COVID-19 and systemic lupus erythematosus genetics: A balance between autoimmune disease risk and protection against infection

Impact of SARS-CoV-2 pre-delta/delta and omicron variants on clinical outcomes in a systemic lupus erythematosus cohort from Puerto Rico

ObjectiveTo examine the clinical outcomes of systemic lupus erythematosus (SLE) patients with COVID-19 during the Pre-Delta/Delta and Omicron periods.MethodsA retrospective study was conducted in a cohort of adult Puerto Ricans with SLE. Demographic parameters, SLE and COVID-19 manifestations, comorbidities, pharmacologic treatment, SLE exacerbations, hospitalizations, and mortality were determined. SARS CoV-2 infection was confirmed by polymerase chain reaction or antigen tests. Variables were compared between the Pre-delta/Delta and Omicron periods. Also, the proportion of COVID-19 cases and mortality of SLE patients was compared to the general population of Puerto Rico.ResultsOf the entire SLE cohort (n = 347), 169 patients (48.7%) had COVID-19. Twenty-two patients had COVID-19 during the Pre-delta/Delta period and 147 during the Omicron period. The proportion of COVID-19 cases in the SLE cohort was significantly higher when compared to the adult general population of Puerto Rico (25.7%), but no difference in mortality was found. Overall, the clinical outcomes of COVID-19 in the SLE cohort were favorable, with low rates of lupus flares (3.0%), hospitalizations (3.6%), and mortality (0.6%). Patients with COVID-19 during the Pre-delta/Delta period were more likely to have oral ulcers, anti-Smith antibodies, and chronic kidney disease, whereas those during the Omicron period were more likely to have COVID-19 symptoms (rhinorrhea, sore throat, and cough).ConclusionIn summary, is this group of Puerto Ricans with SLE, a high proportion had COVID-19, but disease exacerbation, hospitalization, and mortality rates were low. Few clinical differences were noted in SLE patients when comparing the Pre-delta/Delta and Omicron periods.

Large-scale cross-trait genetic analysis highlights shared genetic backgrounds of autoimmune diseases

Disorders associated with the immune system burden multiple organs, although the shared biology exists across the diseases. Preceding family-based studies reveal that immune diseases are heritable to varying degrees, providing the basis for immunogenomics. The recent cost reduction in genetic analysis intensively promotes biobank-scale studies and the development of frameworks for statistical genetics. The accumulating multi-layer omics data, including genome-wide association studies (GWAS) and RNA-sequencing at single-cell resolution, enable us to dissect the genetic backgrounds of immune-related disorders. Although autoimmune and allergic diseases are generally categorized into different disease categories, epidemiological studies reveal the high incidence of autoimmune and allergic disease complications, suggesting the shared genetics and biology between the disease categories. Biobank resources and consortia cover multiple immune-related disorders to accumulate phenome-wide associations of genetic variants and enhance researchers to analyze the shared and heterogeneous genetic backgrounds. The emerging post-GWAS and integrative multi-omics analyses provide genetic and biological insights into the multicategorical disease associations.

STAT4 and STAT6, their role in cellular and humoral immunity and in diverse human diseases

Signal transducer and activator of transcription (STAT) 4 and STAT6 play a crucial role in immune cells by transducing signals from specific cytokine receptors, and inducing transcription of genes involved in cell-mediated and humoral immunity. These two different defense mechanisms against pathogens are regulated by two specific CD4+ T helper (Th) cells known as Th1 and Th2 cells. Many studies have shown that several diseases including cancer, inflammatory, autoimmune and allergic diseases are associated with a Th1/Th2 imbalance caused by increased or decreased expression/activity of STAT4 or STAT6 often due to genetic and epigenetic aberrances. An altered expression of STAT4 has been observed in different tumors and autoimmune diseases, while a dysregulation of STAT6 signaling pathway is frequently observed in allergic conditions, such as atopic dermatitis, allergic asthma, food allergy, and tumors such as Hodgkin and non-Hodgkin lymphomas. Recently, dysregulations of STAT4 and STAT6 expression have been observed in SARS-CoV2 and monkeypox infections, which are still public health emergencies in many countries. SARS-CoV-2 can induce an imbalance in Th1 and Th2 responses with a predominant activation of STAT6 in the cytosol and nuclei of pneumocytes that drives Th2 polarization and cytokine storm. In monkeypox infection the virus can promote an immune evasion by inducing a Th2 response that in turn inhibits the Th1 response essential for virus elimination. Furthermore, genetic variations of STAT4 that are associated with an increased risk of developing systemic lupus erythematosus seem to play a role in defense against SARS-CoV-2 infection.

