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Studies on the Pathogenesis of Chromosome Rearrangement
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Studies on the Pathogenesis of Chromosome Rearrangement

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 26605

Special Issue Editors

Prof. Dr. Angela Bentivegna

E-Mail Website
Guest Editor
School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
Interests: glioblastoma; cancer stem cells; urothelial carcinoma; developmental disability; human cytogenetics
Special Issues, Collections and Topics in MDPI journals
Dr. Gaia Roversi

E-Mail Website
Guest Editor
School of Medicine and Surgery, University of Milano - Bicocca, Milan, Italy

Special Issue Information

Dear Colleagues,

Genome instability of meiotic chromosomes contributes enormously to mutational processes during human genome evolution, in association with human diseases and manifesting as polymorphic variation in populations. In addition, genome instability of mitotic chromosomes is the driving force that creates mutations and chromosome rearrangements, which finally lead to the development of cancers. Several major mechanisms have been proposed for human genome rearrangements, and these include nonallelic homologous recombination (NAHR), nonhomologous end-joining (NHEJ), and replication based mechanisms (RBMs), such as fork stalling and template switching (FoSTeS) and microhomology‐mediated break‐induced replication (MMBIR). Of these, NAHR results in recurrent rearrangements mediated by a common genomic structure or architecture in which the rearranged interval is flanked by paralogous repeat sequences or low-copy repeats (LCRs, also known as segmental duplications). Conversely, NHEJ and replication mechanisms are a major contributor to nonrecurrent genomic rearrangements wherein the rearrangement size, genomic extent, and breakpoint position at a genetic locus can differ amongst unrelated subjects. Moreover, complex exonic, genic, and chromosomal rearrangements can be generated in a single mutagenic event by chromothripsis‐like events. Chromothripsis, a chromosome catastrophe involving shattering and subsequent rearrangement of chromosomes in somatic cells, was first recognized in cancers. By contrast, chromoanasynthesis describes the analogous phenomenon in constitutional genomic disorders.

This Special Issue, “Studies on the Pathogenesis of Chromosome Rearrangement”, will cover a selection of recent research topics and current review articles in the field of chromosome rearrangement, both on a meiotic and mitotic level.

Prof. Dr. Angela Bentivegna
Dr. Gaia Roversi
Guest Editors

Manuscript Submission Information

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Keywords

  • Chromosome rearrangement
  • Human genome copy number variation (CNV)
  • DNA repair
  • DNA double-strand breaks (DSBs)
  • Micronuclei
  • NAHR
  • FoSTeS
  • MMBIR
  • Chromothripsis
  • Chromoanasynthesis

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Published Papers (5 papers)

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Research

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17 pages, 4375 KiB  
Article
Human Chromosome 18 and Acrocentrics: A Dangerous Liaison
by Nicoletta Villa, Serena Redaelli, Elena Sala, Donatella Conconi, Lorenza Romitti, Emanuela Manfredini, Francesca Crosti, Gaia Roversi, Marialuisa Lavitrano, Ornella Rodeschini, Maria Paola Recalcati, Rocco Piazza, Leda Dalprà, Paola Riva and Angela Bentivegna
Int. J. Mol. Sci. 2021, 22(11), 5637; https://doi.org/10.3390/ijms22115637 - 26 May 2021
Viewed by 4142
Abstract
The presence of thousands of repetitive sequences makes the centromere a fragile region subject to breakage. In this study we collected 31 cases of rearrangements of chromosome 18, of which 16 involved an acrocentric chromosome, during genetic screening done in three centers. We [...] Read more.
The presence of thousands of repetitive sequences makes the centromere a fragile region subject to breakage. In this study we collected 31 cases of rearrangements of chromosome 18, of which 16 involved an acrocentric chromosome, during genetic screening done in three centers. We noticed a significant enrichment of reciprocal translocations between the centromere of chromosome 18 and the centromeric or pericentromeric regions of the acrocentrics. We describe five cases with translocation between chromosome 18 and an acrocentric chromosome, and one case involving the common telomere regions of chromosomes 18p and 22p. In addition, we bring evidence to support the hypothesis that chromosome 18 preferentially recombines with acrocentrics: (i) the presence on 18p11.21 of segmental duplications highly homologous to acrocentrics, that can justify a NAHR mechanism; (ii) the observation by 2D-FISH of the behavior of the centromeric regions of 18 respect to the centromeric regions of acrocentrics in the nuclei of normal subjects; (iii) the contact analysis among these regions on published Hi-C data from the human lymphoblastoid cell line (GM12878). Full article
(This article belongs to the Special Issue Studies on the Pathogenesis of Chromosome Rearrangement)
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13 pages, 1957 KiB  
Article
RB Regulates DNA Double Strand Break Repair Pathway Choice by Mediating CtIP Dependent End Resection
by Yuning Jiang, Jason C. Yam, Clement C. Tham, Chi Pui Pang and Wai Kit Chu
Int. J. Mol. Sci. 2020, 21(23), 9176; https://doi.org/10.3390/ijms21239176 - 1 Dec 2020
Cited by 16 | Viewed by 3776
Abstract
Inactivation of the retinoblastoma tumor suppressor gene (RB1) leads to genome instability, and can be detected in retinoblastoma and other cancers. One damaging effect is causing DNA double strand breaks (DSB), which, however, can be repaired by homologous recombination (HR), classical [...] Read more.
Inactivation of the retinoblastoma tumor suppressor gene (RB1) leads to genome instability, and can be detected in retinoblastoma and other cancers. One damaging effect is causing DNA double strand breaks (DSB), which, however, can be repaired by homologous recombination (HR), classical non-homologous end joining (C-NHEJ), and micro-homology mediated end joining (MMEJ). We aimed to study the mechanistic roles of RB in regulating multiple DSB repair pathways. Here we show that HR and C-NHEJ are decreased, but MMEJ is elevated in RB-depleted cells. After inducing DSB by camptothecin, RB co-localizes with CtIP, which regulates DSB end resection. RB depletion leads to less RPA and native BrdU foci, which implies less end resection. In RB-depleted cells, less CtIP foci, and a lack of phosphorylation on CtIP Thr847, are observed. According to the synthetic lethality principle, based on the altered DSB repair pathway choice, after inducing DSBs by camptothecin, RB depleted cells are more sensitive to co-treatment with camptothecin and MMEJ blocker poly-ADP ribose polymerase 1 (PARP1) inhibitor. We propose a model whereby RB can regulate DSB repair pathway choice by mediating the CtIP dependent DNA end resection. The use of PARP1 inhibitor could potentially improve treatment outcomes for RB-deficient cancers. Full article
(This article belongs to the Special Issue Studies on the Pathogenesis of Chromosome Rearrangement)
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Review

