Positive epistasis between disease-causing missense mutations and silent polymorphism with effect on mRNA translation velocity

Abstract

Epistasis refers to the dependence of a mutation on other mutation(s) and the genetic context in general. In the context of human disorders, epistasis complicates the spectrum of disease symptoms and has been proposed as a major contributor to variations in disease outcome. The nonadditive relationship between mutations and the lack of complete understanding of the underlying physiological effects limit our ability to predict phenotypic outcome. Here, we report positive epistasis between intragenic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR)—the gene responsible for cystic fibrosis (CF) pathology. We identified a synonymous single-nucleotide polymorphism (sSNP) that is invariant for the CFTR amino acid sequence but inverts translation speed at the affected codon. This sSNP in cis exhibits positive epistatic effects on some CF disease–causing missense mutations. Individually, both mutations alter CFTR structure and function, yet when combined, they lead to enhanced protein expression and activity. The most robust effect was observed when the sSNP was present in combination with missense mutations that, along with the primary amino acid change, also alter the speed of translation at the affected codon. Functional studies revealed that synergistic alteration in ribosomal velocity is the underlying mechanism; alteration of translation speed likely increases the time window for establishing crucial domain–domain interactions that are otherwise perturbed by each individual mutation.

Synonymous and Nonsynonymous Substitutions in Dictyostelium discoideum Ammonium Transporter amtA Are Necessary for Functional Complementation in Saccharomyces cerevisiae

“…Thus, any parameter that alters translational kinetics is likely to cause a nonfunctional protein product. Considering the above-mentioned factors, it is not surprising that many of the detailed studies on the effect of synonymous substitutions on protein function have come from membrane proteins such as multidrug resistance protein (MDR) and cystic fibrosis transmembrane conductance regulator (CFTR) ( 51 , 53 , 61 – 63 ).…”

“…It has been reported that the mechanistic basis of an increase in fitness caused by synonymous and nonsynonymous mutations could not be discriminated ( 67 ). More recently, it has been demonstrated that even the preceding and the succeeding codon contexts have significant roles in determining the translation speed ( 63 , 68 ). Much of our knowledge of the biological consequences of synonymous substitutions comes from studies where the effect of synonymous codons is determined while keeping the rest of the amino acid sequence context intact ( 51 , 61 , 62 ).…”

“…How do we explain the mechanistic basis of the combined role played by synonymous and nonsynonymous substitutions? Recent studies clearly demonstrated an epistatic relationship between synonymous and nonsynonymous substitutions in the CFTR protein ( 62 , 63 ). However, we were unable to detect epistatic effects between various substitutions within amtA M1 and amtA M2 either because our system is not sensitive enough to detect minor activity that could be associated with such intermediates (single, double, or triple mutations, etc.)…”

The Effect of Synonymous Single-Nucleotide Polymorphisms on an Atypical Cystic Fibrosis Clinical Presentation

“…While the positive sweat test, respiratory features and chronic pulmonary infections resemble the CF symptoms, the mild effect of the c.1584G>A sSNP on CFTR expression along with the wild-type morphology of the patient-derived organoids is a feature of a typical non-CF mutation. The patient also bears a rare combination of two other homozygous alleles, i.e., c.2562T>G, c.4389G>A, which are protective and positively influence the CFTR protein expression level [5,23]. Likely, they also contribute to this very mild and atypical CF clinical presentation.…”

Features of CFTR mRNA and implications for therapeutics development

“…Thus, there remains a critical need for efficacious treatment strategies to address presently off-label variants. Increasing evidence places CFTR mRNA quality and utilization as a key contributor to patient heterogeneity and pharmacologic responsiveness ( Clarke et al, 2021 ; Rauscher et al, 2021 ; Bengtson et al, 2022 ). In this brief review, we summarize ways in which mRNA structure, stability, and abundance robustly influence CFTR functional expression.…”