Blood Monocyte Phenotype Is A Marker of Cardiovascular Risk in Type 2 Diabetes

BACKGROUND

Diabetes is a major risk factor for atherosclerotic cardiovascular diseases with a 2-fold higher risk of cardiovascular events in people with diabetes compared with those without. Circulating monocytes are inflammatory effector cells involved in both type 2 diabetes (T2D) and atherogenesis.

METHODS

We investigated the relationship between circulating monocytes and cardiovascular risk progression in people with T2D, using phenotypic, transcriptomic, and metabolomic analyses. cardiovascular risk progression was estimated with coronary artery calcium score in a cohort of 672 people with T2D.

RESULTS

Coronary artery calcium score was positively correlated with blood monocyte count and frequency of the classical monocyte subtype. Unsupervised k-means clustering based on monocyte subtype profiles revealed 3 main endotypes of people with T2D at varying risk of cardiovascular events. These observations were confirmed in a validation cohort of 279 T2D participants. The predictive association between monocyte count and major adverse cardiovascular events was validated through an independent prospective cohort of 757 patients with T2D. Integration of monocyte transcriptome analyses and plasma metabolomes showed a disruption of mitochondrial pathways (tricarboxylic acid cycle, oxidative phosphorylation pathway) that underlined a proatherogenic phenotype.

CONCLUSIONS

In this study, we provide evidence that frequency and monocyte phenotypic profile are closely linked to cardiovascular risk in patients with T2D. The assessment of monocyte frequency and count is a valuable predictive marker for risk of cardiovascular events in patients with T2D.

REGISTRATION

URL: https://www.clinicaltrials.gov; Unique identifier: NCT04353869.

Genetic variants of interferon-response factor 5 are associated with the incidence of chronic kidney disease: the D.E.S.I.R. study

Inflammation has been associated with renal diseases. The Interferon Regulatory Factor (IRF)-5 is a key transcription factor in the pro-inflammatory polarization of M1-like macrophages. GWAS have reported that the IRF5 locus is associated with autoimmune diseases and with the estimated glomerular filtration rate (eGFR). We study whether allelic variations in IRF5 are associated with the incidence of chronic kidney disease (CKD) in a general population. We genotyped eleven IRF5 SNPs in the French D.E.S.I.R. cohort from the general population (n = 4820). Associations of SNPs with baseline renal parameters were assessed. Data were analyzed for three endpoints during a 9-year follow-up, incidence of:at least stage 3 CKD, the KDIGO criterion "certain drop in eGFR", and incidence of micro/macro albuminuria. In the cross-sectional analysis, rs10954213 and rs10954214 were associated with eGFR and rs1874328 with urinary albumin/creatinine ratio (ACR). Rs3807306, rs11761199, rs78658945, rs1874328, rs10954213 and rs11770589 were associated with the incidence of stage 3 CKD in multi-adjusted models. Rs4731532, rs3807306, and rs11761199 were associated with the incidence of CKD defined by the KDIGO. Rs4731532, rs3807306, rs11761199 and rs79288514 were associated with the incidence of micro/macro albuminuria. Our results support the hypothesis of the importance of IRF5 mediated macrophage polarization in the etiology of CKD.

Are there differences in the relationship between respiratory rate and oxygen saturation between patients with COVID-19 and those without COVID-19? Insights from a cohort-based correlational study

BACKGROUND

Physicians have observed patients with COVID-19 without respiratory distress despite marked hypoxaemia and extensive radiographic abnormalities, a controversial phenomenon called 'silent hypoxaemia'. We aimed to compare the relationship between RR and peripheral oxygen saturation (SpO2) in patients with COVID-19 versus patients without COVID-19 when breathing air on admission.

METHODS

We conducted a retrospective multicentre ED cohort correlational study.We used the Spanish Investigators on Emergency Situations TeAm network cohort of patients with COVID-19 admitted to 61 Spanish EDs between March and April 2020. The non-COVID-19 cohort included patients with lower respiratory tract bacterial infections admitted between January 2016 and April 2018.We built a multivariable linear model to investigate the independent predictive factors related to RR and a logistic multivariate regression model to analyse the presence of 'silent hypoxaemia'.

