Single cell sequencing: Capturing the origin and dynamics of chromosomal copy-number heterogeneity
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PROVIDER: EGAS00001003812 | EGA |
REPOSITORIES: EGA
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Project description:Intratumor heterogeneity is a major challenge in cancer treatment. To decipher patterns of chromosomal heterogeneity, we analyzed six colorectal cancer cell lines by multiplex interphase FISH. The mismatch repair deficient cell lines DLD-1 and HCT116 had the most stable copy numbers, whereas aneuploid cell lines displayed a higher degree of instability. We subsequently assessed the clonal evolution of a single cell in two aneuploid cell lines, SW480 and HT-29, which both have near-triploid karyotypes but different degrees of chromosomal instability. The clonal compositions of the single cell-derived daughter cell lines, as assessed by multiplex FISH, differed for HT-29 and SW480. Daughters of HT-29 were stable, clonal, and had little heterogeneity. Daughters of SW480 were more heterogeneous, with the single cell-derived daughter cell lines separating into two distinct populations with different ploidy (hyper-diploid and near-triploid), morphology, gene expression and tumorigenicity. To better understand the evolutionary trajectory for the two SW480 populations, we constructed phylogenetic trees which showed ongoing instability in the daughter cell lines.. When analyzing the evolutionary development over time, most single cell-derived daughter cell lines maintained their major clonal pattern, with the exception of one daughter of SW480 that showed a switch involving a loss of APC. Our meticulous analysis of the clonal evolution and composition of these colorectal cancer models shows that all chromosomes are subject to segregation errors, however, specific net genomic imbalances are maintained. Karyotype evolution is driven by the necessity to arrive at and maintain a specific plateau of chromosomal copy numbers as the drivers of carcinogenesis.
2018-05-01 | GSE102647 | GEO
Project description:Aneuploidy, a hallmark of cancer, often arises from whole chromosome instability (W-CIN). Many cancers exhibiting W-CIN, however, show no direct insult to the mitotic proteins that ensure proper segregation of chromosomes. This has stimulated interest in identifying defects in non-mitotic processes that might disrupt chromosome behavior in mitosis. Here we show in Saccharomyces cerevisiae that re-replication of centromeric DNA, caused by deregulation of replication initiation proteins, efficiently induces chromosome instability––either by causing missegregation of both sister chromatids to one daughter cell or by triggering formation of an extra chromatid through a pathway dependent on homologous recombination. Given the emerging connections between the deregulation of replication initiation proteins and oncogenesis, our findings offer the possibility of a new non-mitotic source of W-CIN and aneuploidy that may be relevant to cancer. Diploid strains containing a re-replicating locus were induced to re-replicate through a centromere. This compilation includes the analysis of the re-replication, as well as the copy-number determination of alleged aneuploid colonies from various backgrounds. Series contains a total of 194 copy number hybridizations and 8 re-replication profile hybridizations. Note that the VALUE field reported for all of the sample tables in this series are the log2 of the normalized Cy3/Cy5 ratio. To convert these into usable copy number profiles raise 2 to the indicated VALUE.
2014-07-25 | E-GEOD-55641 | biostudies-arrayexpress
Project description:Extrachromosomal DNA (ecDNA) are circular DNA bodies that play critical roles in tumor progression and treatment resistance by amplifying oncogenes across a wide range of cancer types. ecDNA lack centromeres and are thus not constrained by typical Mendelian segregation, enabling their unequal accumulation within daughter cells and associated increases in copy number. Despite intrinsic links to their oncogenic potential, the fidelity and mechanisms of ecDNA inheritance are poorly understood. Here, we show that ecDNA are protected against cytosolic mis-segregation through mitotic clustering and by tethering to mitotic chromosome ends. High fidelity nuclear segregation of MYC-amplifying ecDNA depends on BRD4 transcriptional co-activation and mitotic transcription of the long non-coding RNA PVT1, which is co-amplified with MYC in colorectal and prostate cancer cell lines. Disruption of ecDNA mitotic clustering through BRD4 inhibition, PVT1 depletion, or inhibiting mitotic transcription results in cytosolic mis-segregation, ecDNA chromosomal reintegration, and the formation of homogeneously staining regions (HSRs). We propose that nuclear inheritance of ecDNA is facilitated by an RNA-based mechanism that clusters ecDNA during mitosis and protects against cytosolic missegregation and chromosomal reintegration.
