NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency

The National Institute of Health (NIH) Library of integrated network-based cellular signatures (LINCS) program is premised on the generation of a publicly available data resource of cell-based biochemical responses or signatures to genetic or environmental perturbations. NeuroLINCS uses human inducible pluripotent stem cells (hiPSCs), derived from patients and healthy controls, and differentiated into motor neuron cell cultures. This multi-laboratory effort strives to establish i) robust multi-omic workflows for hiPSC and differentiated neuronal cultures, ii) public annotated data sets and iii) relevant and targetable biological pathways of spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Here, we focus on the proteomics and the quality of the developed workflow of hiPSC lines from 6 individuals, though epigenomics and transcriptomics data are also publicly available. Known and commonly used markers representing 73 proteins were reproducibly quantified with consistent expression levels across all hiPSC lines. Data quality assessments, data levels and metadata of all 6 genetically diverse human iPSCs analysed by DIA-MS are parsable and available as a high-quality resource to the public.

Automated summary

The NIH LINCS program aims to create a publicly available data resource of cell-based biochemical responses or signatures to genetic or environmental perturbations. NeuroLINCS focuses on using hiPSCs to study SMA and ALS, and establishes multi-omic workflows, annotated datasets, and biological pathways. This study focuses on proteomics and the quality of hiPSC lines from 6 individuals, with epigenomics and transcriptomics data also available. The data generated by DIA-MS analysis of the genetically diverse hiPSCs is of high quality and accessible to the public.