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Di Stazio M, Zanus C, Faletra F, Pesaresi A, Ziccardi I, Morgan A, Girotto G, Costa P, Carrozzi M, d’Adamo AP, Musante L. Haploinsufficiency as a Foreground Pathomechanism of Poirer-Bienvenu Syndrome and Novel Insights Underlying the Phenotypic Continuum of CSNK2B-Associated Disorders. Genes (Basel) 2023; 14:genes14020250. [PMID: 36833176 PMCID: PMC9957394 DOI: 10.3390/genes14020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
CSNK2B encodes for the regulatory subunit of the casein kinase II, a serine/threonine kinase that is highly expressed in the brain and implicated in development, neuritogenesis, synaptic transmission and plasticity. De novo variants in this gene have been identified as the cause of the Poirier-Bienvenu Neurodevelopmental Syndrome (POBINDS) characterized by seizures and variably impaired intellectual development. More than sixty mutations have been described so far. However, data clarifying their functional impact and the possible pathomechanism are still scarce. Recently, a subset of CSNK2B missense variants affecting the Asp32 in the KEN box-like domain were proposed as the cause of a new intellectual disability-craniodigital syndrome (IDCS). In this study, we combined predictive functional and structural analysis and in vitro experiments to investigate the effect of two CSNK2B mutations, p.Leu39Arg and p.Met132LeufsTer110, identified by WES in two children with POBINDS. Our data prove that loss of the CK2beta protein, due to the instability of mutant CSNK2B mRNA and protein, resulting in a reduced amount of CK2 complex and affecting its kinase activity, may underlie the POBINDS phenotype. In addition, the deep reverse phenotyping of the patient carrying p.Leu39Arg, with an analysis of the available literature for individuals with either POBINDS or IDCS and a mutation in the KEN box-like motif, might suggest the existence of a continuous spectrum of CSNK2B-associated phenotypes rather than a sharp distinction between them.
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Affiliation(s)
- Mariateresa Di Stazio
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
| | - Caterina Zanus
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
| | - Alessia Pesaresi
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
| | - Ilaria Ziccardi
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
| | - Anna Morgan
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
| | - Giorgia Girotto
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Paola Costa
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
| | - Marco Carrozzi
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
| | - Adamo P. d’Adamo
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
- Correspondence:
| | - Luciana Musante
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”—Trieste, 34137 Trieste, Italy
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2
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Vervoort L, Vermeesch JR. The 22q11.2 Low Copy Repeats. Genes (Basel) 2022; 13:2101. [PMID: 36421776 PMCID: PMC9690962 DOI: 10.3390/genes13112101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 07/22/2023] Open
Abstract
LCR22s are among the most complex loci in the human genome and are susceptible to nonallelic homologous recombination. This can lead to a variety of genomic disorders, including deletions, duplications, and translocations, of which the 22q11.2 deletion syndrome is the most common in humans. Interrogating these phenomena is difficult due to the high complexity of the LCR22s and the inaccurate representation of the LCRs across different reference genomes. Optical mapping techniques, which provide long-range chromosomal maps, could be used to unravel the complex duplicon structure. These techniques have already uncovered the hypervariability of the LCR22-A haplotype in the human population. Although optical LCR22 mapping is a major step forward, long-read sequencing approaches will be essential to reach nucleotide resolution of the LCR22s and map the crossover sites. Accurate maps and sequences are needed to pinpoint potential predisposing alleles and, most importantly, allow for genotype-phenotype studies exploring the role of the LCR22s in health and disease. In addition, this research might provide a paradigm for the study of other rare genomic disorders.
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Nam DE, Jung SC, Yoo DH, Choi SS, Seo SY, Kim GH, Kim SJ, Nam SH, Choi BO, Chung KW. Axonal Charcot-Marie-Tooth neuropathy concurrent with distal and proximal weakness by translational elongation of the 3' UTR in NEFH. J Peripher Nerv Syst 2018; 22:200-207. [PMID: 28544463 DOI: 10.1111/jns.12223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/18/2017] [Accepted: 05/20/2017] [Indexed: 11/27/2022]
Abstract
Mutations in the NEFH gene encoding the heavy neurofilament protein are usually associated with neuronal damage and susceptibility to amyotrophic lateral sclerosis (ALS). Recently, frameshift variants in NEFH (p.Asp1004Glnfs*58 and p.Pro1008Alafs*56) have been reported to be the underlying cause of axonal Charcot-Marie-Tooth disease type 2CC (CMT2CC). The frameshift mutation resulted in a stop loss and translation of a cryptic amyloidogenic element (CAE) encoded by the 3' untranslated region (UTR). This study also identified a de novo c.3015_3027dup frameshift mutation predicting p.Lys1010Glnfs*57 in NEFH from a CMT2 family with an atypical clinical symptom of prominent proximal weakness. This mutation is located near the previously reported frameshift mutations, suggesting a mutational hotspot. Lower limb magnetic resonance imaging (MRI) revealed marked hyperintense signal changes in the thigh muscles compared with those in the calf muscles. Therefore, this study suggests that the stop loss and translational elongations by the 3' UTR of the NEFH mutations may be a relatively frequent genetic cause of axonal peripheral neuropathy with the specific characteristics of proximal dominant weakness.