TYK2: an emerging therapeutic target in rheumatic disease

Tyrosine kinase 2 (TYK2) is a member of the JAK kinase family of intracellular signalling molecules. By participating in signalling pathways downstream of type I interferons, IL-12, IL-23 and IL-10, TYK2 elicits a distinct set of immune events to JAK1, JAK2 and JAK3. TYK2 polymorphisms have been associated with susceptibility to various rheumatic diseases including systemic lupus erythematosus and dermatomyositis. In vitro and animal studies substantiate these findings, highlighting a role for TYK2 in diseases currently managed by antagonists of cytokines that signal through TYK2. Various inhibitors of TYK2 have now been studied in human disease, and one of these inhibitors, deucravacitinib, has now been approved for the treatment of psoriasis. Phase II trials of deucravacitinib have also reported positive results in the treatment of psoriatic arthritis and systemic lupus erythematosus, with a preliminary safety profile that seems to differ from that of the JAK1, JAK2 and JAK3 inhibitors. Two other inhibitors of TYK2, brepocitinib and ropsacitinib, are also in earlier stages of clinical trials. Overall, TYK2 inhibitors hold promise for the treatment of a distinct spectrum of autoimmune diseases and could potentially have a safety profile that differs from other JAK inhibitors.

Systemic lupus erythematosus is associated with increased risk of mortality and acute kidney injury in patients with COVID-19 hospitalization: Insights from a National Inpatient Sample analysis

INTRODUCTION

The COVID-19 pandemic has significantly impacted global health, especially for patients with chronic diseases that may compromise the immune system. This study investigates the association between systemic lupus erythematosus (SLE) and COVID-19 outcomes.

METHODS

Data from the National Inpatient Sample (NIS) were analyzed to create a retrospective cohort of COVID-19 hospitalizations, comparing patients with and without SLE. Propensity-score matched analysis was conducted to assess the association between SLE and clinical outcomes in COVID-19 hospitalizations.

RESULTS

The study included over a million COVID-19 hospitalizations, with approximately 0.5% having a secondary diagnosis of SLE. The SLE-COVID hospitalizations were predominantly female and younger, with a median age of 57.2, while the non-SLE-COVID group had a median age of 64.8 years. Comorbidities such as chronic obstructive pulmonary disease, renal failure, liver disease, and others were more prevalent in the SLE-COVID group. Patients with SLE and COVID-19 had a significantly higher incidence of acute kidney injury requiring dialysis than those without SLE. In-hospital mortality was higher in the SLE group, particularly in the 18-44 year age group (6.15% vs 2.47%, p = .022).

CONCLUSION

COVID-19 patients with SLE are at an increased mortality risk, especially in the younger age group, and a higher incidence of acute kidney injury requiring dialysis. The elevated risk of adverse outcomes underscores the vulnerability of SLE patients to COVID-19. These findings emphasize the importance of special precautions and patient education for individuals with SLE to mitigate the risks associated with COVID-19.

Autoimmune response after SARS-CoV-2 infection and SARS-CoV-2 vaccines

The complicated relationships between autoimmunity, COVID-19, and COVID-19 vaccinations are described, giving insight into their intricacies. Antinuclear antibodies (ANA), anti-Ro/SSA, rheumatoid factor, lupus anticoagulant, and antibodies against interferon (IFN)-I have all been consistently found in COVID-19 patients, indicating a high prevalence of autoimmune reactions following viral exposure. Furthermore, the discovery of human proteins with structural similarities to SARS-CoV-2 peptides as possible autoantigens highlights the complex interplay between the virus and the immune system in initiating autoimmunity. An updated summary of the current status of COVID-19 vaccines is presented. We present probable pathways underpinning the genesis of COVID-19 autoimmunity, such as bystander activation caused by hyperinflammatory conditions, viral persistence, and the creation of neutrophil extracellular traps. These pathways provide important insights into the development of autoimmune-related symptoms ranging from organ-specific to systemic autoimmune and inflammatory illnesses, demonstrating the wide influence of COVID-19 on the immune system.