2025-07-03 | GSE299272 | GEO
Project description:High-grade serous ovarian carcinoma (HGSOC) is the most genomically complex cancer, characterised by ubiquitous TP53 mutation, profound structural variation and heterogeneity. Multiple mutational processes driving chromosomal instability can be distinguished by specific copy number signatures. To develop clinically relevant models of these mutational processes we derived 15 continuous HGSOC patient-derived organoids (PDOs) and provide detailed transcriptomic and genomic profiles using shallow whole genome sequencing single cell and bulk analysis. We show that PDOs comprise communities of different clonal populations and represent models of CCNE1 amplification, chromothripsis, tandem-duplicator phenotype and whole genome duplication. PDOs can also be used as exploratory tools to study transcriptional effects of copy number alterations as well as compound-sensitivity tests. In summary, HGSOC PDO cultures provide a genomic tool for studies of specific mutational processes and precision therapeutics.
2022-07-17 | GSE208216 | GEO
Project description:Chromosome segregation errors have been linked to DNA damage and genomic rearrangements. Accumulating evidence has shown that catastrophic genomic rearrangements, like chromothripsis, can result from lagging chromosomes undergoing aberrant DNA replication and DNA damage in micronuclei. Detailed characterization of genomic rearrangements resulting from DNA damage in micronuclei has been hampered because of difficulties in culturing daughter cells with DNA damage. Here, we employ a method by which a specific single chromosome is trapped in a micronucleus, followed by transfer to an acceptor cell. Next, stably propagating clonal cell lines with an extra chromosome were established and analyzed by copy number profiling and whole genome sequencing. While non-transformed, p53 proficient and telomerase-immortalized RPE1 cells showed a stable genome following addition of the transferred chromosome, we observed frequent de novo genomic rearrangements in cells derived from the HCT116 colorectal cancer cell line after chromosome transfer. The de novo rearrangements varied from simple deletions and duplications to complex rearrangements. Phase-informative SNPs revealed that the rearrangements specifically occurred on the transferred chromosome. We found that the complex rearrangements recapitulated all features of chromothripsis, including massive oscillation between two copy number states, localization to a single chromosome, random joining of chromosome fragments and non-homologous or micro-homologous repair. We describe an approach that enables the isolation of clonal cell lines with genomic rearrangements and chromothripsis on a specific chromosome in p53 proficient cells. The procedure enables further investigation of the exact mechanism leading to chromothripsis and the analysis of its consequences for cell survival (viability) and cancer development. We analyzed 38 cell clones, originating from HCT116 or RPE1 cells respectively, with Illumina beadchip arrays to test for unique de novo copy number variants and to determine the chromosome affacted by the CNAs.
2015-08-13 | E-GEOD-71928 | biostudies-arrayexpress
Project description:Chromosome segregation errors have been linked to DNA damage and genomic rearrangements. Accumulating evidence has shown that catastrophic genomic rearrangements, like chromothripsis, can result from lagging chromosomes undergoing aberrant DNA replication and DNA damage in micronuclei. Detailed characterization of genomic rearrangements resulting from DNA damage in micronuclei has been hampered because of difficulties in culturing daughter cells with DNA damage. Here, we employ a method by which a specific single chromosome is trapped in a micronucleus, followed by transfer to an acceptor cell. Next, stably propagating clonal cell lines with an extra chromosome were established and analyzed by copy number profiling and whole genome sequencing. While non-transformed, p53 proficient and telomerase-immortalized RPE1 cells showed a stable genome following addition of the transferred chromosome, we observed frequent de novo genomic rearrangements in cells derived from the HCT116 colorectal cancer cell line after chromosome transfer. The de novo rearrangements varied from simple deletions and duplications to complex rearrangements. Phase-informative SNPs revealed that the rearrangements specifically occurred on the transferred chromosome. We found that the complex rearrangements recapitulated all features of chromothripsis, including massive oscillation between two copy number states, localization to a single chromosome, random joining of chromosome fragments and non-homologous or micro-homologous repair. We describe an approach that enables the isolation of clonal cell lines with genomic rearrangements and chromothripsis on a specific chromosome in p53 proficient cells. The procedure enables further investigation of the exact mechanism leading to chromothripsis and the analysis of its consequences for cell survival (viability) and cancer development. We analyzed 38 cell clones, originating from HCT116 or RPE1 cells respectively, with Illumina beadchip arrays to test for unique de novo copy number variants and to determine the chromosome affacted by the CNAs.
