Protective Haplotype Research Articles

Molecular fragment characteristics and distribution of tangle associated TDP-43 (TATs) and other TDP-43 lesions in Alzheimer's disease.

TAR DNA binding protein 43 (TDP-43) pathology is a defining feature of frontotemporal lobar degeneration (FTLD). In FTLD-TDP there is a moderate-to-high burden of morphologically distinctive TDP-43 immunoreactive inclusions distributed throughout the brain. In Alzheimer's disease (AD), similar TDP-43 immunoreactive inclusions are observed. In AD, however, there is a unique phenomenon of neurofibrillary tangle-associated TDP-43 (TATs) whereby TDP-43 intermingles with neurofibrillary tangles. Little is known about the characteristics and distribution of TATs, or how burden and distribution of TATs compares to burden and distribution of other FTLD-TDP-like lesions observed in AD. Here we characterize molecular fragment characteristics, burden and distribution of TATs and assess how these features compare to features of other TDP-43 lesions. We performed TDP-43 immunohistochemistry with anti-phosphorylated, C- and N-terminal TDP-43 antibodies in 20 high-probability AD cases and semi-quantitative burden of seven inclusion types within five brain regions (entorhinal cortex, subiculum, CA1 and dentate gyrus of hippocampus, occipitotemporal cortex). Hierarchical cluster analysis was used to analyze the dataset that consisted of 75 different combinations of neuropathological features. TATs were nonspherical with heterogeneous staining patterns and present in all regions except hippocampal dentate. All three antibodies detected TATs although N-terminal antibody sensitivity was low. Three clusters were identified: Cluster-1 had mild-moderate TATs, moderate-frequent neuronal cytoplasmic inclusions, dystrophic neurites, neuronal intranuclear inclusions and fine neurites, and perivascular and granular inclusions identified only with the N-terminal antibody throughout the brain; Cluster-2 had scant TATs in limbic regions and Cluster-3 mild-moderate TATs and mild-moderate neuronal cytoplasmic inclusions and dystrophic neurites throughout the brain and moderate fine neurites. Only 17% of cluster 1 cases had the TMEM106b GG (protective) haplotype and 83% had hippocampal sclerosis. Both features differed across clusters (p=0.03 & p=0.01). TATs have molecular characteristics, distribution and burden, and genetic and pathologic associations like FTLD-TDP lesions.

High-risk genotypes for type 1 diabetes are associated with the imbalance of gut microbiome and serum metabolites.

The profile of gut microbiota, serum metabolites, and lipids of type 1 diabetes (T1D) patients with different human leukocyte antigen (HLA) genotypes remains unknown. We aimed to explore gut microbiota, serum metabolites, and lipids signatures in individuals with T1D typed by HLA genotypes. We did a cross-sectional study that included 73 T1D adult patients. Patients were categorized into two groups according to the HLA haplotypes they carried: those with any two of three susceptibility haplotypes (DR3, DR4, DR9) and without any of the protective haplotypes (DR8, DR11, DR12, DR15, DR16) were defined as high-risk HLA genotypes group (HR, n=30); those with just one or without susceptibility haplotypes as the non-high-risk HLA genotypes group (NHR, n=43). We characterized the gut microbiome profile with 16S rRNA gene amplicon sequencing and analyzed serum metabolites with liquid chromatography-mass spectrometry. Study individuals were 32.5 (8.18) years old, and 60.3% were female. Compared to NHR, the gut microbiota of HR patients were characterized by elevated abundances of Prevotella copri and lowered abundances of Parabacteroides distasonis. Differential serum metabolites (hypoxanthine, inosine, and guanine) which increased in HR were involved in purine metabolism. Different lipids, phosphatidylcholines and phosphatidylethanolamines, decreased in HR group. Notably, Parabacteroides distasonis was negatively associated (p ≤ 0.01) with hypoxanthine involved in purine metabolic pathways. The present findings enabled a better understanding of the changes in gut microbiome and serum metabolome in T1D patients with HLA risk genotypes. Alterations of the gut microbiota and serum metabolites may provide some information for distinguishing T1D patients with different HLA risk genotypes.

Systems genomics in age-related macular degeneration.

