UCSF

Background: Recent advancements in Next Generation Sequencing (NGS) and high throughput multiplexed single-cell multi-omics present an unprecedented opportunity to investigate cell composition, gene expression, map associations between single nucleotide polymorphisms and quantitative molecular traits in heterogenous cell populations across hundreds of donors and perform context relevant functional validation studies. Here we present work (i) using multiplexed single-cell RNA sequencing (scRNA-seq) to study cellular and genetic correlates of systemic lupus erythematosus (SLE), (ii) generating an atlas of healthy immune cells from a diverse cohort, using multiplexed multi-omic profiling of RNA and open chromatin. (iii) We streamlined lentiviral Massively Parallel Reporter Assay (lentiMPRA) protocols and established a computational pipeline to support these assays and (iiii) worked to extend this method to single cells (scMPRA). Methods: (i) We profiled 1.2 million cells using multiplexed scRNA-seq (mux-seq) from 261 donors. We evaluated changes in cell composition and gene expression between cases and controls. We mapped cell type specific expression quantitative trail loci. (ii) We profiled over 1 million cells using multiplexed multi-omics from ~400 donors. We evaluated cell composition across a diverse cohort, mapped immune regulatory networks, and investigated genetic architecture of chromatin accessibility and gene expression. (iii) We established a robust protocol for lentiMPRA and developed pipeline using Nextflow for seamless data analysis to functionally validate putative non-coding regulatory sequences. (iv) We have designed an approach for scMPRA and have generated promising preliminary results. Results and Conclusions: (i) Our mux-seq platform is robust and scalable (ii) and can be applied to multi-omic datasets. (iii) Genetic associations can be validated using lentiMPRA with our streamlined methods. (iv) scMPRA holds promise as an option for validating genetic associations in distinct cellular environments.