RESULTS

We included 1094 patients with COVID-19 and 477 patients without COVID-19. On admission, RR was lower (20±7 vs 24±8/min, p<0.0001), while SpO2 higher (95±5% vs 90±7%, p<0.0001) in patients with COVID-19 versus patients without COVID-19. RR was negatively associated with SpO2 (RR decreasing with increasing age, beta=-0.37, 95% CI (-0.43; -0.31), p<0.0001), positively associated with age (RR increasing with increasing age, beta=0.05, 95% CI (0.03; 0.07), p<0.0001) and negatively associated with COVID-19 status (RR lower in patients with COVID-19, beta=-1.90, 95% CI (-2.65; -1.15), p<0.0001). The negative RR/SpO2 correlation differed between patients with COVID-19 aged <80 and ≥80 years old (p=0.04). Patients with COVID-19 aged ≥80 years old had lower RR than patients without COVID-19 aged ≥80 years old at SpO2 values <95% (22±7 vs 24±8/min, p=0.004). 'Silent hypoxaemia' defined as RR <20/min with SpO2 <95% was observed in 162 (14.8%) patients with COVID-19 and in 79 (16.6%) patients without COVID-19 (p=0.4). 'Silent hypoxaemia' was associated with age ≥80 years (OR=1.01 (1.01; 1.03), p<0.0001) but not with gender, comorbidities and COVID-19 status.

CONCLUSION

The RR/SpO2 relationship before oxygen administration does not differ between patients with COVID-19 and those without COVID-19, except in elderly patients.

How dysregulation of the immune system promotes diabetes mellitus and cardiovascular risk complications

Diabetes mellitus (DM) is a chronic metabolic disorder characterized by persistent hyperglycemia due to insulin resistance or failure to produce insulin. Patients with DM develop microvascular complications that include chronic kidney disease and retinopathy, and macrovascular complications that mainly consist in an accelerated and more severe atherosclerosis compared to the general population, increasing the risk of cardiovascular (CV) events, such as stroke or myocardial infarction by 2- to 4-fold. DM is commonly associated with a low-grade chronic inflammation that is a known causal factor in its development and its complications. Moreover, it is now well-established that inflammation and immune cells play a major role in both atherosclerosis genesis and progression, as well as in CV event occurrence. In this review, after a brief presentation of DM physiopathology and its macrovascular complications, we will describe the immune system dysregulation present in patients with type 1 or type 2 diabetes and discuss its role in DM cardiovascular complications development. More specifically, we will review the metabolic changes and aberrant activation that occur in the immune cells driving the chronic inflammation through cytokine and chemokine secretion, thus promoting atherosclerosis onset and progression in a DM context. Finally, we will discuss how genetics and recent systemic approaches bring new insights into the mechanisms behind these inflammatory dysregulations and pave the way toward precision medicine.

Regulation of inflammation in diabetes: From genetics to epigenomics evidence

Background

Diabetes is one of the greatest public health challenges worldwide, and we still lack complementary approaches to significantly enhance the efficacy of preventive and therapeutic approaches. Genetic and environmental factors are the culprits involved in diabetes risk. Evidence from the last decade has highlighted that deregulation in the immune and inflammatory responses increase susceptibility to type 1 and type 2 diabetes. Spatiotemporal patterns of gene expression involved in immune cell polarisation depend on genomic enhancer elements in response to inflammatory and metabolic cues. Several studies have reported that most regulatory genetic variants are located in the non-protein coding regions of the genome and particularly in enhancer regions. The progress of high-throughput technologies has permitted the characterisation of enhancer chromatin properties. These advances support the concept that genetic alteration of enhancers may influence the immune and inflammatory responses in relation to diabetes.

Scope of review

Results from genome-wide association studies (GWAS) combined with functional and integrative analyses have elucidated the impacts of some diabetes risk-associated variants that are involved in the regulation of the immune system. Additionally, genetic variant mapping to enhancer regions may alter enhancer status, which in turn leads to aberrant expression of inflammatory genes associated with diabetes susceptibility. The focus of this review was to provide an overview of the current indications that inflammatory processes are regulated at the genetic and epigenomic levels in diabetes, along with perspectives on future research avenues that may improve understanding of the disease.