2015-08-13 | E-GEOD-71978 | biostudies-arrayexpress
Project description:Preservation of chromosome integrity is key for the survival of any organism. To assure segregation of intact chromosomes, cell division is presumed to be under strict control of cell-cycle checkpoints. Estimates of chromosomal mutation rates per generation based on cytogenetic analyses of newborns and products of conception, range between 4.57x10-5 and 3.42x10-4. In contrast, the high incidence of segmental imbalances detected by single-cell genome-wide copy number profiling indicates that the error rate per cell division might be more than an order of magnitude higher. To directly measure the de novo incidence of segmental chromosomal imbalances, we plated a single fibroblast and analyzed the genomes of the two sister cells following a single cell division. Analysis of 89 pairs of sister cells (178 single cells in total) from 5 different cell lines revealed megabase-sized chromosomal imbalances in 21 fibroblasts, 14 of which derived from 7 mitoses with complementary segmental aneuploidies in the two daughter cells. The mutation rate of segmental imbalances is thus at least 7.9%, indicating that compared to the per generation chromosome stability is at least 100 times lower in vitro and likely underestimated in vivo.
2016-05-01 | GSE75098 | GEO
Project description:Preservation of chromosome integrity is key for the survival of any organism. To assure segregation of intact chromosomes, cell division is presumed to be under strict control of cell-cycle checkpoints. Estimates of chromosomal mutation rates per generation based on cytogenetic analyses of newborns and products of conception, range between 4.57x10-5 and 3.42x10-4. In contrast, the high incidence of segmental imbalances detected by single-cell genome-wide copy number profiling indicates that the error rate per cell division might be more than an order of magnitude higher. To directly measure the de novo incidence of segmental chromosomal imbalances, we plated a single fibroblast and analyzed the genomes of the two sister cells following a single cell division. Analysis of 89 pairs of sister cells (178 single cells in total) from 5 different cell lines revealed megabase-sized chromosomal imbalances in 21 fibroblasts, 14 of which derived from 7 mitoses with complementary segmental aneuploidies in the two daughter cells. The mutation rate of segmental imbalances is thus at least 7.9%, indicating that compared to the per generation chromosome stability is at least 100 times lower in vitro and likely underestimated in vivo.
2016-05-01 | GSE75093 | GEO
Project description:Preservation of chromosome integrity is key for the survival of any organism. To assure segregation of intact chromosomes, cell division is presumed to be under strict control of cell-cycle checkpoints. Estimates of chromosomal mutation rates per generation based on cytogenetic analyses of newborns and products of conception, range between 4.57x10-5 and 3.42x10-4. In contrast, the high incidence of segmental imbalances detected by single-cell genome-wide copy number profiling indicates that the error rate per cell division might be more than an order of magnitude higher. To directly measure the de novo incidence of segmental chromosomal imbalances, we plated a single fibroblast and analyzed the genomes of the two sister cells following a single cell division. Analysis of 89 pairs of sister cells (178 single cells in total) from 5 different cell lines revealed megabase-sized chromosomal imbalances in 21 fibroblasts, 14 of which derived from 7 mitoses with complementary segmental aneuploidies in the two daughter cells. The mutation rate of segmental imbalances is thus at least 7.9%, indicating that compared to the per generation chromosome stability is at least 100 times lower in vitro and likely underestimated in vivo.
2016-05-01 | GSE75089 | GEO
Project description:Preservation of chromosome integrity is key for the survival of any organism. To assure segregation of intact chromosomes, cell division is presumed to be under strict control of cell-cycle checkpoints. Estimates of chromosomal mutation rates per generation based on cytogenetic analyses of newborns and products of conception, range between 4.57x10-5 and 3.42x10-4. In contrast, the high incidence of segmental imbalances detected by single-cell genome-wide copy number profiling indicates that the error rate per cell division might be more than an order of magnitude higher. To directly measure the de novo incidence of segmental chromosomal imbalances, we plated a single fibroblast and analyzed the genomes of the two sister cells following a single cell division. Analysis of 89 pairs of sister cells (178 single cells in total) from 5 different cell lines revealed megabase-sized chromosomal imbalances in 21 fibroblasts, 14 of which derived from 7 mitoses with complementary segmental aneuploidies in the two daughter cells. The mutation rate of segmental imbalances is thus at least 7.9%, indicating that compared to the per generation chromosome stability is at least 100 times lower in vitro and likely underestimated in vivo.
2016-05-01 | GSE75088 | GEO