Genomic Characterization of Chromosomal Insertions: Insights into the Mechanisms Underlying Chromothripsis

Takema Kato; Yuya Ouchi; Hidehito Inagaki; Yoshio Makita; Seiji Mizuno; Mitsuharu Kajita; Toshiro Ikeda; Kazuhiro Takeuchi; Hiroki Kurahashi

doi:10.1159/000481586

Genomic Characterization of Chromosomal Insertions: Insights into the Mechanisms Underlying Chromothripsis

Cytogenetic and Genome Research ◽

10.1159/000481586 ◽

2017 ◽

Vol 153 (1) ◽

pp. 1-9 ◽

Cited By ~ 12

Author(s):

Takema Kato ◽

Yuya Ouchi ◽

Hidehito Inagaki ◽

Yoshio Makita ◽

Seiji Mizuno ◽

...

Keyword(s):

Molecular Mechanisms ◽

Genomic Region ◽

Nonhomologous End Joining ◽

Parental Origin ◽

Copy Number Alterations ◽

End Joining ◽

Chromosomal Breakage ◽

Genomic Characterization ◽

Trisomy Rescue

Chromosomal insertions are rare structural rearrangements, and the molecular mechanisms underlying their origin are unknown. In this study, we used whole genome sequencing to analyze breakpoints and junction sequences in 4 patients with chromosomal insertions. Our analysis revealed that none of the 4 cases involved a simple insertion mediated by a 3-chromosomal breakage and rejoining events. The inserted fragments consisted of multiple pieces derived from a localized genomic region, which were shuffled and rejoined in a disorderly fashion with variable copy number alterations. The junctions were blunt ended or with short microhomologies or short microinsertions, suggesting the involvement of nonhomologous end-joining. In one case, analysis of the parental origin of the chromosomes using nucleotide variations within the insertion revealed that maternal chromosomal segments were inserted into the paternal chromosome. This patient also carried both maternal alleles, suggesting the presence of zygotic trisomy. These data indicate that chromosomal shattering may occur in association with trisomy rescue in the early postzygotic stage.

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Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2′-guanosine

Nucleic Acids Research ◽

10.1093/nar/gkz680 ◽

2019 ◽

Vol 47 (17) ◽

pp. 9410-9422 ◽

Cited By ~ 1

Author(s):

Andrea M Kaminski ◽

Kishore K Chiruvella ◽

Dale A Ramsden ◽

Thomas A Kunkel ◽

Katarzyna Bebenek ◽

...

Keyword(s):

Double Strand Breaks ◽

Nonhomologous End Joining ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Steady State Kinetics ◽

Ligase Iv ◽

Template Dna ◽

Dna Substrate

Abstract DNA double-strand breaks (DSBs) resulting from reactive oxygen species generated by exposure to UV and ionizing radiation are characterized by clusters of lesions near break sites. Such complex DSBs are repaired slowly, and their persistence can have severe consequences for human health. We have therefore probed DNA break repair containing a template 8-oxo-7,8-dihydro-2′-guanosine (8OG) by Family X Polymerase μ (Pol μ) in steady-state kinetics and cell-based assays. Pol μ tolerates 8OG-containing template DNA substrates, and the filled products can be subsequently ligated by DNA Ligase IV during Nonhomologous end-joining. Furthermore, Pol μ exhibits a strong preference for mutagenic bypass of 8OG by insertion of adenine. Crystal structures reveal that the template 8OG is accommodated in the Pol μ active site with none of the DNA substrate distortions observed for Family X siblings Pols β or λ. Kinetic characterization of template 8OG bypass indicates that Pol μ inserts adenosine nucleotides with weak sugar selectivity and, given the high cellular concentration of ATP, likely performs its role in repair of complex 8OG-containing DSBs using ribonucleotides.

