Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells

Rouhani, Foad J.; Zou, Xueqing; Danecek, Petr; Badja, Cherif; Amarante, Tauanne Dias; Koh, Gene; Wu, Qili; Memari, Yasin; Durbin, Richard; Martincorena, Iñigo; Bassett, Andrew; Gaffney, Daniel J.; Nik-Zainal, Serena

doi:10.1038/s41588-022-01147-3

Cited by 43 publications

(36 citation statements)

References 85 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to the development of newer mouse models ( Kazuki et al, 2020 ), human-induced pluripotent stem cells (hiPSCs) ( Takahashi and Yamanaka, 2006 ) ( Takahashi et al, 2007 ) generated by reprogramming of the DS patient somatic cells have been used to explore DS impaired neurogenesis. Although earlier studies using human iPSCs have benefited us in understanding DS neurological disorder, they have generated conflicting results for impaired neurogenesis in DS, perhaps due to a lack of standardized in vitro neural differentiation protocols ( Shi et al, 2012 ; Briggs et al, 2013 ; Lu et al, 2013 ; Weick et al, 2013 ; Hibaoui et al, 2014 ; Sobol et al, 2019 ) or variations in hiPSC lines ( Rouhani et al, 2022 ). For instance, initial studies reported synaptic deficit in DS neurons ( Weick et al, 2013 ) and detected amyloid plaques ( Shi et al, 2012 ) but found normal neurogenesis in DS cells compared to control cells.…”

Section: Introductionmentioning

confidence: 99%

Biphasic cell cycle defect causes impaired neurogenesis in down syndrome

Sharma

Nehra²,

Long³

et al. 2022

Front. Genet.

View full text Add to dashboard Cite

Impaired neurogenesis in Down syndrome (DS) is characterized by reduced neurons, increased glial cells, and delayed cortical lamination. However, the underlying cause for impaired neurogenesis in DS is not clear. Using both human and mouse iPSCs, we demonstrate that DS impaired neurogenesis is due to biphasic cell cycle dysregulation during the generation of neural progenitors from iPSCs named the “neurogenic stage” of neurogenesis. Upon neural induction, DS cells showed reduced proliferation during the early phase followed by increased proliferation in the late phase of the neurogenic stage compared to control cells. While reduced proliferation in the early phase causes reduced neural progenitor pool, increased proliferation in the late phase leads to delayed post mitotic neuron generation in DS. RNAseq analysis of late-phase DS progenitor cells revealed upregulation of S phase-promoting regulators, Notch, Wnt, Interferon pathways, and REST, and downregulation of several genes of the BAF chromatin remodeling complex. NFIB and POU3F4, neurogenic genes activated by the interaction of PAX6 and the BAF complex, were downregulated in DS cells. ChIPseq analysis of late-phase neural progenitors revealed aberrant PAX6 binding with reduced promoter occupancy in DS cells. Together, these data indicate that impaired neurogenesis in DS is due to biphasic cell cycle dysregulation during the neurogenic stage of neurogenesis.

show abstract

Section: Introductionmentioning

confidence: 99%

Biphasic cell cycle defect causes impaired neurogenesis in down syndrome

Sharma

Nehra²,

Long³

et al. 2022

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…Moreover, such mutations may be selected for during LCL culture, consistent with their higher prevalence in older cell lines (although we cannot discriminate between mutation load and culture age as being causally linked to BCL6 mutation prevalence). If this were the case, BCL6 could be the equivalent of BCOR ( BCL6 corepressor) mutations that are selected for in iPS cell culture 58 ; indeed, BCOR functions together with BCL6 to repress cell cycle arrest in cells with active SHM. Further research will be required to characterize the role of BCL6 (and other genes) in the proliferation and mutational landscape of LCLs.…”

Section: Resultsmentioning

confidence: 99%

Multifactorial heterogeneity of the human mutation landscape related to DNA replication dynamics

