scholarly journals Analysis of Complex DNA Rearrangements During Early Stages of HAC Formation

2020 ◽  
Author(s):  
Elisa Pesenti ◽  
Mikhail Liskovykh ◽  
Koei Okazaki ◽  
Alessio Mallozzi ◽  
Caitlin Reid ◽  
...  
Keyword(s):  
Genomic Organization ◽  
Cell Clone ◽  
Chromosome Instability ◽  
Human Chromosomes ◽  
Dna Rearrangements ◽  
Structural Domains ◽  
Artificial Chromosomes ◽  
Early Stages ◽  
Ht1080 Cells ◽  
Cancer Types

AbstractHuman Artificial Chromosomes (HACs) are important tools for epigenetic engineering, for measuring chromosome instability (CIN) and possible gene therapy. However, their use in the latter is potentially limited because the input HAC-seeding DNA can undergo an unpredictable series of rearrangements during HAC formation. As a result, after transfection and HAC formation, each cell clone contains a HAC with a unique structure that cannot be precisely predicted from the structure of the HAC-seeding DNA. Although it has been reported that these rearrangements can happen, the timing and mechanism of their formation has yet to be described. Here we synthesized a HAC-seeding DNA with two distinct structural domains and introduced it into HT1080 cells. We characterized a number of HAC-containing clones and subclones to track DNA rearrangements during HAC establishment. We demonstrated that rearrangements can occur early during HAC formation. Subsequently, the established HAC genomic organization is stably maintained across many cell generations. Thus, early stages in HAC formation appear to at least occasionally involve a process of DNA shredding and shuffling that resembles chromothripsis, an important hallmark of many cancer types. Understanding these events during HAC formation has critical implications for future efforts aimed at synthesizing and exploiting synthetic human chromosomes.

scholarly journals Analysis of Complex DNA Rearrangements during Early Stages of HAC Formation

2020 ◽  
Vol 9 (12) ◽  
pp. 3267-3287
Author(s):  
Elisa Pesenti ◽  
Mikhail Liskovykh ◽  
Koei Okazaki ◽  
Alessio Mallozzi ◽  
Caitlin Reid ◽  
...  
Keyword(s):  
Dna Rearrangements ◽  
Early Stages

scholarly journals Meiosis and Kinetochore genes are used by cancer cells as genome destabilizers and transformation catalysts

2019 ◽  
Author(s):  
Roshina Thapa ◽  
Swetha Vasudevan ◽  
Mimi Abo-Ayoub Ashqar ◽  
Eli Reich ◽  
Nataly Kravchenko-Balasha ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Cancer Progression ◽  
Genome Instability ◽  
Chromosome Instability ◽  
Information Theoretic ◽  
Cancer Types ◽  
Altered Gene ◽  
The Relationship ◽  
Hct116 Cells

AbstractCancer cells have an altered transcriptome which contributes to their altered behaviors compared to normal cells. Indeed, many tumors express high levels of genes participating in meiosis or kinetochore biology, but the role of this high expression has not been fully elucidated. In this study we explore the relationship between this overexpression and genome instability and transformation capabilities of cancer cells. For this, we obtained expression data from 5 different cancer types which were analyzed using computational information-theoretic analysis. We were able to show that highly expressed meiotic/kinetochore genes were enriched in the altered gene expression subnetworks characterizing unstable cancer types with high chromosome instability (CIN). However, altered subnetworks found in the cancers with low CIN did not include meiotic and kinetochore genes. Representative gene candidates, found by the analysis to be correlated with a CIN phenotype, were further explored by transfecting genomically-stable (HCT116) and unstable (MCF7) cancer cell lines with vectors overexpressing those genes. This overexpression resulted in an increase in the numbers of abnormal cell divisions and defective spindle formations and in increased transformation properties in stable cancer HCT116 cells. Interestingly, the same properties were less affected by the overexpressed genes in the unstable MCF7 cancer cells. Our results indicate that overexpression of both meiosis and kinetochore genes is capable of driving genomic instability and cancer progression.

Deletions of the Normal ABL1 at the Non-Translocated Chromosome 9 in CML Associated with TKI Resistance.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3254-3254
Author(s):  
Anna Virgili ◽  
Diana Brazma ◽  
Colin Grace ◽  
Elisabeth P Nacheva
Keyword(s):  
Tyrosine Kinase ◽  
Conflicts Of Interest ◽  
Cell Clone ◽  
Philadelphia Chromosome ◽  
Chromosome 9 ◽  
The Other ◽  
Comparative Genomic ◽  
Derivative Chromosome ◽  
Artificial Chromosomes ◽  
Tki Resistance

