A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency

Abstract

N-Glycanase 1 (NGLY1) is a cytoplasmic deglycosylating enzyme. Loss-of-function mutations in the NGLY1 gene cause NGLY1 deficiency, which is characterized by developmental delay, seizures, and a lack of sweat and tears. To model the phenotypic variability observed among patients, we crossed a Drosophila model of NGLY1 deficiency onto a panel of genetically diverse strains. The resulting progeny showed a phenotypic spectrum from 0 to 100% lethality. Association analysis on the lethality phenotype, as well as an evolutionary rate covariation analysis, generated lists of modifying genes, providing insight into NGLY1 function and disease. The top association hit was Ncc69 (human NKCC1/2), a conserved ion transporter. Analyses in NGLY1-/- mouse cells demonstrated that NKCC1 has an altered average molecular weight and reduced function. The misregulation of this ion transporter may explain the observed defects in secretory epithelium function in NGLY1 deficiency patients.

Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter

“…In the course of the present studies, we used ERC, a bioinformatics assay, to predict the localization of a poorly understood ion transporter. While ERC has been described and tested before (Brunette et al, 2019; Clark et al, 2012; Findlay et al, 2014; Raza et al, 2019; Talsness et al, 2020; Ziegler et al, 2016), our approach utilized a novel idea that tracking evolutionary histories of functionally linked proteins may inform their functional context, such as localization. Therefore, using this approach we were able to predict protein localization in the absence of obvious clearly defined functional domains.…”

“…This evolutionary rate covariation occurs in physically interacting proteins that coevolve as well as functionally related proteins such as gene regulatory elements, membrane traffic adaptors, and transporters. As a result, ERC has been used to identify the functions of uncharacterized genes, including novel DNA damage-induced apoptosis suppressor, sex peptide network components, regulators of cell adhesion, and ion and aminoacid transporters (Brunette et al, 2019; Clark et al, 2012; Findlay et al, 2014; Raza et al, 2019; Talsness et al, 2020; Ziegler et al, 2016). ERC is calculated as correlation between evolutionary rates throughout a phylogeny.…”

Epistasis for head morphology in Drosophila melanogaster

“…In D. melanogaster , a powerful strategy to convert a two-dimensional epistasis mapping screen to a one-dimensional screen, thus increasing the power to detect epistatic interactions, is to introgress or cross a candidate focal allele into the DGRP ( Mackay et al 2012 ; Huang et al 2014 ) or another mapping population. However, most of these studies ( Polaczyk et al 1998 ; Dworkin et al 2009 ; Chow et al 2016 ; Lavoy et al 2018 ; Palu et al 2019 ; Talsness et al 2020 ) utilized dominant-negative mutations with large effects or the GAL4 - UAS system to over-express, mis-express or knockdown expression of the focal gene. Only a few studies utilized mutations with subtle, quantitative effects as focal genes ( Yamamoto et al 2009 ; Swarup et al 2012 ; He et al 2016 ).…”

“…If the difference between the quantitative effects of the mutant and wild type varies significantly, there is epistasis, and the modifying loci can be mapped with the same power as for a single marker analysis of the same population. Many such studies in D. melanogaster have revealed extensive cryptic natural variation that modifies effects of mutations with large effects ( Rendel 1959 ; Gibson and van Helden 1997 ; Polaczyk et al 1998 ; Rutherford and Lindquist 1998 ; Gibson et al 1999 ; Dworkin et al 2009 ; Chow et al 2016 ; Lavoy et al 2018 ; Palu et al 2019 ; Talsness et al 2020 ). However, there are relatively few studies that have quantified the extent to which naturally occurring variation epistatically modifies the effects of mutations with subtle quantitative effects ( Yamamoto et al 2009 ; Swarup et al 2012 ; He et al 2016 ).…”

Genomic Context and Mechanisms of the ACVR1 Mutation in Fibrodysplasia Ossificans Progressiva

“…Another example of this type of study is provided by the use of genetically diverse Drosophila strains, known as the Drosophila Genetic Reference Panel (DGRP), to identify components of the genetic background that affect symptoms and severity of the rare NGLY1 deficiency [ 47 ]. As already mentioned, a Drosophila FOP model has been reported [ 4 ]; thus, in principle it would be possible to apply a similar approach to search for genetic modifiers also for the FOP phenotype.…”