Caballero

Boos

Koren

2022

Preprint

View full text Add to dashboard Cite

Mutations do not occur uniformly across genomes but instead show biased associations with various genomic features, most notably late replication timing. However, it remains contested which mutation types in human cells relate to DNA replication dynamics and to what extents. Previous studies have been limited by the absence of cell-type-specific replication timing profiles and lack of consideration of inter-individual variation. To overcome these limitations, we performed high-resolution comparisons of mutational landscapes between and within lymphoblastoid cell lines from 1662 individuals, 151 chronic lymphocytic leukemia patients, and three colon adenocarcinoma cell lines including two with mismatch repair deficiency. Using cell type-matched replication timing profiles, we demonstrate how mutational pathways can exhibit heterogeneous replication timing associations. We further identified global mutation load as a novel, pervasive determinant of mutational landscape heterogeneity across individuals. Specifically, elevated mutation load corresponded to increased late replication timing bias as well as replicative strand asymmetries of clock-like mutations and off-target somatic hypermutation. The association of somatic hypermutation with DNA replication timing was further influenced by mutational clustering. Considering these multivariate factors, and by incorporating mutation phasing at an unprecedented scale, we identified a unique mutational landscape on the inactive X-chromosome. Overall, we report underappreciated complexity of mutational pathways and their relationship to replication timing and identify specific factors underlying differential mutation landscapes among cell types and individuals.

show abstract

“…To gain insight into the origin of these variants, we manually reviewed sequencing data from the KOLF fibroblasts from which the KOLF-C1 parental line was derived and found that the vast majority of these variants (37/40, 93%) were already present in the donor fibroblasts and many of them were likely inherited form the germline. Other variants were only seen in a subset of sequencing reads, suggesting they arose as somatic mutations in a subset of the fibroblasts rather than during iPSC reprogramming, culture, or sub-cloning (Rouhani et al 2022).…”

Section: Resultsmentioning

confidence: 99%

A reference induced pluripotent stem cell line for large-scale collaborative studies

Pantazis

Yang

Lara

et al. 2021

Preprint

View full text Add to dashboard Cite

Human induced pluripotent stem cells (iPSCs) are a powerful tool for studying development and disease. However, different iPSC lines show considerable phenotypic variation. The lack of common well-characterized cell lines that are used widely frustrates efforts to integrate data across research groups or replicate key findings. Inspired by model organism communities who addressed this issue by establishing a limited number of widely accepted strains, we characterised candidate iPSC lines in unprecedented detail to select a well-performing line to underpin collaborative studies. Specifically, we characterised the morphology, growth rates, and single-cell transcriptomes of iPSC lines in the pluripotent state and assessed their genomic integrity using karyotyping, DNA microarrays, whole genome sequencing, and functional assays for p53 activity. We further tested their ability to be edited by CRISPR/Cas9 and used single-cell RNA sequencing to compare the efficiency with which they could be differentiated into multiple lineages. We found that there was significant variability in the performance of lines across the tested assays that enabled the rational selection of a lead line, KOLF2.1J, which is a gene-corrected derivative of a publicly available line from the Human Induced Pluripotent Stem Cells Initiative (HipSci) resource. We are now using this line in an initiative from the NIH Center for Alzheimer’s and Related Dementias to derive hundreds of gene-edited and functionalized sub-clones to be distributed widely throughout the research community along with associated datasets, with the aim of promoting the standardisation required for large-scale collaborative science in the stem cell field.SummaryThe authors of this collaborative science study describe a deep characterization of widely available induced pluripotent stem cell (iPSC) lines to rationally select a line that performs well in multiple experimental approaches. Analysis of transcriptional patterns in the pluripotent state, whole genome sequencing, genomic stability after highly efficient CRISPR-mediated gene editing, integrity of the p53 pathway, and differentiation efficiency towards multiple lineages identified KOLF2.1J as a well-performing cell line. The widespread distribution and use of this line makes it an attractive cell line for comparative and collaborative efforts in the stem cell field.HighlightsDeep genotyping and phenotyping reveals KOLF2.1J as well-performing cell line that is readily distributed and could serve as common reference lineDespite rare copy-neutral loss of heterozygosity (CN-LOH) events, iPSC lines retain genomic fidelity after CRISPR/Cas9-based gene editingOur multifactorial pipeline serves as a blueprint for future efforts to identify other lead iPSC linesGraphical abstract

show abstract

Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells

Cited by 43 publications

References 85 publications

Biphasic cell cycle defect causes impaired neurogenesis in down syndrome

Biphasic cell cycle defect causes impaired neurogenesis in down syndrome

Multifactorial heterogeneity of the human mutation landscape related to DNA replication dynamics

A reference induced pluripotent stem cell line for large-scale collaborative studies

Contact Info

Product

Resources

About