Abstract Abstract 3254 Poster Board III-1 Chronic myeloid leukaemia (CML) is characterized by the expression of the BCR/ABL1 fusion gene, a constitutively activated tyrosine kinase that commonly results from the formation of the Philadelphia chromosome (Ph) after a t(9;22)(q34;q11) or variant rearrangement. Some 10% to 15% of CML patients present with cryptic deletions adjacent to the translocation breakpoint junction on the derivative chromosome 9. These deletions are believed to occur during the formation of the Ph translocation and are associated with a worse prognosis for CML patients treated with hydroxyurea or interferon. However there is still conflicting data regarding the significance of these deletions in patients receiving imatinib therapy, which appears to overcome the poor prognosis associated with the genome loss. Here we present data of three BCR/ABL1 positive CML patients on tyrosine kinase inhibitors (TKI) who developed therapy resistance. In all patients loss of the ABL1 sequences was identified. Surprisingly, these deletions affected not the ABL1 sequences of the ABL1/BCR fusion on the der(9) chromosome but the normal ABL1 allele on the non- translocated homologue of chromosome 9. This loss was not present at the time of diagnosis but was a new event developed during disease progression and found along with other additional chromosome rearrangements in the BCR/ABL1 positive cells. Bone marrow chromosome suspensions were studied by array comparative genomic hybridization (aCGH) analysis and/or fluorescent in situ hybridization (FISH) using and a range of commercial and bacterial artificial chromosomes (BAC) probes. While one patient carried a large deletion del(9)(q31q34) that spanned several megabases and was detectable by G-banding analysis, the other two patients had small cryptic losses (from 1.8 Mbp to 2.6 Mbp). The loss involved 3' ABL1 sequences in one patient whereas it affected the whole gene in the other two cases. Since the negative control exercised by the normal ABL1 allele over the BCR/ABL1 expression has been documented, the sensitivity to the TKI might be affected in the BCR/ABL1 positive cell clone bearing the genome loss. In summary, we report a new type of ABL1 loss in Ph positive cells - deletions at the 9q34 associated with TKI resistance in CML patients. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Sequence Diversity and Genomic Organization of Vomeronasal Receptor Genes in the Mouse

2000 ◽  
Vol 10 (12) ◽  
pp. 1958-1967
Author(s):  
Karina Del Punta ◽  
Andrea Rothman ◽  
Ivan Rodriguez ◽  
Peter Mombaerts
Keyword(s):  
Genomic Organization ◽  
Vomeronasal Organ ◽  
Sequence Diversity ◽  
Sequence Information ◽  
Bacterial Artificial Chromosomes ◽  
Vomeronasal System ◽  
Coding Region ◽  
Artificial Chromosomes ◽  
Coding Regions ◽  
Vomeronasal Receptor

The vomeronasal system of mice is thought to be specialized in the detection of pheromones. Two multigene families have been identified that encode proteins with seven putative transmembrane domains and that are expressed selectively in subsets of neurons of the vomeronasal organ. The products of these vomeronasal receptor (Vr) genes are regarded as candidate pheromone receptors. Little is known about their genomic organization and sequence diversity, and only five sequences of mouse V1r coding regions are publicly available. Here, we have begun to characterize systematically the V1r repertoire in the mouse. We isolated 107 bacterial artificial chromosomes (BACs) containing V1r genes from a 129 mouse library. Hybridization experiments indicate that at least 107 V1r-like sequences reside on these BACs. We assembled most of the BACs into six contigs, of which one major contig and one minor contig were characterized in detail. The major contig is 630–860 kb long, encompasses a cluster of 21–48 V1r genes, and contains markerD6Mit227. Sequencing of the coding regions was facilitated by the absence of introns. We determined the sequence of the coding region of 25 possibly functional V1r genes and seven pseudogenes. The functional V1rs can be arranged into three groups; V1rs of one group are novel and substantially divergent from the other V1rs. The genomic and sequence information described here should be useful in defining the biological function of these receptors.

scholarly journals Overexpression of the E2 ubiquitin–conjugating enzyme UbcH10 causes chromosome missegregation and tumor formation

2010 ◽  
Vol 188 (1) ◽  
pp. 83-100 ◽  
Author(s):  
Janine H. van Ree ◽  
Karthik B. Jeganathan ◽  
Liviu Malureanu ◽  
Jan M. van Deursen
Keyword(s):  
Transgenic Mice ◽  
Ubiquitin Ligase ◽  
Human Cancer ◽  
Chromosome Instability ◽  
Tumor Formation ◽  
Anaphase Promoting Complex ◽  
Central Question ◽  
Ubiquitin Conjugating Enzyme ◽  
Cancer Types ◽  
Conjugating Enzyme

