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Gene-editing in Induced Pluripotent Stem Cells Reveals How Risk Locus Influences Cardiovascular Disease

Review of “Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing” from Cell by Stuart P. Atkinson 

A cardiovascular disease locus present at 9p21.3 strongly influences the risk of coronary artery disease, stroke, and aneurysms [1]; however, deciphering the function of this sizeable human-specific coding gene-free risk haplotype has proven problematic. Subsequent studies have implicated a crucial role for the vascular smooth muscle cells (VSMCs) that compose the majority of blood vessel walls [2], although the senescence of VSMCs in vitro and their known phenotypic heterogeneity across individuals, tissues, and disease states have made them difficult to study [3].

To solve these problems, researchers from the laboratory of Kristin K. Baldwin (The Scripps Research Institute, La Jolla, CA, USA) combined gene-editing and induced pluripotent stem cell technologies to generate a large cohort of stem cells and subsequently differentiated VSMCs from both risk and non-risk individuals with and without the homozygous deletion of the coronary artery disease risk locus haplotype. Reporting in Cell, Lo Sardo et al. now report that a small number of single nucleotide changes across the 60 kilobase-long risk locus can impact a network of genes that alter VSMC function, thereby influencing the risk of coronary artery disease and possibly other CVDs [4].

The authors generated induced pluripotent stem cells from risk and non-risk individuals and employed transcription activator-like effector nuclease-mediated gene-editing to delete the risk locus haplotype to permit a range of comparisons following differentiation into VSMCs. Gene expression profiling during induced pluripotent stem cell differentiation identified a network of around 3,000 genes implicated in VSMC proliferation, adhesion, and contraction driven by the risk haplotype that prompted reduced contraction and adhesion and increased proliferation, thereby recapitulating key phenotypes of VSMCs discovered in atherosclerotic plaques. The authors note that their findings confirm 38 of 91 coronary artery disease risk genes identified in previous genome-wide association studies [5, 6].

Excitingly, deletion of the risk haplotype restored gene expression and function of VSMCs to levels similar to VSMCs displaying the non-risk haplotype; however, the deletion of the non-risk region in VSMCs generated only a minimal effect, suggesting that only a small number of single nucleotide changes across a 60 kb region in the risk haplotype exerts an additive gain of function effect. Further analysis of the RNA sequencing data employed for the gene expression analysis identified candidate pathogenic isoforms of the long non-coding RNA ANRIL expressed in risk VSMCs that induced a risk-like phenotype when overexpressed in non-risk VSMCs.

The authors hope that their findings will open the door to new arterial wall-focused therapeutic interventions for cardiovascular disease patients and highlight the power of haplotype editing in induced pluripotent stem cells to uncover new functions of human-specific and non-coding genomic regions relevant to human-specific genome biology and disease. 

For more on gene-editing of induced pluripotent stem cells can reveal risk factors for cardiovascular disease, stay tuned to the Stem Cells Portal!


  1. Gransbo K, Almgren P, Sjogren M, et al., Chromosome 9p21 genetic variation explains 13% of cardiovascular disease incidence but does not improve risk prediction. Journal of Internal Medicine 2013;274:233-40.
  2. Alexander MR and Owens GK, Epigenetic Control of Smooth Muscle Cell Differentiation and Phenotypic Switching in Vascular Development and Disease. Annual Review of Physiology 2012;74:13-40.
  3. Almontashiri NAM, Antoine D, Zhou X, et al., 9p21.3 Coronary Artery Disease Risk Variants Disrupt TEAD Transcription Factor-Dependent Transforming Growth Factor β Regulation of p16 Expression in Human Aortic Smooth Muscle Cells. Circulation 2015;132:1969-1978.
  4. Lo Sardo V, Chubukov P, Ferguson W, et al., Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing. Cell 2018;175:1796-1810.e20.
  5. Howson JMM, Zhao W, Barnes DR, et al., Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms. Nature Genetics 2017;49:1113-1119.
  6. Nikpay M, Goel A, Won HH, et al., A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease. Nat Genet 2015;47:1121-1130.