Genomic studies in age-related macular degeneration (AMD) have identified genetic variants that account for the majority of AMD risk. An important next step is to understand the functional consequences and downstream effects of the identified AMD-associated genetic variants. Instrumental for this next step are 'omics' technologies, which enable high-throughput characterization and quantification of biological molecules, and subsequent integration of genomics with these omics datasets, a field referred to as systems genomics. Single cell sequencing studies of the retina and choroid demonstrated that the majority of candidate AMD genes identified through genomic studies are expressed in non-neuronal cells, such as the retinal pigment epithelium (RPE), glia, myeloid and choroidal cells, highlighting that many different retinal and choroidal cell types contribute to the pathogenesis of AMD. Expression quantitative trait locus (eQTL) studies in retinal tissue have identified putative causal genes by demonstrating a genetic overlap between gene regulation and AMD risk. Linking genetic data to complement measurements in the systemic circulation has aided in understanding the effect of AMD-associated genetic variants in the complement system, and supports that protein QTL (pQTL) studies in plasma or serum samples may aid in understanding the effect of genetic variants and pinpointing causal genes in AMD. A recent epigenomic study fine-mapped AMD causal variants by determing regulatory regions in RPE cells differentiated from induced pluripotent stem cells (iPSC-RPE). Another approach that is being employed to pinpoint causal AMD genes is to produce synthetic DNA assemblons representing risk and protective haplotypes, which are then delivered to cellular or animal model systems. Pinpointing causal genes and understanding disease mechanisms is crucial for the next step towards clinical translation. Clinical trials targeting proteins encoded by the AMD-associated genomic loci C3, CFB, CFI, CFH, and ARMS2/HTRA1 are currently ongoing, and a phase III clinical trial for C3 inhibition recently showed a modest reduction of lesion growth in geographic atrophy. The EYERISK consortium recently developed a genetic test for AMD that allows genotyping of common and rare variants in AMD-associated genes. Polygenic risk scores (PRS) were applied to quantify AMD genetic risk, and may aid in predicting AMD progression. In conclusion, genomic studies represent a turning point in our exploration of AMD. The results of those studies now serve as a driving force for several clinical trials. Expanding to omics and systems genomics will further decipher function and causality from the associations that have been reported, and will enable the development of therapies that will lessen the burden of AMD.

County-wide assessments of Illinois white-tailed deer (Odocoileus virginianus) prion protein gene variation using improved primers and potential implications for management.

Chronic wasting disease (CWD) is a fatal, highly infectious prion disease that affects captive and wild cervids. Chronic wasting disease is the only known transmissible spongiform encephalopathy affecting free-ranging wildlife. In CWD-positive deer, some haplotypes of the prion protein gene PRNP are detected at lower frequencies as compared to CWD-negative deer, as are some variants of the prion protein PrP. Here, we examined wild, hunter-harvested CWD-negative white-tailed deer (Odocoileus virginianus) to determine whether there were geographical or temporal differences in the PRNP haplotypes, PRNP diplotypes, PrP proteoforms, and in the proportion of deer with at least one protective haplotype. We sampled 96-100 hunter-harvested deer per county at two time points in the Illinois counties of Jo Daviess, LaSalle, and Winnebago, chosen based on their geographic locations and known occurrence of CWD. The entire coding region of PRNP was sequenced, with haplotypes, diplotypes, and PrP proteoforms inferred. Across time, in Winnebago there was a significant increase in PrP proteoform F (p = 0.034), which is associated with a lower vulnerability to CWD. In every county, there was an increase over time in the frequency of deer carrying at least one protective haplotype to CWD, with a significant increase (p = 0.02) in the Jo Daviess County CWD infected region. We also found that primer combination was important as there was an 18.7% difference in the number of the deer identified as homozygous depending on primer usage. Current Illinois state management practices continue to remove CWD infected deer from locally infected areas helping to keep CWD prevalence low. Nonetheless, continued research on spatial and temporal changes in PRNP haplotypes, PrP proteoforms, and levels of deer vulnerability among Illinois deer will be important for the management of CWD within the state of Illinois and beyond.

Association of Predisposing Haplotype Snp-Markers of HBB Gene in Thalassaemia

Most of the beta thalassaemia cases are heterogeneous at the molecular level. The genetic variation arises due to the mutation of a single beta-globin gene (HBB) on chromosome 11p15.5. Eventhough, the basis and natural history of this disorder are still not well understood and the clinical presentation in certain patients was not always correlated well with the single gene diagnosis [1].
 
