efficacy of crizotinib as first-line therapy was evaluated in 112 patients according to the retention of 5'-ALK. RESULTS Among the 150 patients with NSCLC, nonreciprocal/reciprocal translocation was detected in 18.7% (28 of 150), and 3'-ALK fusion alone was detected in 81.3% (122 of 150). Among the 112 patients who received first-line crizotinib, 89 had 3'-ALK fusion alone (79 echinoderm microtubule associated protein-like 4 [EML4]-ALK and 10 non-EML4-ALK), and 23 had nonreciprocal/reciprocal ALK translocation. Among the patients with nonreciprocal/reciprocal ALK translocation, three patients harbored dual concurrent 3'-ALK fusions. Patients with nonreciprocal/reciprocal ALK translocation had higher incidence of brain metastasis at baseline than those with 3'-ALK fusion alone (39.1% versus 13.4%, p = 0.028). Crizotinib-treated patients with nonreciprocal/reciprocal ALK translocation had significantly shorter median progression-free survival (PFS) compared with patients carrying 3'-ALK fusion alone (6.1 m versus 12.0 m, p = 0.001) or with EML4-ALK fusion alone (6.1 m versus 12.6 m, p = 0.001). Multivariate analysis revealed that harboring nonreciprocal/reciprocal ALK translocation was an independent predictor of worse PFS for crizotinib-treated ALK-rearranged NSCLC (p = 0.0046). CONCLUSIONS Presence of nonreciprocal/reciprocal ALK translocation was predictive for worse PFS and greater likelihood of baseline brain metastases in patients with ALK-rearranged NSCLC who received first-line crizotinib.
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Affiliation(s)
- Yongchang Zhang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Liang Zeng
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Chunhua Zhou
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Yizhi Li
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Lin Wu
- Department of Medical Oncology, Second Chest Cancer Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, People's Republic of China
| | - Chen Xia
- Department of Hepatology, Hunan Cancer Hospital, Changsha, People's Republic of China
| | - Wenjuan Jiang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Yijuan Hu
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Dehua Liao
- Department of Pharmacy, Hunan Cancer Hospital, Changsha, People's Republic of China
| | - Lili Xiao
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Li Liu
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Haiyan Yang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Yi Xiong
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Rui Guan
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China
| | - Analyn Lizaso
- Burning Rock Biotech, Guangzhou, People's Republic of China
| | | | - Nong Yang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, People's Republic of China.
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Pellestor F, Gatinois V. Chromoanagenesis: a piece of the macroevolution scenario. Mol Cytogenet 2020; 13:3. [PMID: 32010222 PMCID: PMC6988253 DOI: 10.1186/s13039-020-0470-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/05/2020] [Indexed: 01/04/2023] Open
Abstract
Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution. Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of “Hopeful Monsters” and the “Punctuated Equilibrium”. In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms. In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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Haploid Induction and Genome Instability. Trends Genet 2019; 35:791-803. [DOI: 10.1016/j.tig.2019.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/26/2019] [Accepted: 07/10/2019] [Indexed: 11/24/2022]
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Gökpınar İli E, Altıner Ş, Karabulut HG. Cytogenetic, Molecular, and Phenotypic Characterization of a Patient with de novo Derivative Chromosome 18 and Review of the Literature. Cytogenet Genome Res 2019; 159:74-80. [PMID: 31658462 DOI: 10.1159/000503574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 11/19/2022] Open
Abstract
We present a patient with a de novo derivative chromosome 18 which includes a terminal deletion of 18p and a terminal duplication of 18q accompanied by a cryptic duplication of 18p. The girl had mild dysmorphic features such as micro-retrognathia, upslanted palpebral fissures, bilateral epicanthus, high palate, low-set ears, short neck, and full cheeks. She also had an H-type tracheoesophageal fistula which required surgery. Her cognitive and motor skills were delayed. Karyotype analysis showed an additional segment on the short arm of chromosome 18. Chromosomal microarray revealed a 7.3-Mb terminal loss from 18p11.32 to 18p11.23, a 22.2-Mb terminal gain from 18q21.31 to 18q23, and a 3.9-Mb interstitial gain from 18p11.22 to 18p11.21. We hypothesize that the mother has gonadal mosaicism for normal chromosome 18, der(18)dup(p11.22p11.21), and der(18)dup(p11. 22p11.21)inv(18)(p11.22q21.31), or both the terminal del/dup and the interstitial duplication occurred simultaneously.
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Reece AS, Hulse GK. Impacts of cannabinoid epigenetics on human development: reflections on Murphy et. al. 'cannabinoid exposure and altered DNA methylation in rat and human sperm' epigenetics 2018; 13: 1208-1221. Epigenetics 2019; 14:1041-1056. [PMID: 31293213 PMCID: PMC6773386 DOI: 10.1080/15592294.2019.1633868] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recent data from the Kollins lab (‘Cannabinoid exposure and altered DNA methylation in rat and human sperm’ Epigenetics 2018; 13: 1208–1221) indicated epigenetic effects of cannabis use on sperm in man parallel those in rats and showed substantial shifts in both hypo- and hyper-DNA methylation with the latter predominating. This provides one likely mechanism for the transgenerational transmission of epigenomic instability with sperm as the vector. It therefore contributes important pathophysiological insights into the probable mechanisms underlying the epidemiology of prenatal cannabis exposure potentially explaining diverse features of cannabis-related teratology including effects on the neuraxis, cardiovasculature, immune stimulation, secondary genomic instability and carcinogenesis related to both adult and pediatric cancers. The potentially inheritable and therefore multigenerational nature of these defects needs to be carefully considered in the light of recent teratological and neurobehavioural trends in diverse jurisdictions such as the USA nationally, Hawaii, Colorado, Canada, France and Australia, particularly relating to mental retardation, age-related morbidity and oncogenesis including inheritable cancerogenesis. Increasing demonstrations that the epigenome can respond directly and in real time and retain memories of environmental exposures of many kinds implies that the genome-epigenome is much more sensitive to environmental toxicants than has been generally realized. Issues of long-term multigenerational inheritance amplify these concerns. Further research particularly on the epigenomic toxicology of many cannabinoids is also required.
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Affiliation(s)
- Albert Stuart Reece
- Division of Psychiatry, University of Western Australia , Crawley , Western Australia Australia.,School of Medical and Health Sciences, Edith Cowan University , Joondalup , Western Australia , Australia
| | - Gary Kenneth Hulse
- Division of Psychiatry, University of Western Australia , Crawley , Western Australia Australia.,School of Medical and Health Sciences, Edith Cowan University , Joondalup , Western Australia , Australia
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