Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis

Abstract

Human pluripotent stem cells (PSCs) have become popular tools within the research community to study developmental and model diseases. While many induced-PSCs (iPSCs) from various genetic background sources are currently available, scientific advancement has been hampered by the considerable phenotypic variations observed between different iPSC lines. A recent collaborative effort selected a novel iPSC line to address this and encourage the adoption of a standardized iPSC line termed KOLF2.1J. Here, leveraging the multiplexing power of isobaric labeling, we systematically investigate, at the 10k proteome level, the relative protein abundance profiles of the KOLF2.1J reference iPSC line upon two distinct cell state differentiation trajectories. In addition, we side-by-side systematically compare this line with the H9 line, an established embryonically derived PSC line that we previously characterized. We noticed differences in the basal proteome of the two cell lines and highlighted the differentially expressed proteins. While the difference between the cell line's proteome subsisted upon differentiation, the global proteome remodeling trajectory was highly similar during the tested differentiation routes. We thus conclude that the KOLF2.1J line performs well at the proteome level upon the neuro and cardiomyogenesis differentiation protocol used. We believe this dataset will serve as a resource of value for the research community.

High density SNP array and reanalysis of genome sequencing uncovers CNVs associated with neurodevelopmental disorders in KOLF2.1J iPSCs

“…reduced amplitude of evoked excitatory postsynaptic currents in derived neurons) 13 . Furthermore, a recent study shows that the proteome remodeling trajectory during neural induction is similar between KOLF2.1J iPSCs and H9 hESCs, although at steady state level the two lines show profound protein expression differences 51 . Whether KOLF2.1J iPSC-derived neurons display specific neurological disease phenotypes or higher susceptibility to genetic variants associated to neurological disorders remain unknown, but our findings urge to consider these possibilities when working with KOLF2.1J iPSCs.…”

“…Chr6 and Chr9 CNVs cause a complete deletion of DTNBP1 and partial deletions predicting loss of expression of JARID2 and ASTN2. Indeed, a recent proteomic study shows that compared to H9 hESCs, KOLF2.1J iPSCs express about half of ASTN2, JARID2 and DTNBP1 both at pluripotent and neural progenitor stages (Fig 4C ,D) 51 .…”

“…Thus, the impact of these CNVs for pluripotency and neural cell phenotypes, as well as their interaction with other variants that researchers may want to introduce to generate experimental models of neurological disorders, remain unknown. 51 show that JARID2, DTNBP1 and ASTN2 protein levels are ~half in KOLF2.1J compared to the reference H9 line at both pluripotency (C) and neural progenitor stage (D). Graphs show mean +/-SD of n=4 cultures and q-values as calculated in the reference proteomic analysis with Welsch's t-test and FDR correction for multiple comparisons 51 .…”

“…Horizontal lines and red dots depict SNPs that fall within KOLF2.1J CNV regions. (C, D) Quantitative proteomic data retrieved from Nam et al51 show that JARID2, DTNBP1 and ASTN2 protein levels are ~half in KOLF2.1J compared to the reference H9 line at both pluripotency (C) and neural progenitor stage (D). Graphs show mean +/-SD of n=4 cultures and q-values as calculated in the reference proteomic analysis with Welsch's t-test and FDR correction for multiple comparisons51 .…”