The anaphase-promoting complex/cyclosome (APC/C) E3 ubiquitin ligase functions with the E2 ubiquitin–conjugating enzyme UbcH10 in the orderly progression through mitosis by marking key mitotic regulators for destruction by the 26-S proteasome. UbcH10 is overexpressed in many human cancer types and is associated with tumor progression. However, whether UbcH10 overexpression causes tumor formation is unknown. To address this central question and to define the molecular and cellular consequences of UbcH10 overexpression, we generated a series of transgenic mice in which UbcH10 was overexpressed in graded fashion. In this study, we show that UbcH10 overexpression leads to precocious degradation of cyclin B by the APC/C, supernumerary centrioles, lagging chromosomes, and aneuploidy. Importantly, we find that UbcH10 transgenic mice are prone to carcinogen-induced lung tumors and a broad spectrum of spontaneous tumors. Our results identify UbcH10 as a prominent protooncogene that causes whole chromosome instability and tumor formation over a wide gradient of overexpression levels.

scholarly journals Quantified CIN Score From Cell-free DNA as a Novel Noninvasive Predictor of Survival in Patients With Spinal Metastasis

2021 ◽  
Vol 9 ◽  
Author(s):  
Su Chen ◽  
Minglei Yang ◽  
Nanzhe Zhong ◽  
Dong Yu ◽  
Jiao Jian ◽  
...  
Keyword(s):  
Spinal Metastasis ◽  
Metastatic Cancer ◽  
Chromosome Instability ◽  
Validation Dataset ◽  
Survival Prediction ◽  
Survival Prognosis ◽  
Tokuhashi Score ◽  
Number Variation ◽  
Cancer Types ◽  
Low Coverage

Purpose: Most currently available scores for survival prediction of patients with bone metastasis lack accuracy. In this study, we present a novel quantified CIN (Chromosome Instability) score modeled from cfDNA copy number variation (CNV) for survival prediction.Experimental Design: Plasma samples collected from 67 patients with bone metastases from 11 different cancer types between November 2015 and May 2016 were sent through low-coverage whole genome sequencing followed by CIN computation to make a correlation analysis between the CIN score and survival prognosis. The results were validated in an independent cohort of 213 patients.Results: During the median follow-up period of 598 (95% CI 364–832) days until December 25, 2018, 124 (44.3%) of the total 280 patients died. Analysis of the discovery dataset showed that CIN score = 12 was the optimal CIN cutoff. Validation dataset showed that CIN was elevated (score ≥12) in 87 (40.8%) patients, including 5 (5.75%) with head and neck cancer, 11 (12.6%) with liver and gallbladder cancer, 11 (12.6%) with cancer from unidentified sites, 21 (24.1%) with lung cancer, 7 (8.05%) with breast cancer, 4 (4.60%) with thyroid cancer, 6 (6.90%) with colorectal cancer, 4 (4.60%) with kidney cancer, 2 (2.30%) with prostate cancer, and 16 (18.4%) with other types of cancer. Further analysis showed that patients with elevated CIN were associated with worse survival (p < 0.001). For patients with low Tokuhashi score (≤8) who had predictive survival of less than 6 months, the CIN score was able to distinguish patients with a median overall survival (OS) of 443 days (95% CI 301–585) from those with a median OS of 258 days (95% CI 184–332).Conclusion: CNV examination in bone metastatic cancer from cfDNA is superior to the traditional predictive model in that it provides a noninvasive and objective method of monitoring the survival of patients with spine metastasis.

scholarly journals Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2

2021 ◽  
Vol 4 (11) ◽  
pp. e202101083
Author(s):  
Melanie L Bailey ◽  
David Tieu ◽  
Andrea Habsid ◽  
Amy Hin Yan Tong ◽  
Katherine Chan ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Regulatory Gene ◽  
Chromosome Instability ◽  
Genetic Interactions ◽  
Complex Nature ◽  
Whole Genome ◽  
Cohesin Complex ◽  
Synthetic Lethal ◽  
Cancer Types

STAG2, a component of the mitotically essential cohesin complex, is highly mutated in several different tumour types, including glioblastoma and bladder cancer. Whereas cohesin has roles in many cancer-related pathways, such as chromosome instability, DNA repair and gene expression, the complex nature of cohesin function has made it difficult to determine how STAG2 loss might either promote tumorigenesis or be leveraged therapeutically across divergent cancer types. Here, we have performed whole-genome CRISPR-Cas9 screens for STAG2-dependent genetic interactions in three distinct cellular backgrounds. Surprisingly, STAG1, the paralog of STAG2, was the only negative genetic interaction that was shared across all three backgrounds. We also uncovered a paralogous synthetic lethal mechanism behind a genetic interaction between STAG2 and the iron regulatory gene IREB2. Finally, investigation of an unusually strong context-dependent genetic interaction in HAP1 cells revealed factors that could be important for alleviating cohesin loading stress. Together, our results reveal new facets of STAG2 and cohesin function across a variety of genetic contexts.

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