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Affiliation(s)
- Da Eun Nam
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Sung-Chul Jung
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea
| | - Da Hye Yoo
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Sun Seong Choi
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Sung-Yum Seo
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Gwang Hoon Kim
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Song Ja Kim
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Soo Hyun Nam
- Department of Biological Sciences, Kongju National University, Gongju, Korea.,Department of Neurology, and Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byung-Ok Choi
- Department of Neurology, and Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju, Korea
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Delihas N. A family of long intergenic non-coding RNA genes in human chromosomal region 22q11.2 carry a DNA translocation breakpoint/AT-rich sequence. PLoS One 2018; 13:e0195702. [PMID: 29668722 PMCID: PMC5906017 DOI: 10.1371/journal.pone.0195702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
FAM230C, a long intergenic non-coding RNA (lincRNA) gene in human chromosome 13 (chr13) is a member of lincRNA genes termed family with sequence similarity 230. An analysis using bioinformatics search tools and alignment programs was undertaken to determine properties of FAM230C and its related genes. Results reveal that the DNA translocation element, the Translocation Breakpoint Type A (TBTA) sequence, which consists of satellite DNA, Alu elements, and AT-rich sequences is embedded in the FAM230C gene. Eight lincRNA genes related to FAM230C also carry the TBTA sequences. These genes were formed from a large segment of the 3’ half of the FAM230C sequence duplicated in chr22, and are specifically in regions of low copy repeats (LCR22)s, in or close to the 22q.11.2 region. 22q11.2 is a chromosomal segment that undergoes a high rate of DNA translocation and is prone to genetic deletions. FAM230C-related genes present in other chromosomes do not carry the TBTA motif and were formed from the 5’ half region of the FAM230C sequence. These findings identify a high specificity in lincRNA gene formation by gene sequence duplication in different chromosomes.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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5
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Alternative outcomes of pathogenic complex somatic structural variations in the genomes of NF1 and NF2 patients. Neurogenetics 2017; 18:169-174. [PMID: 28285357 DOI: 10.1007/s10048-017-0512-x] [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: 10/04/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
Abstract
Multiplex ligation-dependent probe amplification (MLPA) has been widely used to identify copy-number variations (CNVs), but MLPA's sensitivity and specificity in mosaic CNV detection are largely unknown. Here, we present two mosaic deletions identified by MLPA as NF1 deletion of exons 17-21 and NF2 deletion of exons 9-10. Through cDNA analysis, genomic breakpoint-spanning PCR and Sanger sequencing, we found however both NF1 and NF2 deletions are each composed of two consecutive deletions, which cannot be differentiated by MLPA. Importantly, these consecutive deletions are most likely originating from a single genomic rearrangement and have been preserved independently in different populations of cells.
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Nilsson D, Pettersson M, Gustavsson P, Förster A, Hofmeister W, Wincent J, Zachariadis V, Anderlid BM, Nordgren A, Mäkitie O, Wirta V, Käller M, Vezzi F, Lupski JR, Nordenskjöld M, Lundberg ES, Carvalho CMB, Lindstrand A. Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. Hum Mutat 2017; 38:180-192. [PMID: 27862604 PMCID: PMC5225243 DOI: 10.1002/humu.23146] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 11/07/2022]
Abstract
Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.
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Affiliation(s)
- Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Alisa Förster
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Children's Hospital, Helsinki University Central Hospital and University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Valtteri Wirta
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, 171 71 Stockholm, Sweden
| | - Max Käller
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, 171 71 Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston TX, USA
- Texas Children’s Hospital, 77030 Houston TX, USA
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Claudia M. B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston TX, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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7
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Effects of Replication and Transcription on DNA Structure-Related Genetic Instability. Genes (Basel) 2017; 8:genes8010017. [PMID: 28067787 PMCID: PMC5295012 DOI: 10.3390/genes8010017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/21/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.
