GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19

Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown1 to be highly efficient for discovery of genetic associations2. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group3. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

Novel genes and sex differences in COVID-19 severity

Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10-8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10-22 and P = 8.1 × 10-12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10-8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10-8) and ARHGAP33 (P = 1.3 × 10-8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10-8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.

T3 acutely increases GH mRNA translation rate and GH secretion in hypothyroid rats

Cytoskeleton controls the stability of transcripts, by mechanisms that involve mRNAs and eEF1A attachment to it. Besides, it plays a key role in protein synthesis and secretion, which seems to be impaired in somatotrophs of hypothyroid rats, whose cytoskeleton is disarranged. This study investigated the: eEF1A and GH mRNA binding to cytoskeleton plus GH mRNA translation rate and GH secretion, in sham-operated and thyroidectomized rats treated with T3 or saline, and killed 30min thereafter. Thyroidectomy reduced: (a) pituitary F-actin content, and eEF1A plus GH mRNA binding to it; (b) GH mRNA recruitment to polysome; and (c) liver IGF-I mRNA expression, indicating that GH mRNA stability and translation rate, as well as GH secretion were impaired. T3 acutely reversed all these changes, which points toward a nongenomic action of T3 on cytoskeleton rearrangement, which might contribute to the increase on GH mRNA translation rate and GH secretion.

MSX1 gene polymorphisms in non-syndromic cleft lip and/or palate

OBJECTIVE

The aim of this study was to investigate the contribution of 6 polymorphic variants of the MSX1 gene in non-syndromic cleft lip and/or palate (NSCL/P).

METHODS

Three hundred and fifty-eight individuals (158 NSCL/P cases and 200 controls) were genotyped by TaqMan allelic discrimination using predesigned SNP assays. Statistical analyses were conducted using the software spss 15.0 and the r statistical suite. Haplotype block structure and haplotype frequencies were determined using the Haploview. A P-value of 0.05 and confidence interval of 95% were used for all of statistical tests.

RESULTS

The patients with non-syndromic cleft lip and/or palate were characterized by similar distribution of MSX1 genotypes and allele in comparison to subjects without oral clefts (P > 0.05). Two haplotype blocks were constructed with polymorphisms of MSX1 gene and haplotypes formed showed a similar frequency in patients with and without oral clefts.

CONCLUSIONS

The present study provides no evidence that MSX1 polymorphisms (rs3775261, rs1042484, rs12532, rs6446693, rs4464513 and rs1907998) play a major role in NSCL/P.

mRNA-miRNA integrative analysis of diabetes-induced cardiomyopathy in rats

An integrative analysis of miRNA and mRNA expression profiles in left ventricle (LV) of diabetes-induced rats was performed to elucidate the role of miRNAs and their mRNAs target in diabetic cardiomyopathy (DCM). mRNA (GSE4745) and miRNA (GSE44179) datasets were downloaded from Gene Expression Omnibus 2R (GEO2R) and differentially expressed mRNAs and miRNAs were selected. Cardiotoxicity-related mRNAs (n=7) were analyzed by Ingenuity Pathway Analyses 6 (IPA) and regulatory miRNAs (n=639) were identified using TargetScan 7.1. web dataset. The integrative analysis was performed between miRNAs differentially expressed in GSE44179 and regulatory TargetScan-detected miRNAs of mRNAs differentially expressed in GSE4745. Pla2g2a and Hk2 mRNAs were up-and-down regulated, respectively, in GSE4745 on days 3 and 42 after diabetes-induction. The Pla2g2a regulatory miRNAs, rno-miR-877, rno-miR-320 and rno-miR-214, were down-regulated, and Hk2 regulatory miRNAs, rno-miR-17, rno-miR-187, rno-miR-34a, rno-miR-322, rno-miR-188, rno-miR-532 and rno-miR-21, were up-regulated in GSE44179 dataset. These results are suggestive that Pla2g2a and Hk2 mRNAs and their regulatory miRNAs play a role in DCM pathogenesis and they may be potential circulating biomarkers to detect early cardiovascular complications in diabetic patients.