Major conclusions

In this review, we provide genetic evidence in support of a deregulated immune response as a risk factor in diabetes. We also argue about the importance of enhancer regions in the regulation of immune cell polarisation and how the recent advances using genome-wide methods for enhancer identification have enabled the determination of the impact of enhancer genetic variation on diabetes onset and phenotype. This could eventually lead to better management plans and improved treatment responses in human diabetes.

Genetic association of molecular traits: A help to identify causative variants in complex diseases

In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies. The genetic variants that modulate them are called expression quantitative trait loci. Their study has been extended to other molecular quantitative trait loci (molQTLs) that regulate gene expression at the various levels, from chromatin state to cellular responses. Altogether, these studies have generated a wealth of basic information on the genome-wide patterns of gene expression and their inter-individual variation. Most importantly, molQTLs have become an invaluable asset in the genetic study of complex diseases. Although the identification of the disease-causing variants on the basis of their overlap with molQTLs requires caution, molQTLs can help to prioritize the relevant candidate gene(s) in the disease-associated regions and bring a functional interpretation of the associated variants, therefore, bridging the gap between genotypes and clinical phenotypes.

Network-based analysis of omics data: the LEAN method

Motivation

Most computational approaches for the analysis of omics data in the context of interaction networks have very long running times, provide single or partial, often heuristic, solutions and/or contain user-tuneable parameters.

Results

We introduce local enrichment analysis (LEAN) for the identification of dysregulated subnetworks from genome-wide omics datasets. By substituting the common subnetwork model with a simpler local subnetwork model, LEAN allows exact, parameter-free, efficient and exhaustive identification of local subnetworks that are statistically dysregulated, and directly implicates single genes for follow-up experiments.

Evaluation on simulated and biological data suggests that LEAN generally detects dysregulated subnetworks better, and reflects biological similarity between experiments more clearly than standard approaches. A strong signal for the local subnetwork around Von Willebrand Factor (VWF), a gene which showed no change on the mRNA level, was identified by LEAN in transcriptome data in the context of the genetic disease Cerebral Cavernous Malformations (CCM). This signal was experimentally found to correspond to an unexpected strong cellular effect on the VWF protein. LEAN can be used to pinpoint statistically significant local subnetworks in any genome-scale dataset.

Availability and Implementation

The R-package LEANR implementing LEAN is supplied as supplementary material and available on CRAN (https://cran.r-project.org).

Supplementary information

Supplementary data are available at Bioinformatics online.

Fine mapping genetic determinants of the highly variably expressed MHC gene ZFP57

ZFP57 is an important transcriptional regulator involved in DNA methylation and genomic imprinting during development. Here we demonstrate that gene expression also occurs at a low level in adult peripheral blood cells and other tissues including the kidney and thymus, but is critically dependent on underlying local genetic variation within the MHC. We resolve a highly significant expression quantitative trait locus for ZFP57 involving single-nucleotide polymorphisms (SNPs) in the first intron of the gene co-localizing with a DNase I hypersensitive site and evidence of CTCF recruitment. These data identify ZFP57 as a candidate gene underlying reported MHC disease associations, notably for putative regulatory variants associated with cancer and HIV-1. The work highlights the role that ZFP57 may play in DNA methylation and epigenetic regulation beyond early development into adult life dependent on genetic background, with important potential implications for disease.

Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex

The human major histocompatibility complex (MHC) on chromosome 6p21 is a paradigm for genomics, showing remarkable polymorphism and striking association with immune and non-immune diseases. The complex genomic landscape of the MHC, notably strong linkage disequilibrium, has made resolving causal variants very challenging. A promising approach is to investigate gene expression levels considered as tractable intermediate phenotypes in mapping complex diseases. However, how transcription varies across the MHC, notably relative to specific haplotypes, remains unknown. Here, using an original hybrid tiling and splice junction microarray that includes alternate allele probes, we draw the first high-resolution strand-specific transcription map for three common MHC haplotypes (HLA-A1-B8-Cw7-DR3, HLA-A3-B7-Cw7-DR15, and HLA-A26-B18-Cw5-DR3-DQ2) strongly associated with autoimmune diseases including type 1 diabetes, systemic lupus erythematosus, and multiple sclerosis. We find that haplotype-specific differences in gene expression are common across the MHC, affecting 96 genes (46.4%), most significantly the zing finger protein gene ZFP57. Differentially expressed probes are correlated with polymorphisms between haplotypes, consistent with cis effects that we directly demonstrate for ZFP57 in a cohort of healthy volunteers (P = 1.2 × 10(-14)). We establish that alternative splicing is significantly more frequent in the MHC than genome-wide (72.5% vs. 62.1% of genes, P ≤ 1 × 10(-4)) and shows marked haplotypic differences. We also unmask novel and abundant intergenic transcription involving 31% of transcribed blocks identified. Our study reveals that the renowned MHC polymorphism also manifests as transcript diversity, and our novel haplotype-based approach marks a new step toward identification of regulatory variants involved in the control of MHC-associated phenotypes and diseases.

Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1)

BACKGROUND

Asthma is a common, chronic inflammatory airway disease of major public health importance with multiple genetic determinants. Previously, we found by positional cloning that PHD finger protein 11 (PHF11) on chromosome 13q14 modifies serum immunoglobulin E (IgE) concentrations and asthma susceptibility. No coding variants in PHF11 were identified.

OBJECTIVE

Here we investigate the 3 single nucleotide polymorphisms (SNPs) in this gene most significantly associated with total serum IgE levels--rs3765526, rs9526569, and rs1046295--for a role in transcription factor binding.

METHODS

We used electrophoretic mobility shift assays to examine the effect of the 3 SNPs on transcription factor binding in 3 cell lines relevant to asthma pathogenesis. Relative preferential expression of alleles was investigated by using the allelotyping method.

RESULTS

Electrophoretic mobility shift assays show that rs1046295 modulates allele-specific binding by the octamer-binding transcription factor 1 (Oct-1). Analysis of the relative expression levels of the 2 alleles of this SNP in heterozygous individuals showed a modest, but highly significant (P = 6.5 × 10(-16)), preferential expression of the A allele consistent with a functional role for rs1046295.

CONCLUSION

These results suggest a mechanism by which rs1046295 may act as a regulatory variant modulating transcription at this locus and altering asthma susceptibility.

The human Major Histocompatibility Complex as a paradigm in genomics research

Since its discovery more than 50 years ago, the human Major Histocompatibility Complex (MHC) on chromosome 6p21.3 has been at the forefront of human genetic research. Here, we review from a historical perspective the major advances in our understanding of the nature and consequences of genetic variation which have involved the MHC, as well as highlighting likely future directions. As a consequence of its particular genomic structure, its remarkable polymorphism and its early implication in numerous diseases, the MHC has been considered as a model region for genomics, being the first substantial region to be sequenced and establishing fundamental concepts of linkage disequilibrium, haplotypic structure and meiotic recombination. Recently, the MHC became the first genomic region to be entirely re-sequenced for common haplotypes, while studies mapping gene expression phenotypes across the genome have strongly implicated variation in the MHC. This review shows how the MHC continues to provide new insights and remains in the vanguard of contemporary research in human genomics.

Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations

BACKGROUND

Localising regulatory variants that control gene expression is a challenge for genome research. Several studies have recently identified non-coding polymorphisms associated with inter-individual differences in gene expression. These approaches rely on the identification of signals of association against a background of variation due to other genetic and environmental factors. A complementary approach is to use an Allele-Specific Expression (ASE) assay, which is more robust to the effects of environmental variation and trans-acting genetic factors.

METHODOLOGY/PRINCIPAL FINDINGS

Here we apply an ASE method which utilises heterozygosity within an individual to compare expression of the two alleles of a gene in a single cell. We used individuals from three HapMap population groups and analysed the allelic expression of genes with cis-regulatory regions previously identified using total gene expression studies. We were able to replicate the results in five of the six genes tested, and refined the cis- associated regions to a small number of variants. We also showed that by using multi-populations it is possible to refine the associated cis-effect DNA regions.