 The study aimed to evaluate the predisposing effect of HBB polymorphisms and their haplotypes in conferring beta-thalassaemia in Malaysia using a bioinformatics tool. Archived genotype data for five tagging SNPs of HBB gene assigned as c.9T/C, IVS2-16G/C, IVS2-74T/G, 3'UTR +314G/A and 3'UTR +316A/C across thalassaemia patient group (n=433) and normal control group (n=794) controls were retrieved from the year 2011 to 2016 at Institute for Medical Research (IMR). The genotype data were analysed for individual SNP-based association analysis and haplotype-based association analysis using SHEsis online software.
 
 The study in all races in Malaysia showed significant association in four SNPs of the HBB gene (c.9T/C, P-value = 0.014; IVS2-16G/C, P-value = 0.017; 3'UTR+314G/A, P value = 2.08x108; 3'UTR+316A/C, P-value = 0.021). However, IVS2-74T/G did not show significant association with a P-value of 0.763 (Table 1). We further revealed two susceptible haplotypes in all races (haplotype TGTAA, P-value = 1.68x10-7, OR = 2.382 [1.707~3.325]; haplotype CCTGC, P-value = 0.003, OR = 1.300 [1.089~1.551]). Meanwhile, one protective haplotype observed was haplotype TGTGA (P-value = 2.99x10-7, OR = 0.625 [0.522~0.749]) (Table 2).
 In conclusion, this study suggests the potential susceptible and protective haplotypes of the HBB gene in predisposing to beta-thalassaemia in Malaysia

Autoimmune-associated genetics impact probiotic colonization of the infant gut

To exemplify autoimmune-associated genetic influence on the colonization of bacteria frequently used in probiotics, microbial composition of stool from 1326 one-year-old infants was analyzed in a prospective general-population cohort, All Babies In Southeast Sweden (ABIS). We show that an individual's HLA haplotype composition has a significant impact on which common Bifidobacterium strains thrive in colonizing the gut. The effect HLA has on the gut microbiome can be more clearly observed when considered in terms of allelic dosage. HLA DR1-DQ5 showed the most significant and most prominent effect on increased Bifidobacterium relative abundance. Therefore, HLA DR1-DQ5 is proposed to act as a protective haplotype in many individuals. Protection-associated HLA haplotypes are more likely to influence the promotion of specific bifidobacteria. In addition, strain-level differences are correlated with colonization proficiency in the gut depending on HLA haplotype makeup. These results demonstrate that HLA genetics should be considered when designing effective probiotics, particularly for those at high genetic risk for autoimmune diseases.

Associations between Extracellular Matrix Protein 1 Gene Polymorphism and Progression of Liver Disease.

Background Our study aimed to investigate the relationship between extracellular matrix 1 (ECM1) gene polymorphism and progression of liver fibrosis in the Chinese population. Methods A total 656 patients with hepatitis B virus (HBV) infection and 298 healthy individuals of the Chinese Han population were recruited for a retrospective case-control study. Of the disease group, 104 cases had chronic hepatitis B (CHB), 266 had LC, and 286 had hepatocellular carcinoma (HCC). Subjects were frequency-matched according to age and gender. Polymorphisms of the ECM1 gene were examined using the MassARRAY SNP genotyping method. Results There were no associations between genotype and allele frequencies of ECM1 rs3737240 and rs13294 loci with the risk of CHB and CHB-related HCC. After adjustment for age, sex, smoking status, and drinking habits, the GT genotype was dramatically related to a reduced risk of chronic HBV infection in both non-HCC (OR = 0.68, 95% CI: 0.49-0.94) and total chronic HBV infection patients (OR = 0.75, 95% CI: 0.56-1.00). Haplotype analyses revealed twelve protective haplotypes against total chronic HBV infection and four against non-HCC chronic HBV infection. Conclusion ECM1 gene polymorphism in rs3834087 and rs3754217 loci is associated with a reduced risk of chronic HBV infection but not with liver fibrosis development and the occurrence of HCC.

Association between CARD14 gene polymorphisms and psoriasis vulgaris in Hainan Han population based on exon sequencing: A case-control study.

