Identification of QTL genes for BMD variation using both linkage and gene-based association approaches

Shedding new light on the role of ERAP1 in Type 1 diabetes: A perspective on disease management

Type 1 diabetes mellitus (T1D) is a multifactorial organ specific autoimmune disease which originates from the destruction of insulin-producing beta cells within the pancreatic islets by autoreactive CD8⁺ T lymphocytes. The autoimmune responses are raised against autoantigenic peptides presented in the context of the Major Histocompatibility Complex (MHC) class I molecules. Peptides are generated in the cytoplasm of the beta cell by degradation through the proteasome activity and other proteases. Proteolytic intermediate protein fragments are then vehicled into the endoplasmic reticulum (ER) by transporters associated with antigen processing TAP1 and TAP2. In the ER, Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) and 2 (ERAP2) shape the intermediate proteins to produce the optimal peptide size for loading into the MHC class I molecules. Subsequently complexes are shuttled to the cell surface for antigen presentation. Genome Wide Association Studies (GWAS) have identified different SNPs of ERAP1 associated to several autoimmune diseases and in particular the T1D-related ERAP1 SNP rs30187 encoding for K528R ERAP1. An association between the ER stress and the increased exposure of beta cells to the immune system has been hypothesized to further contribute to the etiopathogenesis. In particular in a recent study by Thomaidou et al. 2020 (doi: https://doi.org/10.2337/db19-0984) the posttranscriptional regulation of ERAP1 is shown to shaping the recognition of the preproinsulin (PPI) signal peptide by cytotoxic T lymphocytes. In the light of foregoing ERAP1 inhibitors could potentially prevent the activation of epitope-specific autoimmune-promoting T cells and their cytokine production; further regulating ERAP1 expression at posttranscriptional level under stress conditions of the beta cells could help to reverse autoimmune process through limiting epitope-presentation to autoreactive T cells. In this article we provide a perspective on the role of ERAP1 as implicated in the pathogenesis of insulin-dependent diabetes mellitus by reviewing studies reported in literature and discussing our own experimental evidence.

A single genetic locus associated with pediatric fractures: A genome-wide association study on 3,230 patients

The understanding of the biological and environmental risk factors of fractures in pediatrics is limited. Previous studies have reported that fractures involve heritable traits, but the genetic factors contributing to the risk of fractures remain elusive. Furthermore, genetic influences specific to immature bone have not been thoroughly studied. Therefore, the aim of the present study was to identify genetic variations that are associated with fractures in early childhood. The present study used a prospective Northern Finland Birth Cohort (year 1986; n=9,432). The study population was comprised of 3,230 cohort members with available genotype data. A total of 48 members of the cohort (1.5%) had in-hospital treated bone fractures during their first 6 years of life. Furthermore, individuals without fracture (n=3,182) were used as controls. A genome-wide association study (GWAS) was performed using a frequentist association test. In the GWAS analysis, a linear regression model was fitted to test for additive effects of single-nucleotide polymorphisms (SNPs; genotype dosage) adjusting for sex and performing population stratification using genotypic principal components. Using the GWAS analysis, the present study identified one locus with a significant association with fractures during childhood on chromosome 10 (rs112635931) and six loci with a suggested implication. The lead SNP rs112635931 was located near proline- and serine-rich 2 (PROSER2) antisense RNA 1 (PROSER2-AS1) and PROSER2, thus suggesting that these may be novel candidate genes associated with the risk of pediatric fractures.

An allelic variant in the intergenic region between ERAP1 and ERAP2 correlates with an inverse expression of the two genes

The Endoplasmatic Reticulum Aminopeptidases ERAP1 and ERAP2 are implicated in a variety of immune and non-immune functions. Most studies however have focused on their role in shaping the HLA class I peptidome by trimming peptides to the optimal size. Genome Wide Association Studies highlighted non-synonymous polymorphisms in their coding regions as associated with several immune mediated diseases. The two genes lie contiguous and oppositely oriented on the 5q15 chromosomal region. Very little is known about the transcriptional regulation and the quantitative variations of these enzymes. Here, we correlated the level of transcripts and proteins of the two aminopeptidases in B-lymphoblastoid cell lines from 44 donors harbouring allelic variants in the intergenic region between ERAP1 and ERAP2. We found that the presence of a G instead of an A at SNP rs75862629 in the ERAP2 gene promoter strongly influences the expression of the two ERAPs with a down-modulation of ERAP2 coupled with a significant higher expression of ERAP1. We therefore show here for the first time a coordinated quantitative regulation of the two ERAP genes, which can be relevant for the setting of specific therapeutic approaches.

Novel Candidate Genes Underlying Extreme Trophic Specialization in Caribbean Pupfishes

The genetic changes responsible for evolutionary transitions from generalist to specialist phenotypes are poorly understood. Here we examine the genetic basis of craniofacial traits enabling novel trophic specialization in a sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist species and two novel specialists: a small-jawed "snail-eater" and a large-jawed "scale-eater." We genotyped 12 million single nucleotide polymorphisms (SNPs) by whole-genome resequencing of 37 individuals of all three species from nine populations and integrated genome-wide divergence scans with association mapping to identify divergent regions containing putatively causal SNPs affecting jaw size-the most rapidly diversifying trait in this radiation. A mere 22 fixed variants accompanied extreme ecological divergence between generalist and scale-eater species. We identified 31 regions (20 kb) containing variants fixed between specialists that were significantly associated with variation in jaw size which contained 11 genes annotated for skeletal system effects and 18 novel candidate genes never previously associated with craniofacial phenotypes. Six of these 31 regions showed robust signs of hard selective sweeps after accounting for demographic history. Our data are consistent with predictions based on quantitative genetic models of adaptation, suggesting that the effect sizes of regions influencing jaw phenotypes are positively correlated with distance between fitness peaks on a complex adaptive landscape.