Differentiation of African components of ancestry to stratify groups in a case-control study of a Brazilian urban population

BACKGROUND

Balancing the subject composition of case and control groups to create homogenous ancestries between each group is essential for medical association studies.

METHODS

We explored the applicability of single-tube 34-plex ancestry informative markers (AIM) single nucleotide polymorphisms (SNPs) to estimate the African Component of Ancestry (ACA) to design a future case-control association study of a Brazilian urban sample.

RESULTS

One hundred eighty individuals (107 case group; 73 control group) self-described as white, brown-intermediate or black were selected. The proportions of the relative contribution of a variable number of ancestral population components were similar between case and control groups. Moreover, the case and control groups demonstrated similar distributions for ACA <0.25 and >0.50 categories. Notably a high number of outlier values (23 samples) were observed among individuals with ACA <0.25. These individuals presented a high probability of Native American and East Asian ancestral components; however, no individuals originally giving these self-described ancestries were observed in this study.

CONCLUSIONS

The strategy proposed for the assessment of ancestry and adjustment of case and control groups for an association study is an important step for the proper construction of the study, particularly when subjects are taken from a complex urban population. This can be achieved using a straight forward multiplexed AIM-SNPs assay of highly discriminatory ancestry markers.

Maternal autoantibodies to the sodium potassium pump α1 subunit AT1A1 and fetal autoimmune congenital heart block: a case-control study

BACKGROUND

Fetal autoimmune congenital heart block is a rare but life-threatening condition that is difficult to predict. This study sought to identify a serological biomarker predictive of autoimmune congenital heart block in pregnancies at risk due to maternal systemic lupus erythematosus, Sjögren's disease, undifferentiated connective tissue disease, or a history of congenital heart block offspring.

METHODS

This case-control study analysed maternal blood samples from pregnancies affected and unaffected by autoimmune congenital heart block from two centres (The Hospital for Sick Children, Canada, and The University of Padua, Italy). Serum samples collected across varying gestational ages were used for biomarker discovery, verification, and validation. The key inclusion criterion was a positive clinical test for maternal anti-Sjögren's syndrome-related antigen A/Ro autoantibodies, and the key exclusion criterion was structural congenital heart disease associated with heart block. Cases were pregnancies that resulted in fetal or neonatal congenital heart block and controls were pregnancies that resulted in offspring with a normal heart rhythm. Two-dimensional western blotting was used to identify maternal autoantibodies targeting fetal cardiac proteins, using fetal heart tissue and stem-cell-derived cardiomyocytes. Findings were validated using commercial proteins. Sensitivity and specificity for predicting fetal heart block outcomes were assessed using receiver-operating characteristic curves. The primary study outcomes were the presence and specificity of anti-cardiac autoantibodies in autoimmune congenital heart block cases versus controls, the association between specific autoantibodies and congenital heart block development, and the predictive accuracy of identified autoantibodies. This study did not involve individuals with lived experience in the study design or implementation.

FINDINGS

Serum samples were collected between Jan 1, 2010, and Dec 31, 2020, in the discovery cohort (The Hospital for Sick Children), between Aug 1, 1999, and Dec 31, 2019 in the verification cohort (University Hospital of Padua), and between June 1, 2018, and Aug 31, 2023, in the validation cohort (The Hospital for Sick Children). Mean maternal age was 34·2 years (SD 5·2) in the discovery cohort, 33·5 years (4·6) in the verification cohort, and 32·8 years (4·3) in the validation cohort. Maternal serum samples from pregnancies affected by fetal autoimmune congenital heart block (cases; n=46) showed an expanded repertoire of anti-cardiac autoantibodies compared with unaffected pregnancies (controls; n=65). Mass spectrometry identified 11 potential cardiac protein targets for maternal autoantibodies and the presence of seven autoantibodies were confirmed in serum samples from affected pregnancies. Four targets were identified before the onset of congenital heart block (ANXA1, BIP, MYPC3, and AT1A1). Maternal autoantibodies against the Na+ and K+ ATPase α1 isoform (AT1A1) were detected as early as 7 weeks gestation and were present in all affected pregnancies of mothers with and without previous fetal heart block history (six [100%] of six in the discovery cohort, 22 [100%] of 22 in the verification cohort, and 16 [100%] of 16 in the validation cohort). Anti-AT1A1 autoantibodies were absent in all unaffected pregnancies in pregnant women with no fetal heart block history (54/65 [83%]).

