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Non-clonal mosaicism in human somatic and embryonic stem cells revealed by single-cell array-based copy-number variation analysis

ABSTRACT: Although it is known that cultured human cells acquire copy number variations over time, little is known about the mutation frequency in individual cells. Here we describe that human somatic and embryonic stem cell cultures show significant fractions of cells carrying unique chromosomal abnormalities, forming a non-clonal genetic mosaic. We studied 85 human single cells by array-based comparative genomic hybridisation and found that 14-31% of hESC and 8-26% of somatic cells are chromosomally abnormal. Remarkably, only 2 cells showed full-chromosome aneuploidy, while 93% of detected abnormalities were segmental, most of them telomere-spanning. Furthermore, fluorescent in situ hybridisation confirmed this finding and revealed an increased instability of the subtelomeric regions in hESC as compared to somatic cells. We first validated the aCGH method by studying single cells with known genetic imbalances of different sizes. We analysed 2 amniocytes (Amniocyte C 01 - Amniocyte C 02) with a trisomy 18, eight amniocytes carrying a deletion of 5p33.3p15.55 and a duplication of 9q33q34.3 (Amniocyte A 01 - Amniocyte A 08), two amniocytes carrying a deletion of 5p15.33p15.1 (Amniocyte B 01 - Amniocyte B 02) and three hESC carrying a duplication of 3q26.33q27.3 (VUB07 P165BBB7 01 - VUB07 P165BBB7 03). From this, we found that we can reliably detect at the single-cell level CNVs that span seven consecutive BAC clones on the microarray.

ORGANISM(S): Homo sapiens

SUBMITTER: Kurt Jacobs

PROVIDER: E-GEOD-51126 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Non-clonal mosaicism in human somatic and embryonic stem cells revealed by single-cell array-based copy-number variation analysis

Project description:Although it is known that cultured human cells acquire copy number variations over time, little is known about the mutation frequency in individual cells. Here we describe that human somatic and embryonic stem cell cultures show significant fractions of cells carrying unique chromosomal abnormalities, forming a non-clonal genetic mosaic. We studied 85 human single cells by array-based comparative genomic hybridisation and found that 14-31% of hESC and 8-26% of somatic cells are chromosomally abnormal. Remarkably, only 2 cells showed full-chromosome aneuploidy, while 93% of detected abnormalities were segmental, most of them telomere-spanning. Furthermore, fluorescent in situ hybridisation confirmed this finding and revealed an increased instability of the subtelomeric regions in hESC as compared to somatic cells.

2014-06-24 | GSE51126 | GEO

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Project description:Somatic mutations in cancer are a potential source of cancer specific neoantigens. Acute myeloid leukemia (AML) has common recurrent mutations shared between patients in addition to private mutations specific to individuals. We hypothesized that neoantigens derived from recurrent shared mutations would be attractive targets for future immunotherapy and sought to study the Class I and II HLA ligandomes of thirteen primary AML tumor samples and two AML cell lines (OCI-AML3 and MV4-11) using mass spectrometry. We identified two endogenous, mutation-bearing HLA Class I ligands from NPM1, which are predicted to bind the common HLA haplotypes, HLA-A*03:01 and HLA-A*02:01 respectively. We further derived CD8+ T cells from healthy donor peripheral blood samples which bound mutant-peptide loaded A*03:01 and A*02:01 tetramers, suggesting a new source of NPM1 mutation-specific T cell receptors (TCRs) for future evaluation. Since NPM1 is mutated in approximately one-third of patients with AML, the finding of endogenous NPM1 neoantigens supports future studies evaluating immunotherapeutic approaches against this target, for this subset of patients with AML.

2019-07-17 | PXD012083 | Pride

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Project description:Tankyrase, a poly(ADP-ribose) polymerase family member, destabilizes Axin and positively regulates the Wnt/β-catenin signaling. We demonstrated that tankyrase inhibitors can target the colorectal cancer stem-like cells. Tankyrase inhibitors efficiently suppress colorectal cancer stem-like cell proliferation via AXIN-dependent manner. We sorted CD44-positive COLO-320DM cells, which showed a characteristic of CSCs and were targeted by tankyrase inhibitors. We analyzed gene expression profile of CD44-positive cells (CD44-positive 01, 02, 03) and CD44-negative cells (CD44-negative 01, 02, 03).

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Project description:Analysis of peptide presentation by Human Leukocyte Antigen (HLA) class I of influenza B infected C1R cells expressing HLA-B*07:02, -B*08:01 or -B*35:01.

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2020-07-27 | PXD014754 | Pride

MicroRNA profiling of human cholangiocyte H69 cells after culturing with lipopolysaccharide

Project description:H69 cells were cultured in H69 medium with 1 ng/ml lipopolysaccharide(LPS, for smaples 04, 05 and 06) or without LPS(for samples 01, 02 and 03) for 8 hours and then collected for array analysis. <br>

2010-02-11 | E-MEXP-2052 | biostudies-arrayexpress

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2016-01-01 | GSE71792 | GEO

476b50f4-b297-43f4-aeca-71d156f38e81 - samples

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