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Bladder Cancer in the Genomic Era

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2018-0329-ra ◽

2019 ◽

Vol 143 (6) ◽

pp. 695-704 ◽

Cited By ~ 6

Author(s):

Charles C. Guo ◽

Bogdan Czerniak

Keyword(s):

Bladder Cancer ◽

Molecular Mechanisms ◽

Complex Disease ◽

Human Cancer ◽

Wide Spectrum ◽

Clinicopathologic Features ◽

Pathologic Features ◽

Genomic Characterization

Context.— Bladder cancer is a heterogeneous disease that exhibits a wide spectrum of clinical and pathologic features. The classification of bladder cancer has been traditionally based on morphologic assessment with the aid of immunohistochemistry. However, recent genomic studies have revealed that distinct alterations of DNA and RNA in bladder cancer may underlie its diverse clinicopathologic features, leading to a novel molecular classification of this common human cancer. Objective.— To update recent developments in genomic characterization of bladder cancer, which may shed insights on the molecular mechanisms underlying the origin of bladder cancer, dual-track oncogenic pathways, intrinsic molecular subtyping, and development of histologic variants. Data Sources.— Peer-reviewed literature retrieved from PubMed search and authors' own research. Conclusions.— Bladder cancer is likely to arise from different uroprogenitor cells through papillary/luminal and nonpapillary/basal tracks. The intrinsic molecular subtypes of bladder cancer referred to as luminal and basal exhibit distinct expression signatures, clinicopathologic features, and sensitivities to standard chemotherapy. Genomic characterization of bladder cancer provides new insights to understanding the biological nature of this complex disease, which may lead to more effective treatment.

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Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2024512118 ◽

2021 ◽

Vol 118 (8) ◽

pp. e2024512118

Author(s):

Wei Xie ◽

Shengliu Wang ◽

Juncheng Wang ◽

M. Jason de la Cruz ◽

Guotai Xu ◽

...

Keyword(s):

Molecular Mechanisms ◽

Atp Hydrolysis ◽

Ternary Complexes ◽

Double Strand Breaks ◽

Nonhomologous End Joining ◽

Repair Pathway ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

N Terminus

The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA+ ATPase TRIP13 remodels Shieldin to regulate DNA repair pathway choice. Here we report crystal structures of human SHLD3–REV7 binary and fused SHLD2–SHLD3–REV7 ternary complexes, revealing that assembly of Shieldin requires fused SHLD2–SHLD3 induced conformational heterodimerization of open (O-REV7) and closed (C-REV7) forms of REV7. We also report the cryogenic electron microscopy (cryo-EM) structures of the ATPγS-bound fused SHLD2–SHLD3–REV7–TRIP13 complexes, uncovering the principles underlying the TRIP13-mediated disassembly mechanism of the Shieldin complex. We demonstrate that the N terminus of REV7 inserts into the central channel of TRIP13, setting the stage for pulling the unfolded N-terminal peptide of C-REV7 through the central TRIP13 hexameric channel. The primary interface involves contacts between the safety-belt segment of C-REV7 and a conserved and negatively charged loop of TRIP13. This process is mediated by ATP hydrolysis-triggered rotatory motions of the TRIP13 ATPase, thereby resulting in the disassembly of the Shieldin complex.

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Efficacy of immune checkpoint inhibitors (ICI) and genomic characterization of sarcomatoid and/or rhabdoid (S/R) metastatic renal cell carcinoma (mRCC).

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.4514 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 4514-4514 ◽

Cited By ~ 3

Author(s):

Ziad Bakouny ◽

Natalie Vokes ◽

Xin Gao ◽

Amin Nassar ◽

Sarah Abou Alaiwi ◽

...