Psoriasis is a serious non-communicable, chronic immune-inflammatory mediated disease affecting about 125 million people worldwide. Its effects go beyond skin manifestation. Through genome-wide association studies, the caspase recruitment domain family member 14 (CARD14) gene and other gene variants have been implicated to have an association with Psoriasis, and as we move towards individualized therapy the discovery of single nucleotide polymorphism (SNP) is of great importance. This study aimed to determine whether the CARD14 gene is a susceptible gene for psoriasis vulgaris. In this study, 101 psoriasis patients and 79 healthy controls were subjected to exome sequencing. The CARD14 gene regions upstream and downstream of 1kb were sequenced. SNP-based association analysis and haplotype-based association analysis were performed in SNPs with minimum allele frequency (MAF) greater than 1%. Bioinformatic methods were used to predict the impact of risk loci on gene function. A total of 32 polymorphisms were identified in this study, of which 3 SNPs (1 in exon and 2 in intron) were susceptible to psoriasis (P < .05, OR = 0.19~0.53, 95%CI = 0.05~0.70). Bioinformatics analysis showed that rs144475004 located on the exon led to an amino acid change from aspartate to histidine. On the other hand, results of haplotype-based association analysis showed that 2 haplotypes (CARD14-1 and CARD14-2) were protective haplotypes of the disease (P < .05, OR = 0.18~0.38, 95%CI = 0.05~0.88), the frequencies in healthy controls and patients was 6.96% and 1.49%, respectively. CARD14 gene is associated with susceptibility to psoriasis vulgaris in the Hainan Han population.

Large registry-based analysis of genetic predisposition to tuberculosis identifies genetic risk factors at HLA.

Tuberculosis is a significant public health concern resulting in the death of over 1 million individuals each year worldwide. While treatment options and vaccines exist, a substantial number of infections still remain untreated or are caused by treatment resistant strains. Therefore, it is important to identify mechanisms that contribute to risk and prognosis of tuberculosis as this may provide tools to understand disease mechanisms and provide novel treatment options for those with severe infection. Our goal was to identify genetic risk factors that contribute to the risk of tuberculosis and to understand biological mechanisms and causality behind the risk of tuberculosis. A total of 1895 individuals in the FinnGen study had International Classification of Diseases-based tuberculosis diagnosis. Genome-wide association study analysis identified genetic variants with statistically significant association with tuberculosis at the human leukocyte antigen (HLA) region (P < 5e-8). Fine mapping of the HLA association provided evidence for one protective haplotype tagged by HLA DQB1*05:01 (P = 1.82E-06, OR = 0.81 [CI 95% 0.74-0.88]), and predisposing alleles tagged by HLA DRB1*13:02 (P = 0.00011, OR = 1.35 [CI 95% 1.16-1.57]). Furthermore, genetic correlation analysis showed association with earlier reported risk factors including smoking (P < 0.05). Mendelian randomization supported smoking as a risk factor for tuberculosis (inverse-variance weighted P < 0.05, OR = 1.83 [CI 95% 1.15-2.93]) with no significant evidence of pleiotropy. Our findings indicate that specific HLA alleles associate with the risk of tuberculosis. In addition, lifestyle risk factors such as smoking contribute to the risk of developing tuberculosis.

LTBP4, SPP1, and CD40 Variants: Genetic Modifiers of Duchenne Muscular Dystrophy Analyzed in Serbian Patients.

Background: Clinical course variability in Duchenne muscular dystrophy (DMD) is partially explained by the mutation location in the DMD gene and variants in modifier genes. We assessed the effect of the SPP1, CD40, and LTBP4 genes and DMD mutation location on loss of ambulation (LoA). Methods: SNPs in SPP1-rs28357094, LTBP4-rs2303729, rs1131620, rs1051303, rs10880, and CD40-rs1883832 were genotyped, and their effect was assessed by survival and hierarchical cluster analysis. Results: Patients on glucocorticoid corticosteroid (GC) therapy experienced LoA one year later (p = 0.04). The modifying effect of SPP1 and CD40 variants, as well as LTBP4 haplotypes, was not observed using a log-rank test and multivariant Cox regression analysis. Cluster analysis revealed two subgroups with statistical trends in differences in age at LoA. Almost all patients in the cluster with later LoA had the protective IAAM LTBP4 haplotype and statistically significantly fewer CD40 genotypes with harmful T allele and “distal” DMD mutations. Conclusions: The modifying effect of SPP1, CD40, and LTBP4 was not replicated in Serbian patients, although our cohort was comparable in terms of its DMD mutation type distribution, SNP allele frequencies, and GC-positive effect with other European cohorts. Cluster analysis may be able to identify patient subgroups carrying a combination of the genetic variants that modify LoA.

