Consistent Assignment of Risk and Benign Allele at rs2303153 in the CF Modifier Gene SCNN1B in Three Independent F508del-CFTR Homozygous Patient Populations

CFTR encodes for a chloride and bicarbonate channel expressed at the apical membrane of polarized epithelial cells. Transepithelial sodium transport mediated by the amiloride-sensitive sodium channel ENaC is thought to contribute to the manifestation of CF disease. Thus, ENaC is a therapeutic target in CF and a valid cystic fibrosis modifier gene. We have characterized SCNN1B as a genetic modifier in the three independent patient cohorts of F508del-CFTR homozygotes. We could identify a regulatory element at SCNN1B to the genomic segment rs168748-rs2303153-rs4968000 by fine-mapping (Pbest = 0.0177), consistently observing the risk allele rs2303153-C and the contrasting benign allele rs2303153-G in all three patient cohorts. Furthermore, our results show that expression levels of SCNN1B are associated with rs2303153 genotype in intestinal epithelia (P = 0.003). Our data confirm that the well-established biological role of SCNN1B can be recognized by an association study on informative endophenotypes in the rare disease cystic fibrosis and calls attention to reproducible results in association studies obtained from small, albeit carefully characterized patient populations.

Gene modification research has potential, from diagnostic to therapeutic levels. The most promising metabolic pathways include the TGF-1 signaling system, inflammation and protein transport

A human disease modifier gene is a gene that regulates another gene's function or effects. The presence of a modifier gene is not sufficient to cause a disease. Nonetheless, the presence of a modifier gene alters the disease's onset and severity. A genetic modifier can interact in several ways with another gene product. Changes in penetration and expressiveness, direct interaction with the target gene product, mechanistic contribution to the same biological process and/or functional compensation through other routes might all have effects. Despite long hypothesized genetic modifiers, their influence is yet unclear. Improved computational tools, international consortia with larger patient cohorts, improved laboratory precision procedures, and high-throughput technology have all helped find and verify genetic modifiers in recent years. As new possible genetic modifiers are found, common pathways can be established linking some modifying genes or neuromuscular diseases. The most promising metabolic pathways include the TGF-1 signaling system, inflammation, endoplasmic reticulum metabolism, axon formation, regeneration, extracellular matrix, RNA metabolism and protein transport. Perhaps in the future, we will conceive of neuromuscular diseases in terms of impaired molecular processes and the amount involving multiple metabolic pathways, rather than main genetic variations or medical nomenclature. Another fascinating feature of genetic modifiers in neuromuscular diseases is the involvement of genetic moderators in oligogenic inheritance. Preliminary research on animal models and people indicates that more rare, non-synonymous mutations in NMD-related genes might worsen muscle damage and lead to a more severe phenotype. Besides oligogenic inheritance, the "diagnostic gap"—individuals who remain unresolved after exome or genome sequencing—can be explained by the action of genetic modifiers. In the coming years, genetic modification research is expected to advance from diagnostic to therapeutic levels, and it would be extremely tempting from a therapeutic point of view to identify "protective" modifiers and comparable metabolic pathways for NMDs.

Quantitative trait locus mapping identifies the Gpnmb gene as a modifier of mouse macrophage lysosome function

We have previously shown that the DBA/2J versus AKR/J mouse strain is associated with decreased autophagy-mediated lysosomal hydrolysis of cholesterol esters. Our objective was to determine differences in lysosome function in AKR/J and DBA/2J macrophages, and identify the responsible genes. Using a novel dual-labeled indicator of lysosome function, DBA/2J versus AKR/J bone marrow derived macrophages had significantly decreased lysosome function. We performed quantitative trait loci mapping of lysosome function in bone marrow macrophages from an AKR/J × DBA/2J strain intercross. Four distinct lysosome function loci were identified, which we named macrophage lysosome function modifier (Mlfm) Mlfm1 through Mlfm4. The strongest locus Mlfm1 harbors the Gpnmb gene, which has been shown to recruit autophagy protein light chain 3 to autophagosomes for lysosome fusion. The parental DBA/2J strain has a nonsense variant in Gpnmb. siRNA knockdown of Gpnmb in AKR/J macrophages decreased lysosome function, and Gpnmb deletion through CRISP/Cas9 editing in RAW 264.7 mouse macrophages also demonstrated a similar result. Furthermore, a DBA/2 substrain, called DBA/2J-Gpnmb+/SjJ, contains the wildtype Gpnmb gene, and macrophages from this Gpnmb-preserved DBA/2 substrain exhibited recovered lysosome function. In conclusion, we identified Gpnmb as a causal modifier gene of lysosome function in this strain pair.

Duplication in ECR near HMX1 and a SNP in GATA6 Genes Regulate Microtia in Awassi Sheep

Microtia and anotia are hereditary traits characterized by an underdevelopment or complete absence of the outer ear. These congenital malformations observed in many species can exist as part of various syndromes or as an isolated trait as seen in the fat-tailed Awassi sheep breed. Our study aims to identify the genetic mutations causing microtia in Awassi sheep by DNA sequencing. DNA was extracted from blood samples randomly collected from 84 Awassi sheep (16 earless, 41 short ear and 27 normal ear) across different farms. GATA6 exons 1, 2, 4, 6 and 7, CLRN1 intron 3, DCC intron 2, ECR near HMX1 and the intergenic region between GATA6 and MIB1 genes were screened, amplified and sequenced. Allele and genotype frequencies were calculated by direct counting. Association was performed using chi-squared test for goodness-of-fit. Results showed mutations in only two genes significantly associated with microtia in Awassi: duplication in part of ECR near HMX1 (6:114293121-6:114293196) and a SNP at GATA6 exon 7 (23:34498242). Association results revealed that the ECR locus accounts for the microtia phenotype, while GATA6 exon 7 acts as a modifier gene. Genetic screening for these loci can be used to improve selection against microtia in Awassi sheep.