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8
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Banerjee S, Dai Y, Liang S, Chen H, Wang Y, Tang L, Wu J, Huang H. A novel mutation in NF1 is associated with diverse intra-familial phenotypic variation and astrocytoma in a Chinese family. J Clin Neurosci 2016; 31:182-4. [PMID: 27234610 DOI: 10.1016/j.jocn.2015.12.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/29/2015] [Indexed: 11/16/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a dysregulated neurocutaneous disorder, characterized by neurofibromas and café-au-lait spots. NF1 is caused by mutations in the NF1 gene, encoding neurofibromin. Here, we present a clinical molecular study of a three-generation Chinese family with NF1. The proband was a male patient who showed café-au-lait spots and multiple subcutaneous neurofibromas over the whole body, but his siblings only had regional lesions. The man's daughter presented with severe headache and vomiting. Neurological examination revealed an intracranial space occupying lesion. Surgery was undertaken and the histopathological examination showed a grade I-II astrocytoma. Next-Generation sequencing (Illumina HiSeq2500 Analyzers; Illumina, San Diego, CA, USA) and Sanger sequencing (ABI PRISM 3730 automated sequencer; Applied Biosystems, Foster City, CA, USA) identified the c.227delA mutation in the NF1 gene in the man. The mutation is co-segregated with the disease phenotypes among the affected members of this family and was absent in 100 healthy controls. This novel mutation results in a frameshift (p.Asn78IlefsX7) as well as truncation of neurofibromin by formation of a premature stop codon. Our results not only extended the mutational and phenotypic spectra of the gene and the disease, but also highlight the importance of the other genetic or environmental factors in the development and severity of the disease.
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Affiliation(s)
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | | | | | | | - Jing Wu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Hui Huang
- BGI-Shenzhen, Shenzhen, 518083, China.
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9
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Bacolla A, Tainer JA, Vasquez KM, Cooper DN. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Res 2016; 44:5673-88. [PMID: 27084947 PMCID: PMC4937311 DOI: 10.1093/nar/gkw261] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 12/13/2022] Open
Abstract
Gross chromosomal rearrangements (including translocations, deletions, insertions and duplications) are a hallmark of cancer genomes and often create oncogenic fusion genes. An obligate step in the generation of such gross rearrangements is the formation of DNA double-strand breaks (DSBs). Since the genomic distribution of rearrangement breakpoints is non-random, intrinsic cellular factors may predispose certain genomic regions to breakage. Notably, certain DNA sequences with the potential to fold into secondary structures [potential non-B DNA structures (PONDS); e.g. triplexes, quadruplexes, hairpin/cruciforms, Z-DNA and single-stranded looped-out structures with implications in DNA replication and transcription] can stimulate the formation of DNA DSBs. Here, we tested the postulate that these DNA sequences might be found at, or in close proximity to, rearrangement breakpoints. By analyzing the distribution of PONDS-forming sequences within ±500 bases of 19 947 translocation and 46 365 sequence-characterized deletion breakpoints in cancer genomes, we find significant association between PONDS-forming repeats and cancer breakpoints. Specifically, (AT)n, (GAA)n and (GAAA)n constitute the most frequent repeats at translocation breakpoints, whereas A-tracts occur preferentially at deletion breakpoints. Translocation breakpoints near PONDS-forming repeats also recur in different individuals and patient tumor samples. Hence, PONDS-forming sequences represent an intrinsic risk factor for genomic rearrangements in cancer genomes.
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Affiliation(s)
- Albino Bacolla
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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10
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Hsiao MC, Piotrowski A, Callens T, Fu C, Wimmer K, Claes KBM, Messiaen L. Decoding NF1 Intragenic Copy-Number Variations. Am J Hum Genet 2015; 97:238-49. [PMID: 26189818 DOI: 10.1016/j.ajhg.2015.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/05/2015] [Indexed: 11/30/2022] Open
Abstract
Genomic rearrangements can cause both Mendelian and complex disorders. Currently, several major mechanisms causing genomic rearrangements, such as non-allelic homologous recombination (NAHR), non-homologous end joining (NHEJ), fork stalling and template switching (FoSTeS), and microhomology-mediated break-induced replication (MMBIR), have been proposed. However, to what extent these mechanisms contribute to gene-specific pathogenic copy-number variations (CNVs) remains understudied. Furthermore, few studies have resolved these pathogenic alterations at the nucleotide-level. Accordingly, our aim was to explore which mechanisms contribute to a large, unique set of locus-specific non-recurrent genomic rearrangements causing the genetic neurocutaneous disorder neurofibromatosis type 1 (NF1). Through breakpoint-spanning PCR as well as array comparative genomic hybridization, we have identified the breakpoints in 85 unrelated individuals carrying an NF1 intragenic CNV. Furthermore, we characterized the likely rearrangement mechanisms of these 85 CNVs, along with those of two additional previously published NF1 intragenic CNVs. Unlike the most typical recurrent rearrangements mediated by flanking low-copy repeats (LCRs), NF1 intragenic rearrangements vary in size, location, and rearrangement mechanisms. We propose the DNA-replication-based mechanisms comprising both FoSTeS and/or MMBIR and serial replication stalling to be the predominant mechanisms leading to NF1 intragenic CNVs. In addition to the loop within a 197-bp palindrome located in intron 40, four Alu elements located in introns 1, 2, 3, and 50 were also identified as intragenic-rearrangement hotspots within NF1.