Mast cell infiltration of the choroid and protease release are early events in age-related macular degeneration associated with genetic risk at both chromosomes 1q32 and 10q26.

Age-related macular degeneration (AMD) is a leading cause of visual loss. It has a strong genetic basis, and common haplotypes on chromosome (Chr) 1 (CFH Y402H variant) and on Chr10 (near HTRA1/ARMS2) contribute the most risk. Little is known about the early molecular and cellular processes in AMD, and we hypothesized that analyzing submacular tissue from older donors with genetic risk but without clinical features of AMD would provide biological insights. Therefore, we used mass spectrometry–based quantitative proteomics to compare the proteins in human submacular stromal tissue punches from donors who were homozygous for high-risk alleles at either Chr1 or Chr10 with those from donors who had protective haplotypes at these loci, all without clinical features of AMD. Additional comparisons were made with tissue from donors who were homozygous for high-risk Chr1 alleles and had early AMD. The Chr1 and Chr10 risk groups shared common changes compared with the low-risk group, particularly increased levels of mast cell–specific proteases, including tryptase, chymase, and carboxypeptidase A3. Histological analyses of submacular tissue from donors with genetic risk of AMD but without clinical features of AMD and from donors with Chr1 risk and AMD demonstrated increased mast cells, particularly the tryptase-positive/chymase-negative cells variety, along with increased levels of denatured collagen compared with tissue from low–genetic risk donors. We conclude that increased mast cell infiltration of the inner choroid, degranulation, and subsequent extracellular matrix remodeling are early events in AMD pathogenesis and represent a unifying mechanistic link between Chr1- and Chr10-mediated AMD.

Association of gene polymorphisms of ACE, AGT, and ARNT-like protein 1 with susceptibility to gestational diabetes

Background and aimsGestational diabetes mellitus is well-defined as glucose intolerance first documented during pregnancy. In this study, we examined the possible associations between I/D polymorphism of the angiotensin-converting enzyme gene, the M235T variant of angiotensinogen gene, and the rs7950226 polymorphism of the ARNT-like protein-1 (BMAL1) gene and the risk for diabetes in Egyptian pregnant women.Subjects and methodsThis study recruited 160 gestational diabetes cases and 165 controls. Genomic DNA was derived from peripheral blood leukocytes and ACE gene (I/D) genotyping was performed using the method of polymerase chain reaction and the polymerase chain reaction-based restriction fragment length polymorphism was used for identifying the M235T variant of AGT gene and the rs7950226 polymorphism of the BMAL1.ResultsThe II, ID, and DD genotypes of the ACE gene have significant differences in cases compared to controls (P = 0.000 and X2 = 81.77). The M235T polymorphism of the AGT gene was increased with gestational diabetes risk. Furthermore, the AA genotype of the BMAL1 rs7950226 gene was significantly related to the gestational diabetes risk (P = 0.000 and X2 = 52.82). Furthermore, the allele frequencies of the three variants have significant variances between cases and control.ConclusionThis study suggested significant associations between ACE (DD), AGT (TT), and BMAL1 rs7950226 (AA) gene polymorphisms with gestational diabetes susceptibility and there was a possibility to identify that II + MM + GG as protective haplotypes and DD + TT + AA as risk haplotypes for gestational diabetes.

