Human gene knockouts in a cohort with a high rate of consanguinity

A major goal in all of biology and medicine is to understand the function of every gene in the human genome. Loss-of-function (LOF) mutations can disrupt both copies of a given gene in humans. Thus, phenotypic analysis of such ‘human knockouts’ can provide insight into gene function. This has been performed thousands of times in mice –– since the 1980s.

Consanguineous marriages are more likely to result in offspring carrying homozygous LOF mutations. In Pakistan, consanguinity rates are remarkable high. In the attached file, authors used whole-exome sequencing (WES) to sequence the protein-coding regions of 10,503 adult participants in the Pakistan Risk of Myocardial Infarction Study (PROMIS), designed to understand the determinants of cardiometabolic diseases in individuals from South Asia. They identified individuals carrying homozygous predicted loss-of-function (pLoF) mutations, and performed phenotypic analysis involving more than 200 biochemical and disease traits. They counted 49,138 rare (<1% minor-allele frequency; MAF) pLoF mutations. These pLoF mutations were estimated to knock out 1,317 genes –– each in at least one participant.

Homozygosity for pLoF mutations occurred at:

PLA2G7 was associated with absent enzymatic activity of soluble lipoprotein-associated phospholipase A2;

at CYP2F1, with higher plasma interleukin-8 (IL8) concentrations;

at TREH, with lower concentrations of apoB-containing lipoprotein subfractions;

at either A3GALT2 or NRG4, with markedly reduced plasma insulin C-peptide concentrations; and

at SLC9A3R1, with mediators of calcium and phosphate signalling.

Heterozygous deficiency of APOC3 has been shown to protect against coronary heart disease; authors identified APOC3 homozygous pLoF carriers in their cohort. They recruited these human knockouts and challenged them with an oral fat load. Compared with family members lacking the mutation, individuals with APOC3 ablated were found to show marked blunting of the usual post-prandial rise in plasma triglycerides.

Overall, these intriguing observations provide a roadmap for a ‘human knockout project’, a systematic effort to understand the phenotypic consequences of complete disruption of genes in humans..!! For example, this is the first study to show an association between CYP2F1 expression and IL8 levels. Each of you is encouraged to screen these data for the “gene of your choice.”

Nature 13 April 2o17; 544: 235–239

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