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Affiliation(s)
- Meng-Chang Hsiao
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Arkadiusz Piotrowski
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - Tom Callens
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chuanhua Fu
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Peter-Mayr-Straße 1, 6020 Innsbruck, Austria
| | - Kathleen B M Claes
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan, 185 9000 Gent, Belgium
| | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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11
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Mishra D, Kato T, Inagaki H, Kosho T, Wakui K, Kido Y, Sakazume S, Taniguchi-Ikeda M, Morisada N, Iijima K, Fukushima Y, Emanuel BS, Kurahashi H. Breakpoint analysis of the recurrent constitutional t(8;22)(q24.13;q11.21) translocation. Mol Cytogenet 2014; 7:55. [PMID: 25478009 PMCID: PMC4255720 DOI: 10.1186/s13039-014-0055-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/25/2014] [Indexed: 11/23/2022] Open
Abstract
Backgrounds The t(8;22)(q24.13;q11.2) has been identified as one of several recurrent
constitutional translocations mediated by palindromic AT-rich repeats (PATRRs).
Although the breakage on 22q11 utilizes the same PATRR as that of the more
prevalent constitutional t(11;22)(q23;q11.2), the breakpoint region on 8q24 has
not been elucidated in detail since the analysis of palindromic sequence is
technically challenging. Results In this study, the entire 8q24 breakpoint region has been resolved by next
generation sequencing. Eight polymorphic alleles were identified and compared with
the junction sequences of previous and two recently identified t(8;22) cases . All
of the breakpoints were found to be within the PATRRs on chromosomes 8 and 22
(PATRR8 and PATRR22), but the locations were different among cases at the level of
nucleotide resolution. The translocations were always found to arise on symmetric
PATRR8 alleles with breakpoints at the center of symmetry. The translocation
junction is often accompanied by symmetric deletions at the center of both PATRRs.
Rejoining occurs with minimal homology between the translocation partners.
Remarkably, comparison of der (8) to der(22) sequences shows identical breakpoint
junctions between them, which likely represent products of two independent events
on the basis of a classical model. Conclusions Our data suggest the hypothesis that interactions between the two PATRRs prior to
the translocation event might trigger illegitimate recombination resulting in the
recurrent palindrome-mediated translocation.
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Affiliation(s)
- Divya Mishra
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto 390-8621, Nagano, Japan
| | - Keiko Wakui
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto 390-8621, Nagano, Japan
| | - Yasuhiro Kido
- Department of Pediatrics, Dokkyo Medical University Koshigaya Hospital, Koshigaya 343-8555, Saitama, Japan
| | - Satoru Sakazume
- Department of Pediatrics, Dokkyo Medical University Koshigaya Hospital, Koshigaya 343-8555, Saitama, Japan
| | - Mariko Taniguchi-Ikeda
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan
| | - Naoya Morisada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan
| | - Yoshimitsu Fukushima
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto 390-8621, Nagano, Japan
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia 19104, PA, USA.,Department of Pediatrics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia 19104, PA, USA
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
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Hasty P, Montagna C. Chromosomal Rearrangements in Cancer: Detection and potential causal mechanisms. Mol Cell Oncol 2014; 1:e29904. [PMID: 26203462 PMCID: PMC4507279 DOI: 10.4161/mco.29904] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 12/13/2022]
Abstract
Many cancers exhibit chromosomal rearrangements. These rearrangements can be simple with a single balanced fusion preserving the proper complement of genetic information or they can be complex with one or more fusions that distort this balance. A range of technological advances has improved our ability to detect and understand these rearrangements leading to speculation of causal mechanisms including defective DNA double strand break (DSB) repair and faulty DNA replication. A better understanding of these potential cancer-causing mechanisms will lead to novel therapeutic regimes to fight cancer. This review describes the technological advances used to detect simple and complex chromosomal rearrangements, cancers that exhibit these rearrangements, potential mechanisms that rearrange chromosomes and intervention strategies designed to specifically attack fusion gene products and causal DNA repair/synthesis pathways.
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Affiliation(s)
- Paul Hasty
- Department of Molecular Medicine/Institute of Biotechnology; The University of Texas Health Science Center at San Antonio; San Antonio, TX USA
| | - Cristina Montagna
- Department of Genetics and Pathology; Albert Einstein College of Medicine of Yeshiva University; Michael F. Price Center; Bronx, NY USA
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