INTERPRETATION

This study identifies a novel maternal autoantibody targeting the fetal AT1A1 cardiac protein as a potential biomarker for the early and accurate detection of fetal autoimmune congenital heart block in pregnant women who had not previously had an affected pregnancy. This advancement might improve the maternal-fetal management of at-risk pregnancies through enhanced surveillance and timely and informed therapeutic interventions.

FUNDING

Heart and Stroke Foundation of Canada and Canadian Institutes of Health Research.

Novel risk loci for COVID-19 hospitalization among admixed American populations

The genetic basis of severe COVID-19 has been thoroughly studied, and many genetic risk factors shared between populations have been identified. However, reduced sample sizes from non-European groups have limited the discovery of population-specific common risk loci. In this second study nested in the SCOURGE consortium, we conducted a genome-wide association study (GWAS) for COVID-19 hospitalization in admixed Americans, comprising a total of 4702 hospitalized cases recruited by SCOURGE and seven other participating studies in the COVID-19 Host Genetic Initiative. We identified four genome-wide significant associations, two of which constitute novel loci and were first discovered in Latin American populations (BAZ2B and DDIAS). A trans-ethnic meta-analysis revealed another novel cross-population risk locus in CREBBP. Finally, we assessed the performance of a cross-ancestry polygenic risk score in the SCOURGE admixed American cohort. This study constitutes the largest GWAS for COVID-19 hospitalization in admixed Latin Americans conducted to date. This allowed to reveal novel risk loci and emphasize the need of considering the diversity of populations in genomic research.

Interaction between poly(A)-binding protein PABPC4 and nuclear receptor corepressor NCoR1 modulates a metabolic stress response

Mitochondria are organelles known primarily for generating ATP via the oxidative phosphorylation process. Environmental signals are sensed by whole organisms or cells and markedly affect this process, leading to alterations in gene transcription and, consequently, changes in mitochondrial function and biogenesis. The expression of mitochondrial genes is finely regulated by nuclear transcription factors, including nuclear receptors and their coregulators. Among the best-known coregulators is the nuclear receptor corepressor 1 (NCoR1). Muscle-specific knockout of NCoR1 in mice induces an oxidative phenotype, improving glucose and fatty acid metabolism. However, the mechanism by which NCoR1 is regulated remains elusive. In this work, we identified the poly(A)-binding protein 4 (PABPC4) as a new NCoR1 interactor. Unexpectedly, we found that silencing of PABPC4 induced an oxidative phenotype in both C2C12 and MEF cells, as indicated by increased oxygen consumption, mitochondria content, and reduced lactate production. Mechanistically, we demonstrated that PABPC4 silencing increased the ubiquitination and consequent degradation of NCoR1, leading to the derepression of PPAR-regulated genes. As a consequence, cells with PABPC4 silencing had a greater capacity to metabolize lipids, reduced intracellular lipid droplets, and reduced cell death. Interestingly, in conditions known to induce mitochondrial function and biogenesis, both mRNA expression and PABPC4 protein content were markedly reduced. Our study, therefore, suggests that the lowering of PABPC4 expression may represent an adaptive event required to induce mitochondrial activity in response to metabolic stress in skeletal muscle cells. As such, the NCoR1-PABPC4 interface might be a new road to the treatment of metabolic diseases.