Knowledge mapping of COVID-19 and autoimmune diseases: a visual and bibliometric analysis

BACKGROUND

Many studies have shown an association between COVID-19 and autoimmune diseases (ADs). Studies on COVID-19 and ADs have also increased significantly, but there is no bibliometric analysis to summarize the association between COVID-19 and ADs. The purpose of this study was to perform a bibliometric and visual analysis of published studies related to COVID-19 and ADs.

METHODS

Based on the Web of Science Core Collection SCI-Expanded database, we utilize Excel 2019 and visualization analysis tools Co-Occurrence13.2 (COOC13.2), VOSviewer, CiteSpace, and HistCite for analysis.

RESULTS

A total of 1736 related kinds of papers were included, and the number of papers presented an overall increasing trend. The country/region with the most publications is the USA, the institution is the Harvard Medical School, the author is Yehuda Shoenfeld from Israel, and the journal is Frontiers in Immunology. Research hotspots include immune responses (such as cytokines storm), multisystem ADs (such as systemic lupus erythematosus, rheumatoid arthritis, and multiple sclerosis), treatment modalities (such as hydroxychloroquine, rituximab), vaccination and autoimmune mechanisms (such as autoantibodies, molecular mimicry). The future research direction may be the mechanisms and treatment ideas of the association between ADs and COVID-19 (such as NF-κB, hyperinflammation, antiphospholipid antibodies, neutrophil extracellular traps, granulocyte-macrophage colony-stimulating factor), other cross-diseases of COVID-19 and ADs (such as inflammatory bowel disease, chronic mucocutaneous candidiasis, acute respiratory distress syndrome).

CONCLUSION

The growth rate of publications regarding ADs and COVID-19 has risen sharply. Our research results can help researchers grasp the current status of ADs and COVID-19 research and find new research directions in the future.

Shared genetic architecture of COVID-19 and Alzheimer's disease

The severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the сoronavirus disease 2019 (COVID-19) have become a global health threat. At the height of the pandemic, major efforts were focused on reducing COVID-19-associated morbidity and mortality. Now is the time to study the long-term effects of the pandemic, particularly cognitive impairment associated with long COVID. In recent years much attention has been paid to the possible relationship between COVID-19 and Alzheimer's disease, which is considered a main cause of age-related cognitive impairment. Genetic predisposition was shown for both COVID-19 and Alzheimer's disease. However, the analysis of the similarity of the genetic architecture of these diseases is usually limited to indicating a positive genetic correlation between them. In this review, we have described intrinsic linkages between COVID-19 and Alzheimer's disease, pointed out shared susceptibility genes that were previously identified in genome-wide association studies of both COVID-19 and Alzheimer's disease, and highlighted a panel of SNPs that includes candidate genetic risk markers of the long COVID-associated cognitive impairment.

Integrated Analyses of Single-Cell Transcriptome and Mendelian Randomization Reveal the Protective Role of Resistin in Sepsis Survival in Intensive Care Unit

The high morbidity and mortality rates associated with sepsis highlight the challenges of finding specific remedies for this condition in the intensive care unit (ICU). This study aimed to explore the differentially expressed genes (DEGs) specific to cell types in sepsis and investigate the role of resistin in the survival of sepsis patients through Mendelian randomization (MR) analyses. We used single-cell and bulk transcriptome data to identify cell type-specific DEGs between sepsis and healthy controls. MR analyses were then conducted to investigate the causal relationships between resistin (one of the identified DEGs) levels and the survival of sepsis patients. Additionally, we utilized meQTL (methylation quantitative trait loci) to identify cytosine-phosphate-guanine (CpG) sites that may directly affect sepsis. We identified 560 cell type-specific DEGs between sepsis and healthy controls. Notably, we observed the upregulation of resistin levels in macrophages during sepsis. In bulk transcriptome, RETN is also upregulated in sepsis samples compared with healthy controls. MR analyses revealed a negative association existed between the expression of resistin, at both gene and protein levels, and the mortality or severity of sepsis patients in ICU. Moreover, there were no associations observed between resistin levels and death or organ failure due to other causes. We also identified three methylation CpG sites, located in RETN or its promoter region-cg06633066, cg22322184, and cg02346997-that directly affected both resistin protein levels and sepsis death in the ICU. Our findings suggest that resistin may provide feasible protection for sepsis patients, particularly those with severe cases, without serious side effects. Therefore, resistin could be a potential drug candidate for sepsis treatment. Additionally, we identified two CpG sites, cg06633066 and cg22322184, that were associated with RETN protein levels and sepsis death, providing novel insights into the underlying mechanisms of sepsis.