P696 Genetic predisposition to infliximab immunogenicity in patients with immune-mediated inflammatory diseases – secondary analyses from a randomised clinical trial

Abstract Background Immunogenicity is a leading cause of treatment failure to TNF inhibitors. Genetic variations in HLA class II genes have been suggested to predispose to anti-drug antibody formation, but studies using high-resolution HLA typing as well as characterisation of biologically relevant haplotypes are currently lacking. The aim of this study was to assess associations between HLA loci and immunogenicity to infliximab. Methods Patients with immune-mediated inflammatory diseases (IMID) treated with infliximab (N=612) (120 rheumatoid arthritis, 181 spondyloarthritis, 72 psoriatic arthritis, 114 ulcerative colitis, 80 Crohn disease, and 45 psoriasis) were included in the randomised, Norwegian Drug Monitoring (NOR-DRUM) trial. Neutralising anti-drug antibodies were detected with an automated fluorescence assay. Next generation HLA sequencing at G group resolution were performed and trimmed to 2nd field. Haplotype analyses including the most significant HLA loci were performed, and epitope predictions for the infliximab light- and heavy-chain were assessed. Results Anti-drug antibodies to infliximab were detected in 147 (24 %) of patients. The most significant associations with immunogenicity were with the genes HLA-DQB1 (P=1.4x10-6), -DRB1 (P= 2.7x10-5), -DQA1 (P=0.00017) and -B (P=0.0009). Conditional analyses indicated that HLA-DQB1 represents the primary association(Table 1). Haplotype analyses showed that there was significantly increased risk of immnogenicity in patients carrying the HLA-DQ2 haplotypes DQB1*02:01~DQA1*05:01 (P=1.1x10-6) and DQB1*02:02~DQA1*02:01 (P=0.008), while one protective haplotype DQB1*05:01~DQA1*01:01 (P=0.0005) was identified (Figure 1a-c). Presence of HLA-DQ2 more than doubled the risk of anti-drug antibody formation (HR 2.54, 95%CI 1.82–3.56) (Figure 1d), in a model including the covariates age, sex, diagnosis, and concomitant immunosuppressive therapy. Association tests of each level of HLA analyses showed that HLA-DQ2 represents the strongest association(Figure 2). Epitope predictions revealed that the HLA-DQ2 haplotypes DQB1*02:01-DQA1*05:01 and DQB1*02:02-DQA1*02:01 share nine strong binder peptides, originating from the infliximab light chain, encompassing the amino acid core-peptide sequences INTVESEDI and VYACEVTHQ. Conclusion Using high-resolution HLA sequencing, we here demonstrate a genetic association between HLA-DQ2 and infliximab immunogenicity in IMID patients. The presence of either HLA-DQ2 risk haplotypes more than doubled the risk of anti-drug antibody formation across all diagnoses. Testing for HLA-DQ2 could be of clinical value in identifying patients at risk for immunogenicity and facilitate treatment decisions. Whether these findings apply to other TNF inhibitors should be further explored.

Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19

The OAS1/2/3 cluster has been identified as a risk locus for severe COVID-19 among individuals of European ancestry, with a protective haplotype of approximately 75 kilobases (kb) derived from Neanderthals in the chromosomal region 12q24.13. This haplotype contains a splice variant of OAS1, which occurs in people of African ancestry independently of gene flow from Neanderthals. Using trans-ancestry fine-mapping approaches in 20,779 hospitalized cases, we demonstrate that this splice variant is likely to be the SNP responsible for the association at this locus, thus strongly implicating OAS1 as an effector gene influencing COVID-19 severity.

Ancestry‐specific intronic variants on the APOE ɛ4 haplotype influence enhancer activity and interaction with APOE promoter

The risk for late-onset Alzheimer disease (AD) in APOEε4 carriers differs between ancestral groups, where APOEε4's odds ratio for AD risk is lower in African (AFR) homozygous carriers than in non-Hispanic White (NHW) or Japanese (JPT) carriers (odds ratio ∼2-5 vs >15). Local ancestry (LA) analyses in APOEε4 carrier populations have shown the protective effect in AFR relative to EUR/JPT is due to noncoding factors lying in the LA surrounding APOEε4. Thus, regulatory differences between risk and protective LA haplotypes are most likely involved in the differential risk effect seen for APOEε4 on different backgrounds.We identified 56 significant sequence differences between AFR and EUR/JPT APOEε4 haplotypes from the 1000 genomes in the immediate topologically associated domain surrounding APOE. We performed two different Massively Parallel Reporter Assay (MPRA) designs; one assessing small haplotype (∼900bp) effects and one based upon single variant effects. We supplemented these results with single fragment luciferase reporter assays. All assays were performed in at least duplicate in HMC3 (microglia), U118 (astrocytes) and SH-SY5Y (neurons) cell lines. Additionally, we integrated chromatin interaction information from promoter capture C chromatin conformation assays in the same cell types.We identified a region in the first introns of TOMM40 with increased EUR/JPT enhancer activity, supported by both MPRA analyses and APOE promoter interaction in astrocytes and microglia. Two additional regions with differential enhancer activity in neurons, but no promoter interaction, were identified; downstream of APOE and in PVRL2 introns upstream of APOE presenting with higher EUR or higher JPT haplotype variant enhancer activity compared to AFR, respectively.Our results indicate several areas of differential regulation in this LA region on APOEε4 haplotypes dependent on cell type. As APOE is mostly expressed in glial cells, the data in TOMM40 introns points to this region as having the biggest impact on APOE expression in our study and thus highly supports the involvement of this region in the differential risk effects seen for APOEε4. Follow-up of the identified regulatory regions is currently ongoing using in-house iPSC derived cell lines.