CONCLUSIONS/SIGNIFICANCE

We discuss the efficacy and drawbacks of both total gene expression and ASE approaches in the discovery of cis-acting variants. We show that the ASE approach has significant advantages as it is a cleaner representation of cis-acting effects. We also discuss the implication of using different populations to map cis-acting regions and the importance of finding regulatory variants which contribute to human phenotypic variation.

Genetic factors in autoimmune myasthenia gravis

Autoimmune myasthenia gravis (MG) is a multifactorial disease, markedly influenced by genetic factors, even though it shows limited heritability. The clinically typical form of autoimmune MG with thymus hyperplasia shows the most reproducible genetic associations, especially with the A1-B8-DR3 (8.1) haplotype of the major histocompatibility complex (MHC). However, because of strong linkage disequilibrium, the causative polymorphism in this region is not known yet. Increasing the density of genetic markers has nevertheless recently revealed the complex, but highly significant contribution of this essential genetic region in controlling the disease phenotype and the quantitative expression of serum autoantibodies. The advances of the human genome program, the development of genotyping and sequencing tools with increasing throughput, and the availability of powerful statistical methods now make feasible the dissection of a complex genetic region, such as the MHC and beyond, the systematic search throughout the genome for variants influencing disease predisposition. The identification of such functional variants should provide new clues to the pathogenesis of MG, as recently illustrated by the study of a promoter polymorphism of the CHRNA1 locus, influencing its thymic expression and central tolerance, or of a coding variant of the PTPN22 intracellular phosphatase.

Chromatin profiling across the human tumour necrosis factor gene locus reveals a complex, cell type-specific landscape with novel regulatory elements

The TNF locus on chromosome 6p21 encodes a family of proteins with key roles in the immune response whose dysregulation leads to severe disease. Transcriptional regulation is important, with cell type and stimulus-specific enhancer complexes involving the proximal TNF promoter. We show how quantitative chromatin profiling across a 34 kb region spanning the TNF locus has allowed us to identify a number of novel DNase hypersensitive sites and characterize more distant regulatory elements. We demonstrate DNase hypersensitive sites corresponding to the lymphotoxin alpha (LTA) and tumour necrosis factor (TNF) promoter regions, a CpG island in exon 4 of lymphotoxin beta (LTB), the 3′ end of nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1 (NFKBIL1) and 3.4 kb upstream of LTA. These sites co-localize to highly conserved DNA sequences and show evidence of cell type specificity when lymphoblastoid, Jurkat, U937, HeLa and HEK293T cell lines are analysed using Southern blotting. For Jurkat T cells, we define histone modifications across the locus. Peaks of acetylated histone H3 and H4, together with tri-methyl K4 of histone H3, correspond to hypersensitive sites, notably in exon 4 of LTB. We provide evidence of a functional role for an intergenic DNase I hypersensitive site distal to LTA in Jurkat cells based on reporter gene analysis, with evidence of recruitment of upstream stimulatory factors (USF) transcription factors.

An IRF8-binding promoter variant and AIRE control CHRNA1 promiscuous expression in thymus

Promiscuous expression of tissue-restricted auto-antigens in the thymus imposes T-cell tolerance and provides protection from autoimmune diseases. Promiscuous expression of a set of self-antigens occurs in medullary thymic epithelial cells and is partly controlled by the autoimmune regulator (AIRE), a nuclear protein for which loss-of-function mutations cause the type 1 autoimmune polyendocrine syndrome. However, additional factors must be involved in the regulation of this promiscuous expression. Here we describe a mechanism controlling thymic transcription of a prototypic tissue-restricted human auto-antigen gene, CHRNA1. This gene encodes the alpha-subunit of the muscle acetylcholine receptor, which is the main target of pathogenic auto-antibodies in autoimmune myasthenia gravis. On re-sequencing the CHRNA1 gene, we identified a functional bi-allelic variant in the promoter that is associated with early onset of disease in two independent human populations (France and United Kingdom). We show that this variant prevents binding of interferon regulatory factor 8 (IRF8) and abrogates CHRNA1 promoter activity in thymic epithelial cells in vitro. Notably, both the CHRNA1 promoter variant and AIRE modulate CHRNA1 messenger RNA levels in human medullary thymic epithelial cells ex vivo and also in a transactivation assay. These findings reveal a critical function of AIRE and the interferon signalling pathway in regulating quantitative expression of this auto-antigen in the thymus, suggesting that together they set the threshold for self-tolerance versus autoimmunity.