Trps1 differentially modulates the bone mineral density between male and female mice and its polymorphism associates with BMD differently between women and men

The objective of our study was to identify genetic factors that regulate bone mineral density (BMD) in mice using well defined recombinant inbred strains. For this purpose we chose the BXD recombinant inbred (RI) strains derived from progeny of the C57BL/6J (B6) and DBA/2J (D2) progenitor strains. We sampled both male and female mice (∼4 each) of 46 strains at 3 months-of-age, measured their BMD, and conducted QTL mapping. The data were analyzed to identify candidates genes contained within the most significant quantitative trait locus (QTL). Evaluation of candidate genes included functional assessment, single nucleotide polymorphism (SNP) genotyping and direct sequencing. We established that there was a QTL for BMD in males on chromosome 15 that has the impact larger than QTLs on all other chromosomes. The QTL on chromosome 15 was narrowed to a genomic region between 38 Mbp and 52 Mbp. By examining transcripts within this region, we found an important candidate gene: trichorhinophalangeal syndrome, type I (Trps1). SNP analysis identified a nonsynonymous SNP (rs32398060) in Trps1 that co-segregated with bone mineral density. Analysis of association between this SNP within TRPS1 and BMD in a human population confirmed its significance.

Whole genome scanning and association mapping identified a significant association between growth and a SNP in the IFABP-a gene of the Asian seabass

BACKGROUND

Aquaculture is the quickest growing sector in agriculture. However, QTL for important traits have been only identified in a few aquaculture species. We conducted QTL mapping for growth traits in an Asian seabass F(2) family with 359 individuals using 123 microsatellites and 22 SNPs, and performed association mapping in four populations with 881 individuals.

RESULTS

Twelve and nine significant QTL, as well as 14 and 10 suggestive QTL were detected for growth traits at six and nine months post hatch, respectively. These QTL explained 0.9-12.0% of the phenotypic variance. For body weight, two QTL intervals at two stages were overlapped while the others were mapped onto different positions. The IFABP-a gene located in a significant QTL interval for growth on LG5 was cloned and characterized. A SNP in exon 3 of the gene was significantly associated with growth traits in different populations.

CONCLUSIONS

The results of QTL mapping for growth traits suggest that growth at different stages was controlled by some common QTL and some different QTL. Positional candidate genes and association mapping suggest that the IFABP-a is a strong candidate gene for growth. Our data supply a basis for fine mapping QTL, marker-assisted selection and further detailed analysis of the functions of the IFABP-a gene in fish growth.

The putative role of endoplasmic reticulum aminopeptidases in autoimmunity: insights from genomic-wide association studies

Autoimmune diseases represent a heterogeneous group of conditions whose incidence is increasing worldwide. This has stimulated studies on their etiopathogenesis, derived from a complex interaction between genetic and environmental factors, aimed at finally improving prevention and treatment of these diseases. In the autoimmune process, immune responses are generated against self antigens presented by Major Histocompatibility Complex (MHC) class I on the cell surface. These peptide/MHC class I complexes are generated and assembled through MHC class I antigen processing and presentation machinery. In the endoplasmic reticulum (ER), aminopeptidases ERAP1 and ERAP2 display distinct trimming activity before antigenic peptides are loaded onto MHC class I molecules. The advent of new tools such as genome-wide association studies (GWAS) has provided evidence for new susceptibility loci and candidate genes playing a role in the autoimmune process for the recognized immune function of their transcripts. Genetic linkage has been discovered with MHC antigens and various autoimmune conditions. Recent GWAS showed the importance of ERAP1 and ERAP2 in several autoimmune diseases, including ankylosing spondylitis, insulin-dependent diabetes mellitus, psoriasis, multiple sclerosis, Crohn's disease. In this review, we first provide a general overview of ERAP1 and ERAP2 genes, their biological functions and their relevancy in autoimmunity. We then discuss the importance of GWAS and the case-control studies that confirm the relevancy of ERAP single-nucleotide polymorphism associations and their linkage with particular MHC class I haplotypes, supporting a putative functional role in the autoimmune process.

Cortical bone health shows significant linkage to chromosomes 2p, 3p, and 17q in 10-year-old children

Genes play an important role in lifelong skeletal health. Genes that influence bone building during childhood have the potential to affect bone health not only throughout childhood but also into adulthood. Given that peak bone mass is a significant predictor of adult fracture risk, it is imperative that the genetic underpinnings of the normal pediatric skeleton are uncovered. In a sample of 600 10-year-old children from 144 families in the Fels Longitudinal Study, we examined radiographic cortical bone measures of the second metacarpal. Morphometic measurements included bone width, medial and lateral cortical thicknesses, and the calculated cortical index representing the amount of cortex relative to bone width. We then conducted genome-wide linkage analysis on these traits in 440 genotyped individuals using the SOLAR analytic platform. Significant quantitative trait loci (QTL) were identified for bone traits on three separate chromosomes. A QTL for medial cortical thickness was localized to chromosome 2p25.2. A QTL for lateral cortical thickness was localized to chromosomal region 3p26.1-3p25.3. Finally, a QTL detected for cortical index was localized to the 17q21.2 chromosomal region. Each region contains plausible candidate genes for pediatric skeletal health, some of which confirm findings from studies of adulthood bone, and for others represent novel candidate genes for skeletal health.