Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

Abstract

Genome-wide association studies (GWAS) have identified thousands of variants associated with human diseases and traits. However, the majority of GWAS-implicated variants are in non-coding regions of the genome and require in depth follow-up to identify target genes and decipher biological mechanisms. Here, rather than focusing on causal variants, we have undertaken a pooled loss-of-function screen in primary hematopoietic cells to interrogate 389 candidate genes contained in 75 loci associated with red blood cell traits. Using this approach, we identify 77 genes at 38 GWAS loci, with most loci harboring 1–2 candidate genes. Importantly, the hit set was strongly enriched for genes validated through orthogonal genetic approaches. Genes identified by this approach are enriched in specific and relevant biological pathways, allowing regulators of human erythropoiesis and modifiers of blood diseases to be defined. More generally, this functional screen provides a paradigm for gene-centric follow up of GWAS for a variety of human diseases and traits.

The Polygenic and Monogenic Basis of Blood Traits and Diseases

“…rs139178017 (MAF = 0.53%) is a strongly FM variant in a novel association locus for red cell distribution width (RDW) (PP FM = 0.73) and MCV (PP FM = 0.4). It is predicted to induce a donor loss splice alteration for transferrin receptor 2 ( TFR2 ), a partner of the erythropoietin receptor and a known regulator of erythropoiesis ( Nai et al., 2015 ; Nandakumar et al., 2019 ). Compared to non-carriers, the 4 carriers of rs139178017 harbored substantially increased transcripts with intron retention adjacent to this variant ( Figure 4 E).…”

The Polygenic and Monogenic Basis of Blood Traits and Diseases

“…To validate these in silico predictions for select rare and biologically interesting novel splice variants, we examined isoform variation in RNA-sequencing data of 465 participants from the Geuvadis project (Lappalainen et al, 2013). For example, rs139178017 (MAF = 0.0053) is strongly fine-mapped for RDW (PP FM = 0.73) and MCV (PP FM = 0.40) and predicted to induce a donor loss splice alteration for transferrin receptor 2 ( TFR2 ), a partner of the erythropoietin receptor and a known regulator of erythropoiesis (Nai et al, 2015; Nandakumar et al, 2019). Compared to non-carriers, the 4 carriers of rs139178017 harbored substantially increased transcripts with intron retention adjacent to this variant ( Figure 4C ).…”

The genetics of human hematopoiesis and its disruption in disease

“…High‐throughput gene knockdown or knockout screens have also become a popular experimental approach to identify genes that are important for a phenotype of interest. These screens can be implemented with short hairpin RNA or CRISPR‐Cas9 genetic perturbation to systematically test which genes or regulatory elements are essential for a phenotype, such as hematopoietic lineage differentiation (Canver et al , ; Nandakumar et al , ).…”