Quantification of Aneuploidy in Mammalian Systems

Bos, Hilda van den; Bakker, Björn; Taudt, Aaron; Guryev, Victor; Colomé-Tatché, Maria; Lansdorp, Peter M; Foijer, Floris; Spierings, Diana C.J.

doi:10.1007/978-1-4939-8931-7_15

Cited by 41 publications

(40 citation statements)

References 9 publications

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“…To examine the fate of the sperm-induced gains and losses, we performed single-cell WGS (30) of individual blastomeres at the about eight-cell stage of development (~48 hpf). Strand-seq is less efficient on eight-cell-stage embryos, because it depends on BrdU incorporation for exactly one cell cycle, but the cell cycles of all the blastomeres within a four-cell-stage embryo may not be precisely synchronized.…”

Section: Sperm Dna Damage Leads To Chaotic Mosaicismmentioning

confidence: 99%

“…For each chromosome, Strand-seq libraries of diploid cells display either Watson-Watson, Watson-Crick, or Crick-Crick inheritance patterns of the template strands that were inherited by the daughter cell after cell division (29). Strand-seq was originally developed to detect sister chromatid exchanges (SCEs), but Strand-seq is also suitable for the genome-wide detection of copy number changes based on read depth and the detection of copy neutral structural variants based on the strand inheritance patterns between daughter cells (29)(30)(31). Strand-seq was performed on both blastomeres of two-cell-stage embryos [~28 hours post-fertilization (hpf)] produced with sperm that was untreated or subjected to a low (2.5 Gy) or high (10 Gy) dose of radiation.…”

Section: Introductionmentioning

confidence: 99%

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Sperm DNA damage causes genomic instability in early embryonic development

et al. 2020

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Genomic instability is common in human embryos, but the underlying causes are largely unknown. Here, we examined the consequences of sperm DNA damage on the embryonic genome by single-cell whole-genome sequencing of individual blastomeres from bovine embryos produced with sperm damaged by γ-radiation. Sperm DNA damage primarily leads to fragmentation of the paternal chromosomes followed by random distribution of the chromosomal fragments over the two sister cells in the first cell division. An unexpected secondary effect of sperm DNA damage is the induction of direct unequal cleavages, which include the poorly understood heterogoneic cell divisions. As a result, chaotic mosaicism is common in embryos derived from fertilizations with damaged sperm. The mosaic aneuploidies, uniparental disomies, and de novo structural variation induced by sperm DNA damage may compromise fertility and lead to rare congenital disorders when embryos escape developmental arrest.

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Section: Sperm Dna Damage Leads To Chaotic Mosaicismmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Sperm DNA damage causes genomic instability in early embryonic development

et al. 2020

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“…Isolation and sequencing of tumor and liver tissue nuclei was performed as described before (van den Bos et al, 2019). In brief, snap frozen tissues were cut into small pieces and incubated in nuclei isolation buffer (10 mM Tris-HCl pH8.0, 320 mM Sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton X-100).…”

Section: Mini Bulk Whole Genome Sequencing and Data Analysismentioning

confidence: 99%

“…The nuclei pellet was re-suspended into PBS containing 2% bovine serum albumin and 10 µg/ml Hoechst 33358 (ThermoFisher Scientific, Waltham, MA, Cat# H3569) and 10 µg/ml propidium iodide (ThermoFisher Scientific, Waltham, MA, Cat# P1304MP). 30 nuclei per tumor were sorted into a single well for library preparation as described previously (van den Bos et al, 2019). Sequencing was performed using a NextSeq 500 (Illumina, San Diego, CA).…”

Section: Mini Bulk Whole Genome Sequencing and Data Analysismentioning

confidence: 99%

PIDDosome-induced p53-activation for ploidy restriction facilitates hepatocarcinogenesis

Sladky

Knapp

Szabó

et al. 2020

Preprint

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Polyploidization frequently precedes tumorigenesis but also occurs during normal development in several tissues. Hepatocyte ploidy is controlled by the PIDDosome during development and regeneration. The PIDDosome multi-protein complex is activated by supernumerary centrosomes to induce p53 and restrict proliferation of polyploid cells, otherwise prone for chromosomal instability.PIDDosome-deficiency in the liver results in drastically increased polyploidy. To investigate PIDDosome-induced p53-activation in the pathogenesis of liver cancer, we chemically induced hepatocellular carcinoma (HCC) in mice. Strikingly, PIDDosome-deficiency reduced tumor number and burden, despite the inability to activate p53 in polyploid cells. Liver tumors arise primarily from cells with low ploidy, indicating an intrinsic pro-tumorigenic effect of PIDDosome-mediated ploidy restriction. These data suggest that hyperpolyploidization caused by PIDDosome-deficiency protects from HCC. Moreover, high tumor cell density, as a surrogate marker of low ploidy, predicts of survival of HCC patients receiving liver transplantation. Together, we show that the PIDDosome is a potential therapeutic target to manipulate hepatocyte polyploidization for HCC prevention and tumor cell density serves as a novel prognostic marker for recurrence free survival in HCC patients.

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“…Whole genome sequencing of cryopreserved primary osteosarcoma cells was performed as described in detail previously 39 . In brief, library preparation was performed using a modified 17 single cell whole genome sequencing protocol and 77 base pair single reads were generated using a NextSeq 500 sequencing instrument (Illumina).…”

Section: Whole Genome Low-pass Sequencing Of Single Cellsmentioning

confidence: 99%

Dysregulated gene expression throughTP53promoter swapping in osteosarcoma

Saba

Cornmark

Kováč

et al. 2020

Preprint

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The malignant bone tumor osteosarcoma harbors an extreme number of chromosome rearrangements. How such massive DNA errors confer a competitive advantage to a cancer cell has remained an enigma. Osteosarcoma typically presents mutations disrupting normal 5 TP53 gene function, frequently in the form of structural rearrangements that separate the promoter region from the coding parts of the gene. To unravel the consequences of a TP53 promoter relocated in this manner, we performed in-depth genetic analyses of osteosarcoma biopsies (n=148) and cell models. We show that TP53 structural variations not only facilitate further chromosomal alterations, but also allow the constitutively active TP53 promoter to 10 upregulate putative oncogenes erroneously placed under its control. Paradoxically, many of the induced genes are part of the TP53-associated transcriptome, suggesting a need to counterbalance the initial loss of function. Our findings demonstrate how the promoter region of a tumor suppressor gene can functionally turn into an oncogenic driver. 15

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Quantification of Aneuploidy in Mammalian Systems

Cited by 41 publications

References 9 publications

Sperm DNA damage causes genomic instability in early embryonic development

Sperm DNA damage causes genomic instability in early embryonic development

PIDDosome-induced p53-activation for ploidy restriction facilitates hepatocarcinogenesis

Dysregulated gene expression throughTP53promoter swapping in osteosarcoma

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