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16 pages, 752 KiB  
Review
Insight into the Molecular Basis Underlying Chromothripsis
by Katarzyna Ostapińska, Borys Styka and Monika Lejman
Int. J. Mol. Sci. 2022, 23(6), 3318; https://doi.org/10.3390/ijms23063318 - 19 Mar 2022
Cited by 12 | Viewed by 4655
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Studies on the Pathogenesis of Chromosome Rearrangement)
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37 pages, 8043 KiB  
Review
Congenital Diseases of DNA Replication: Clinical Phenotypes and Molecular Mechanisms
by Megan Schmit and Anja-Katrin Bielinsky
Int. J. Mol. Sci. 2021, 22(2), 911; https://doi.org/10.3390/ijms22020911 - 18 Jan 2021
Cited by 23 | Viewed by 8962
Abstract
Deoxyribonucleic acid (DNA) replication can be divided into three major steps: initiation, elongation and termination. Each time a human cell divides, these steps must be reiteratively carried out. Disruption of DNA replication can lead to genomic instability, with the accumulation of point mutations [...] Read more.
Deoxyribonucleic acid (DNA) replication can be divided into three major steps: initiation, elongation and termination. Each time a human cell divides, these steps must be reiteratively carried out. Disruption of DNA replication can lead to genomic instability, with the accumulation of point mutations or larger chromosomal anomalies such as rearrangements. While cancer is the most common class of disease associated with genomic instability, several congenital diseases with dysfunctional DNA replication give rise to similar DNA alterations. In this review, we discuss all congenital diseases that arise from pathogenic variants in essential replication genes across the spectrum of aberrant replisome assembly, origin activation and DNA synthesis. For each of these conditions, we describe their clinical phenotypes as well as molecular studies aimed at determining the functional mechanisms of disease, including the assessment of genomic stability. By comparing and contrasting these diseases, we hope to illuminate how the disruption of DNA replication at distinct steps affects human health in a surprisingly cell-type-specific manner. Full article
(This article belongs to the Special Issue Studies on the Pathogenesis of Chromosome Rearrangement)
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17 pages, 999 KiB  
Review
Origin, Regulation, and Fitness Effect of Chromosomal Rearrangements in the Yeast Saccharomyces cerevisiae
by Xing-Xing Tang, Xue-Ping Wen, Lei Qi, Yang Sui, Ying-Xuan Zhu and Dao-Qiong Zheng
Int. J. Mol. Sci. 2021, 22(2), 786; https://doi.org/10.3390/ijms22020786 - 14 Jan 2021
Cited by 1 | Viewed by 4002
Abstract
Chromosomal rearrangements comprise unbalanced structural variations resulting in gain or loss of DNA copy numbers, as well as balanced events including translocation and inversion that are copy number neutral, both of which contribute to phenotypic evolution in organisms. The exquisite genetic assay and [...] Read more.
Chromosomal rearrangements comprise unbalanced structural variations resulting in gain or loss of DNA copy numbers, as well as balanced events including translocation and inversion that are copy number neutral, both of which contribute to phenotypic evolution in organisms. The exquisite genetic assay and gene editing tools available for the model organism Saccharomyces cerevisiae facilitate deep exploration of the mechanisms underlying chromosomal rearrangements. We discuss here the pathways and influential factors of chromosomal rearrangements in S. cerevisiae. Several methods have been developed to generate on-demand chromosomal rearrangements and map the breakpoints of rearrangement events. Finally, we highlight the contributions of chromosomal rearrangements to drive phenotypic evolution in various S. cerevisiae strains. Given the evolutionary conservation of DNA replication and recombination in organisms, the knowledge gathered in the small genome of yeast can be extended to the genomes of higher eukaryotes. Full article
(This article belongs to the Special Issue Studies on the Pathogenesis of Chromosome Rearrangement)
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