Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis
- Boston Children's Hospital, United States
- Broad Institute of MIT and Harvard, United States
- Cleveland Clinic, United States
- Brigham and Women's Hospital, United States
- Broad Institute of Harvard and MIT, United States
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.
Data availability
1000 Genomes human variation datasetThe 1000 Genomes Project Consortium. (2015)Recombinant hotspots access at:ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/technical/reference/Phase 1 data (for PLINK) accessed at: https://www.cog-genomics.org/plink/1.9/resourcesPhase 3 data accessed at: http://www.internationalgenome.org/category/phase-3/Pooled screen abundance data for shRNA targeting red blood cell trait GWAS-nominated genes during the course of in vitro differentiation of human CD34+ cellsSK Nandakumar, SK McFarland, et al. (2019)Available on the project's companion GitHub repository: https://github.com/sankaranlab/shRNA_screen/tree/master/ref/shref.csvEffects of shRNA knockdown of SF3A2 on splicing during human erythropoiesisSK Nandakumar, SK McFarland, et al. (2019)ID GSE129603. In the public domain at GEO https://www.ncbi.nlm.nih.gov/geo/Effects of SF3B1 mutants on splicing in human erythropoiesisEA Obeng et al. (2016)ID GSE85712. In the public domain at GEO https://www.ncbi.nlm.nih.gov/geo/SNP sets identified by GWAS of LDL, HDL, and triglyceride traitsCJ Willer et al. (2013)Accessed at: http://csg.sph.umich.edu/willer/public/lipids2013/Human hematopoietic lineage gene expressionMR Corces et al. (2016)ID GSE74912. In the public domain at GEO https://www.ncbi.nlm.nih.gov/geo/Human adult and fetal erythropoiesis gene expressionH Yan et al. (2018)ID GSE107218. In the public domain at GEO https://www.ncbi.nlm.nih.gov/geo/
Article and author information
Author details
Funding
National Institutes of Health (R33HL120791)
- Vijay G Sankaran
New York Stem Cell Foundation
- Vijay G Sankaran
National Institutes of Health (R01DK103794)
- Vijay G Sankaran
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Stephen Parker, University of Michigan, United States
Ethics
Animal experimentation: No human subjects were involved in the study. Human CD34+ HSPCs used in these experiments are deidentified and obtained from external sources. All mouse experiments were performed in full compliance with the approved Institutional Animal Care and Use Committee (IACUC) protocols at Boston Children's Hospital (Protocol # 18-05-3680R) and Brigham and Women's Hospital (Protocol # 2017N000060). These studies were approved by local regulatory committees in accordance with the highest ethical standards for biomedical research involving vertebrate animals.
Version history
- Received: December 2, 2018
- Accepted: May 8, 2019
- Accepted Manuscript published: May 9, 2019 (version 1)
- Version of Record published: May 24, 2019 (version 2)
Copyright
© 2019, Nandakumar et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis
eLife 8:e44080.
https://doi.org/10.7554/eLife.44080
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