ERAP1 Controls the Autoimmune Response against Melanocytes in Psoriasis by Generating the Melanocyte Autoantigen and Regulating Its Amount for HLA-C*06:02 Presentation.

Autoimmune diseases develop when autoantigens activate previously quiescent self-reactive lymphocytes. Gene-gene interaction between certain HLA class I risk alleles and variants of the endoplasmic reticulum aminopeptidase ERAP1 controls the risk for common immune-mediated diseases, including psoriasis, ankylosing spondylitis, and Behçet disease. The functional mechanisms underlying this statistical association are unknown. In psoriasis, HLA-C*06:02 mediates an autoimmune response against melanocytes by autoantigen presentation. Using various genetically modified cell lines together with an autoreactive psoriatic TCR in a TCR activation assay, we demonstrate in this study that in psoriasis, ERAP1 generates the causative melanocyte autoantigen through trimming N-terminal elongated peptide precursors to the appropriate length for presentation by HLA-C*06:02. An ERAP1 risk haplotype for psoriasis produced the autoantigen much more efficiently and increased HLA-C expression and stimulation of the psoriatic TCR by melanocytes significantly more than a protective haplotype. Compared with the overall HLA class I molecules, cell surface expression of HLA-C decreased significantly more upon ERAP1 knockout. The combined upregulation of ERAP1 and HLA-C on melanocytes in psoriasis lesions emphasizes the pathogenic relevance of their interaction in patients. We conclude that in psoriasis pathogenesis, the increased generation of an ERAP1-dependent autoantigen by an ERAP1 risk haplotype enhances the likelihood that autoantigen presentation by HLA-C*06:02 will exceed the threshold for activation of potentially autoreactive T cells, thereby triggering CD8+ T cell-mediated autoimmune disease. These data identify ERAP1 function as a central checkpoint and promising therapeutic target in psoriasis and possibly other HLA class I-associated diseases with a similar genetic predisposition.

Prevalence of protective haplotypes of the SLCO1B1 gene for statin transport in Mexican populations.

Aim: To evaluate the genetic distribution of the rs4149056 and rs2306283 variants inthe SLCO1B1 gene in Mexican Mestizo (admixed) and Native American groups. Materials& methods: We recruited 360 volunteers who were qPCR-genotyped with TaqMan probes. Results: Allele and genotype frequencies are reported. Among the expected rs4149056-rs2306283 haplotypes, T-A (42.35-58.47%) was the most prevalent which relates to the normal activity of the OATP1B1 transporter. This was followed by the T-G haplotype associated with further statin transport and cholesterol reduction (32.49-43.76%). Conclusion: Based on these SLCO1B1 gene variants, we confirmed that a minimum fraction of the Mexican study populations would be at risk from decreasing simvastatin transportand the development of statin-induced myopathy.

Association and Gene-Gene Interactions Study of Late-Onset Alzheimer's Disease in the Russian Population.