Systemic Lupus Erythematosus and COVID-19

PURPOSE OF REVIEW

To describe the current state of knowledge regarding COVID-19 in patients with systemic lupus erythematosus (SLE). We focus on (i) SARS-CoV-2 vaccination uptake, immunogenicity and safety, and (ii) outcomes of COVID-19 in patients with SLE and pertinent risk factors for adverse sequelae.

RECENT FINDINGS

Notwithstanding the potential concern of patients about possible post-vaccination side-effects, the safety of anti-SARS-CoV-2 vaccines in patients with SLE has been undisputedly confirmed in numerous studies. Humoral immunogenicity is generally attained in SLE, although affected by the use of background immunosuppressive drugs, especially rituximab. The latter has also clearly been implicated with adverse COVID-19 outcomes in SLE, including need for hospitalization, mechanical ventilation and death. Although the wide adoption of vaccination has significantly improved COVID-19 outcomes, patients with SLE continue to pose challenges during the pandemic, mainly owing to administered immunosuppressive medications.

Colocalization of expression transcripts with COVID-19 outcomes is rare across cell states, cell types and organs

Identifying causal genes at GWAS loci can help pinpoint targets for therapeutic interventions. Expression studies can disentangle such loci but signals from expression quantitative trait loci (eQTLs) often fail to colocalize-which means that the genetic control of measured expression is not shared with the genetic control of disease risk. This may be because gene expression is measured in the wrong cell type, physiological state, or organ. We tested whether Mendelian randomization (MR) could identify genes at loci influencing COVID-19 outcomes and whether the colocalization of genetic control of expression and COVID-19 outcomes was influenced by cell type, cell stimulation, and organ. We conducted MR of cis-eQTLs from single cell (scRNA-seq) and bulk RNA sequencing. We then tested variables that could influence colocalization, including cell type, cell stimulation, RNA sequencing modality, organ, symptoms of COVID-19, and SARS-CoV-2 status among individuals with symptoms of COVID-19. The outcomes used to test colocalization were COVID-19 severity and susceptibility as assessed in the Host Genetics Initiative release 7. Most transcripts identified using MR did not colocalize when tested across cell types, cell state and in different organs. Most that did colocalize likely represented false positives due to linkage disequilibrium. In general, colocalization was highly variable and at times inconsistent for the same transcript across cell type, cell stimulation and organ. While we identified factors that influenced colocalization for select transcripts, identifying 33 that mediate COVID-19 outcomes, our study suggests that colocalization of expression with COVID-19 outcomes is partially due to noisy signals even after following quality control and sensitivity testing. These findings illustrate the present difficulty of linking expression transcripts to disease outcomes and the need for skepticism when observing eQTL MR results, even accounting for cell types, stimulation state and different organs.

COVID-19 as a trigger of Guillain-Barré syndrome: A review of the molecular mechanism

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic with serious complications. After coronavirus disease 2019 (COVID-19), several post-acute COVID-19 syndromes (PACSs) and long-COVID sequels were reported. PACSs involve many organs, including the nervous, gustatory, and immune systems. One of the PACSs after SARS-CoV-2 infection and vaccination is Guillain-Barré syndrome (GBS). The incidence rate of GBS after SARS-CoV-2 infection or vaccination is low. However, the high prevalence of COVID-19 and severe complications of GBS, for example, autonomic dysfunction and respiratory failure, highlight the importance of post-COVID-19 GBS. It is while patients with simultaneous COVID-19 and GBS seem to have higher admission rates to the intensive care unit, and demyelination is more aggressive in post-COVID-19 GBS patients. SARS-CoV-2 can trigger GBS via several pathways like direct neurotropism and neurovirulence, microvascular dysfunction and oxidative stress, immune system disruption, molecular mimicry, and autoantibody production. Although there are few molecular studies on the molecular and cellular mechanisms of GBS occurrence after SARS-CoV-2 infection and vaccination, we aimed to discuss the possible pathomechanism of post-COVID-19 GBS by gathering the most recent molecular evidence.