Association of the PTPN22*R620W polymorphism with autoimmune myasthenia gravis

OBJECTIVE

Our objective was to investigate a role of the intracellular tyrosine phosphatase PTPN22*R620W variant in autoimmune myasthenia gravis (MG), considering disease heterogeneity.

METHODS

We used a case-control design, comparing 470 patients and 296 controls, all French whites. Patients were categorized depending on the presence of a thymoma and serum anti-titin antibodies.

RESULTS

The 620W risk allele was increased in 293 nonthymoma patients without anti-titin antibodies (odds ratio, 1.97; 95% confidence interval, 1.32-2.97, p = 0.00059) but not in nonthymoma patients with anti-titin antibodies or in thymoma patients.

INTERPRETATION

Our genetic findings strengthen the concept that these groups of patients correspond to etiologically distinct disease entities.

Genetics of autoimmune myasthenia gravis: The multifaceted contribution of the HLA complex

The HLA complex plays a prominent role in predisposition to many autoimmune diseases. Thus far, the highly polymorphic class I and class II loci have been considered as the prime candidates to explain this role. There is nonetheless growing evidence that other closely linked HLA loci are also involved in autoimmune susceptibility. Their search, however, has been hampered by the often strong linkage disequilibria, i.e. the non-random association of alleles at linked loci, across the HLA complex. Here, we discuss recent work from our laboratory on the dissection of this emblematic genetic region in a model autoimmune disease, acquired myasthenia gravis (MG).

Pleiotropic effects of the 8.1 HLA haplotype in patients with autoimmune myasthenia gravis and thymus hyperplasia

The 8.1 haplotype of the HLA complex has been reproducibly associated with several autoimmune diseases and traits, notably with thymus hyperplasia in patients with acquired generalized myasthenia gravis, an autoantibody-mediated disease directed at the muscle acetylcholine receptor. However, the strong linkage disequilibrium across this haplotype has prevented the identification of the causative locus, termed MYAS1. Here, we localized MYAS1 to a 1.2-Mb genome segment by reconstructing haplotypes and assessing their transmission in 73 simplex families. This segment encompasses the class III and proximal class I regions, between the BAT3 and C3-2-11 markers, therefore unambiguously excluding the class II loci. In addition, a case-control study revealed a very strong association with a core haplotype in this same region following an additive model (P=7 x 10(-11), odds ratio 6.5 for one copy and 42 for two copies of the core haplotype). Finally, we showed that this region is associated with a marked increase in serum titers of anti-acetylcholine receptor autoantibodies (P=8 x 10(-6)). Remarkably, this effect was suppressed by a second locus in cis on the 8.1 haplotype and located toward the class II region. Altogether, these data demonstrate the highly significant but complex effects of the 8.1 haplotype on the phenotype of myasthenia gravis patients and might shed light on its role in other autoimmune diseases.

Genetic linkage of progressive pseudorheumatoid dysplasia to a 3-cM interval of chromosome 6q22

Progressive pseudorheumatoid dysplasia (PPD), MIM 208230, is an autosomal-recessive disorder, clinically characterized by spondyloepiphyseal dysplasia and progressive arthropathy. Linkage analysis of three families of different geographic and ethnic origin, including 11 affected individuals, showed strong evidence for localization of a gene for progressive pseudorheumatoid dysplasia to chromosome 6q with a maximum two-point lod score for D6S1647 of 8.34 at theta=0. Analysis of regions of homozygosity placed the gene in a 3-cM interval between D6S 1594 and D6S432. No significant shared haplotype was found for markers of the linked interval in the three families analyzed. Five genes encoding collagen and one encoding a specific procollagen-processing enzyme that map near this interval represent good candidates for the PPD gene.