Alzheimer’s disease (AD) is a neurodegenerative disorder, and represents the most common cause of dementia. In this study, we performed several different analyses to detect loci involved in development of the late onset AD in the Russian population. DNA samples from 472 unrelated subjects were genotyped for 63 SNPs using iPLEX Assay and real-time PCR. We identified five genetic loci that were significantly associated with LOAD risk for the Russian population (TOMM40 rs2075650, APOE rs429358 and rs769449, NECTIN rs6857, APOE ε4). The results of the analysis based on comparison of the haplotype frequencies showed two risk haplotypes and one protective haplotype. The GMDR analysis demonstrated three significant models as a result: a one-factor, a two-factor and a three-factor model. A protein–protein interaction network with three subnetworks was formed for the 24 proteins. Eight proteins with a large number of interactions are identified: APOE, SORL1, APOC1, CD33, CLU, TOMM40, CNTNAP2 and CACNA1C. The present study confirms the importance of the APOE-TOMM40 locus as the main risk locus of development and progress of LOAD in the Russian population. Association analysis and bioinformatics approaches detected interactions both at the association level of single SNPs and at the level of genes and proteins.

Extended haplotypes based on rare single nucleotide polymorphisms of TNFA and HLA DRB1 associated with rheumatoid arthritis

Rheumatoid arthritis (RA) is a multifactorial disease, with genetic component based on intergenic interactions leading to the formation of gene networks. The current trend in RA immunogenetic studies is to assess the gene-to-gene interactions. Among possible genetic factors contributing to RA development, the genes of main histocompatibility complex (HLA class II) play a fundamental role. TNFA gene is among possible candidate genes providing susceptibility to this disorder and contributing to its immune pathogenesis. The special location of this gene suggests arrangement of extended TNFA – HLA haplotypes. This work analyzed the distribution features of two-locus SNP haplotypes (TNFA and HLA DRB1) for their association with rheumatoid arthritis in Russians. The following methods were used: DNA isolation, PCR-based genotyping, RFLP analysis with electrophoretic detection. Calculation of two-locus haplotypes frequencies and linkage disequilibrium (D’; χ2; p) was carried out using the EM algorithm in the Arlequin ver 3.5 program. Comparison of paired samples was carried out using standard immunogenetic criteria. The significance level was 0.05. Analysis of the data showed that the two-locus haplotypes -1031T/C and -863C/A TNFA were not associated with predisposal for rheumatoid arthritis in Russian population sample. The haplotypes associated with predisposition for RA were TNFA -863*a – HLA DRB1*03, TNFA -1031*t – HLA DRB1*04, TNFA -1031*t – HLA DRB1*04. Meanwhile, TNFA -1031*t – HLA DRB1*15; TNFA -1031*t -HLA DRB1*11 proved to be protective haplotypes. Our study showed that, in addition to individual HLA II alleles, the predisposal or resistance to rheumatoid arthritis may be promoted by haplotypes of rare SNPs at positions -1031, -863 C/A of TNFA gene, and HLA DRB1.

A Low-Producing Haplotype of Interleukin-6 Disrupting CTCF Binding Is Protective against Severe COVID-19.

ABSTRACTInterleukin6 (IL-6) is a key driver of hyperinflammation in COVID-19, and its level strongly correlates with disease progression. To investigate whether variability in COVID-19 severity partially results from differential IL-6 expression, functional single-nucleotide polymorphisms (SNPs) of IL-6 were determined in Chinese COVID-19 patients with mild or severe illness. An Asian-common IL-6 haplotype defined by promoter SNP rs1800796 and intronic SNPs rs1524107 and rs2066992 correlated with COVID-19 severity. Homozygote carriers of C-T-T variant haplotype were at lower risk of developing severe symptoms (odds ratio, 0.256; 95% confidence interval, 0.088 to 0.739; P = 0.007). This protective haplotype was associated with lower levels of IL-6 and its antisense long noncoding RNA IL-6-AS1 by cis-expression quantitative trait loci analysis. The differences in expression resulted from the disturbance of stimulus-dependent bidirectional transcription of the IL-6/IL-6-AS1 locus by the polymorphisms. The protective rs2066992-T allele disrupted a conserved CTCF-binding locus at the enhancer elements of IL-6-AS1, which transcribed antisense to IL-6 and induces IL-6 expression in inflammatory responses. As a result, carriers of the protective allele had significantly reduced IL-6-AS1 expression and attenuated IL-6 induction in response to acute inflammatory stimuli and viral infection. Intriguingly, this low-producing variant that is endemic to present-day Asia was found in early humans who had inhabited mainland Asia since ∼40,000 years ago but not in other ancient humans, such as Neanderthals and Denisovans. The present study suggests that an individual's IL-6 genotype underlies COVID-19 outcome and may be used to guide IL-6 blockade therapy in Asian patients.