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Study Suggests Gene Expression at Root of Genetic Background-related Mutant Phenotype Differences

NEW YORK (GenomeWeb) – Gene expression differences between individuals appear to be related to at least some of the ways mutant phenotypes manifest themselves differently in individuals, according to a model organism study published in today's issue of Cell.

University of Toronto researchers relied on an RNA interference screen to trace the phenotypic consequences of loss-of-function mutations affecting some 1,400 genes in Caenorhabditis elegans worms from two genetic backgrounds. In roughly one-fifth of cases, these mutations led to distinct physical features in each background — effects that were partly predictable from individuals' underlying gene expression differences.

"Our results show that there is extensive variation in the severity of loss-of-function phenotypes between individuals and that this variation in mutant phenotypes is partly predictable from variation in gene expression," senior author Andrew Fraser, a molecular genetics researcher at the University of Toronto, and colleagues wrote.

"We thus suggest that variations in personal gene expression levels are one of the key causes of the variation in disease severity in Mendelian disorders," they added.

It was clear from past studies that the same mutation may manifest itself differently depending on a model organism's genetic background, the team explained. But the reason for such effects has been difficult to parse.

In the case of Mendelian diseases in human, for instance, the study's authors noted that "although disease risk may be largely monogenic and its heritability predictable, the severity of the disease phenotype is the outcome of interaction between multiple genes."

"We cannot yet predict these effects of genetic background on disease severity with any accuracy," they added, "nor do we understand the general mechanisms underlying this."

For their part, the researchers attempted to tease this problem apart by pairing their quantitative phenotyping pipeline with an RNAi screen that systematically interfered with the functions of 1,353 genes in C. elegans from a so-called N2 Bristol genetic background and in a Hawaiian background known as CB4856.

After performing multiple rounds of the experiment in each of the genetic backgrounds, the team did manual phenotyping and additional quality control steps to narrow in on loss-of-function mutations — affecting hundreds of genes — that showed more pronounced effects in one genetic background or the other in the initial screen.

The researchers verified findings for a handful of these genes using mutation-containing C. elegans strains, supporting the notion that their screen picked up authentic differences in phenotype for many of the mutations identified.

For example, their results suggest that worms from the N2 genetic background tend to experience especially severe phenotypic consequences when they contain mutations affecting energy-related genes in the electron transport chain pathway and/or sequences coding for RNA-binding proteins.

On the other hand, the team found that mutations falling in protein synthesis genes often produced more pronounced effects in C. elegans representatives from the CB4856 background.

To dig into such differences, the researchers did RNA sequencing on N2 and CB4856 worms sampled at different life stages. Results of those experiments hinted that gene expression variability may be to blame for some of the severe mutational effects detected in each of the genetic backgrounds.

In particular, the N2 worms had somewhat lower expression of electron transport chain and other genes, while protein synthesis genes showed more muted expression in CB4856 worms.