Keyword(s):

Molecular Mechanisms ◽

Cox Regression ◽

Checkpoint Inhibitors ◽

Objective Response ◽

Multivariable Analysis ◽

Sequencing Data ◽

Tumor Mutational Burden ◽

Genomic Characterization

4514 Background: S/R mRCC are poorly characterized rapidly progressing tumors associated with poor prognosis. Although conventional therapies are less effective for these tumors, emerging data suggests that ICIs may be especially effective. Our aim was to characterize the genomic alterations (GA) in S/R mRCC tumors and evaluate their response to ICIs. Methods: We retrospectively compared the activity of first-line ICIs to non-ICI-based therapies for S/R mRCC patients (pts) treated at DFCI and analyzed sequencing data from an NGS panel (275-447 genes) on a subset of these patients (matched by histology to non-S/R mRCC). For S/R mRCC pts treated with ICI vs non-ICI therapies, overall survival (OS) and time to treatment failure (TTF) were compared by Cox regression and objective response rate (ORR) by logistic regression. GA frequencies were compared by Fisher’s test and tumor mutational burden (TMB) by Mann Whitney U between S/R and non-S/R mRCC. Results were considered statistically significant if p < 0.05 or q < 0.10. Results: 125 S/R mRCC pts were included (88 S, 23 R, 14 S&R) among which 103 were clear cell and 48 had sequencing data. GA in BAP1 were significantly more frequent in S/R vs non-S/R (25% vs 4.3%; q = 0.096) while other GA had similar frequencies and TMB (median [IQR]) was similar (7.2 [5.2-8.4] vs 6.8 [5.3-9.1] mut/Mb; p = 0.98). Median follow-up was 35.4 (95% CI = 24.9 – 46.0) months (m). On multivariable analysis, S/R mRCC pts treated with ICI had significantly better clinical outcomes (Table). Conclusions: Pts with S/R mRCC have a higher frequency of BAP1 GA and better outcomes on ICIs compared to non-ICI-based therapies. Future studies should determine the molecular mechanisms underlying the improved response to ICIs in S/R mRCC. [Table: see text]

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Genomic Characterization of a Rare, de Novo Unbalanced ins(3;1)(p25.3;q21.3q23.3) in a Female Child with Multiple Congenital Anomalies

Cytogenetic and Genome Research ◽

10.1159/000511234 ◽

2020 ◽

Vol 160 (10) ◽

pp. 579-588

Author(s):

Martha L. Ornelas-Arana ◽

Guillermo Pérez-Garcia ◽

Carla D. Robles-Espinoza ◽

Martha M. Rangel-Sosa ◽

Carolina Castaneda-Garcia ◽

...

Keyword(s):

De Novo ◽

Clinical Manifestations ◽

Recurrence Risk ◽

Female Child ◽

Clinical Findings ◽

Facial Dysmorphism ◽

End Joining ◽

Position Effects ◽

Genomic Characterization

“Simple” 1-way interchromosomal insertions involving an interstitial 1q segment are rare, and therefore, their characterization at the base pair level remains understudied. Here, we describe the genomic characterization of a previously unreported de novo interchromosomal insertion (3;1) entailing an about 12-Mb pure gain of 1q21.3q23.3 that causes typical (microcephaly, developmental delay, and facial dysmorphism) and atypical (interauricular communication, small feet with bilateral deep plantar creases, syndactyly of II-IV toes, and mild pachyonychia of all toes) clinical manifestations associated with this region. Based on our analyses, we hypothesize that the duplication of a subset of morbid genes (including LMNA, USF1, VANGL2, LOR, and POGZ) could account for most clinical findings in our patient. Furthermore, the apparent disruption of a promoter region (between CPNE9 and BRPF1) and a topologically associated domain also suggests likely pathogenic reconfiguration/position effects to contribute to the patient’s phenotype. In addition to further expanding the clinical spectrum of proximal 1q duplications and evidencing the phenotypical heterogeneity among similar carriers, our genomic findings and observations suggest that randomness – rather than lethality issues – may account for the paucity of “simple” interchromosomal insertions involving the 1q21.3q23.3 region as genomic donor and distal 3p25.3 as receptor. Moreover, the microhomology sequence found at the insertion breakpoint is consistent with a simple nonhomologous end-joining mechanism, in contrast to a chromothripsis-like event, which has previously been seen in other nonrecurrent insertions. Taken together, the data gathered in this study allowed us to inform this family about the low recurrence risk but not to predict the reproductive prognosis for hypothetical carriers. We highlight that genomic-level assessment is a powerful tool that allows the visualization of the full landscape of sporadic chromosomal injuries and can be used to improve genetic counseling.