Diagnostic and prognostic significance of miRNA-15a-5p, 16-5p, and 92a-3p in arrhythmogenic right ventricular cardiomyopathy

BACKGROUND

Arrhythmogenic right ventricular cardiomyopathy (ARVC) presents diagnostic challenges and significant clinical burden because of life-threatening ventricular arrhythmias, compounded by the limited ability to predict patient prognosis using current clinical parameters. MicroRNAs (miRNAs) offer potential as markers in cardiac diseases, including ARVC, providing insights into disease pathogenesis, identification, and prognosis. However, current diagnostic criteria lack sensitivity and specificity, highlighting the need for novel markers such as miRNAs to better understand ARVC's complex pathophysiologic mechanisms.

OBJECTIVE

This multisite study assessed circulating miRNA expression in ARVC patients, stratified by 5-year event-free survival risk, to explore their potential as a marker for improving ARVC diagnosis and prognosis.

METHODS

Blood samples from 102 ARVC patients, 24 Brugada syndrome (BrS) patients, and 22 healthy controls were analyzed for the expression of 20 miRNAs using TaqMan quantitative real-time polymerase chain reaction (PCR), ARVC patients were stratified by 5-year event-free survival risk. Six candidate miRNAs were selected for further analysis, and machine learning algorithms were applied for classification and risk stratification based on miRNA profiles. Additionally, genotyping and functional annotation of miRNA targets were performed.

RESULTS

Six miRNAs exhibited differential expression between high- and low-risk ARVC patients. MiR-15a-5p, miR-16-5p, and miR-92a-3p demonstrated the best performance in risk stratification. MiR-15a-5p also displayed higher expression in patients with adverse cardiac events. Comparative analysis with BrS patients and healthy controls consistently demonstrated increased expression of these miRNAs in ARVC.

CONCLUSION

This study highlights miRNAs' potential to enhance the diagnosis, disease progression, and clinical outcomes of ARVC, supporting further research to improve patient care.

Chlamydophila pneumonia and increased TLR4 gene expression in leukocytes are associated with acute myocardial infarction

We investigated the relationship of the positivity for Chlamydophila pneumoniae (Cpn) and Mycoplasma pneumonia (Mpn), inflammatory and metabolic markers, and mRNA expression and polymorphisms of the TLR2, TLR4, IL-6 and TNFA genes with acute myocardial infarction (AMI). Two hundred and eighteen individuals (98 AMI and 120 non-AMI) were selected at two Clinical Centers. Blood samples were drawn to extract DNA and RNA and to measure laboratory variables including anti-Cpn IgM and IgG. Cpn and Mpn genomic DNA as well as TLR2, TLR4, IL-6 and TNFA mRNA expression were evaluated by quantitative real-time PCR (qPCR). Gene polymorphisms were detected by PCR-HRM. AMI patients had higher positivity for Cpn-DNA (17.3%) than non-AMI group (6.7%, p=0.018). In addition, Cpn-DNA positivity was an independent predictor of risk for AMI (OR: 2.56, CI: 1.08 - 6.04, p=0.031). Positivity for anti-Cpn IgG and Mpn-DNA was similar between AMI and non-AMI (> 0.05). TLR4 mRNA expression was higher in AMI than non-AMI individuals (p=0.005). CD14 -260C> T, TNFA -308A> G, TLR2 c.2258G> A, TLR4 c.896A> G and TLR4 c.1196> T variants were not associated with increased risk for AMI (p> 0.05). In the AMI group, individuals carrying CD14 -260CC genotype had higher hsCRP levels than CT/TT carriers (p=0.041). These results are suggestive that Cpn-DNA positivity and increased TLR4 mRNA expression in blood leukocytes may be associated with AMI and could be useful markers to evaluate the severity and progression of the atherosclerotic disease in AMI patients.