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Characterization of Chromosomal Translocation Breakpoint Sequences in Solid Tumours: “An In Silico Analysis”

The Open Medical Informatics Journal ◽

10.2174/1874431101509010001 ◽

2015 ◽

Vol 9 (1) ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Aditi Daga ◽

Afzal Ansari ◽

Rakesh Rawal ◽

Valentina Umrania

Keyword(s):

Molecular Mechanisms ◽

Genomic Sequence ◽

Chromosomal Rearrangements ◽

Chromosomal Translocation ◽

In Silico Analysis ◽

Translocation Breakpoint ◽

Breakpoint Region ◽

Segmental Duplications ◽

Chromosomal Breakage

Chromosomal translocations that results in formation and activation of fusion oncogenes are observed in numerous solid malignancies since years back. Expression of fusion kinases in these cancers drives the initiation & progression that ultimately leads to tumour development and thus comes out to be clinically imperative in terms of diagnosis and treatment of cancer. Nonetheless, molecular mechanisms beneath these translocations remained unexplored consequently limiting our knowledge of carcinogenesis and hence is the current field where further research is required. The issue of prime focus is the precision with which the chromosomes breaks and reunites within genome. Characterization of Genomic sequences located at Breakpoint region may direct us towards the thorough understanding of mechanism leading to chromosomal rearrangement. A unique computational multi-parametric analysis was performed for characterization of genomic sequence within and around breakpoint region. This study turns out to be novel as it reveals the occurrence of Segmental Duplications flanking the breakpoints of all translocation. Breakpoint Islands were also investigated for the presence of other intricate genomic architecture and various physico-chemical parameters. Our study particularly highlights the probable role of SDs and specific genomic features in precise chromosomal breakage. Additionally, it pinpoints the potential features that may be significant for double-strand breaks leading to chromosomal rearrangements.

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Nickel Carcinogenesis Mechanism: DNA Damage

International Journal of Molecular Sciences ◽

10.3390/ijms20194690 ◽

2019 ◽

Vol 20 (19) ◽

pp. 4690 ◽

Cited By ~ 8

Author(s):

Hongrui Guo ◽

Huan Liu ◽

Hongbin Wu ◽

Hengmin Cui ◽

Jing Fang ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Molecular Mechanisms ◽

Excision Repair ◽

Nonhomologous End Joining ◽

End Joining ◽

Damage Repair ◽

Occupational And Environmental Exposure ◽

Base Excision

Nickel (Ni) is known to be a major carcinogenic heavy metal. Occupational and environmental exposure to Ni has been implicated in human lung and nasal cancers. Currently, the molecular mechanisms of Ni carcinogenicity remain unclear, but studies have shown that Ni-caused DNA damage is an important carcinogenic mechanism. Therefore, we conducted a literature search of DNA damage associated with Ni exposure and summarized known Ni-caused DNA damage effects. In vitro and vivo studies demonstrated that Ni can induce DNA damage through direct DNA binding and reactive oxygen species (ROS) stimulation. Ni can also repress the DNA damage repair systems, including direct reversal, nucleotide repair (NER), base excision repair (BER), mismatch repair (MMR), homologous-recombination repair (HR), and nonhomologous end-joining (NHEJ) repair pathways. The repression of DNA repair is through direct enzyme inhibition and the downregulation of DNA repair molecule expression. Up to now, the exact mechanisms of DNA damage caused by Ni and Ni compounds remain unclear. Revealing the mechanisms of DNA damage from Ni exposure may contribute to the development of preventive strategies in Ni carcinogenicity.

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