The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Characteristic cerebrospinal fluid cytokine/chemokine profiles in neuromyelitis optica, relapsing remitting or primary progressive multiple sclerosis.

BACKGROUND: Differences in cytokine/chemokine profiles among patients with neuromyelitis optica (NMO), relapsing remitting multiple sclerosis (RRMS), and primary progressive MS (PPMS), and the relationships of these profiles with clinical and neuroimaging features are unclear. A greater understanding of these profiles may help in differential diagnosis. METHODS/PRINCIPAL FINDINGS: We measured 27 cytokines/chemokines and growth factors in CSF collected from 20 patients with NMO, 26 with RRMS, nine with PPMS, and 18 with other non-inflammatory neurological diseases (OND) by multiplexed fluorescent bead-based immunoassay. Interleukin (IL)-17A, IL-6, CXCL8 and CXCL10 levels were significantly higher in NMO patients than in OND and RRMS patients at relapse, while granulocyte-colony stimulating factor (G-CSF) and CCL4 levels were significantly higher in NMO patients than in OND patients. In NMO patients, IL-6 and CXCL8 levels were positively correlated with disability and CSF protein concentration while IL-6, CXCL8, G-CSF, granulocyte-macrophage colony-stimulating factor (GM-CSF) and IFN-γ were positively correlated with CSF neutrophil counts at the time of sample collection. In RRMS patients, IL-6 levels were significantly higher than in OND patients at the relapse phase while CSF cell counts were negatively correlated with the levels of CCL2. Correlation coefficients of cytokines/chemokines in the relapse phase were significantly different in three combinations, IL-6 and GM-CSF, G-CSF and GM-CSF, and GM-CSF and IFN-γ, between RRMS and NMO/NMOSD patients. In PPMS patients, CCL4 and CXCL10 levels were significantly higher than in OND patients. CONCLUSIONS: Our findings suggest distinct cytokine/chemokine alterations in CSF exist among NMO, RRMS and PPMS. In NMO, over-expression of a cluster of Th17- and Th1-related proinflammatory cytokines/chemokines is characteristic, while in PPMS, increased CCL4 and CXCL10 levels may reflect on-going low grade T cell and macrophage/microglia inflammation in the central nervous system. In RRMS, only a mild elevation of proinflammatory cytokines/chemokines was detectable at relapse

Genetic and Infectious Profiles of Japanese Multiple Sclerosis Patients

<div><h3>Background</h3><p>Nationwide surveys conducted in Japan over the past thirty years have revealed a four-fold increase in the estimated number of multiple sclerosis (MS) patients, a decrease in the age at onset, and successive increases in patients with conventional MS, which shows an involvement of multiple sites in the central nervous system, including the cerebrum and cerebellum. We aimed to clarify whether genetic and infectious backgrounds correlate to distinct disease phenotypes of MS in Japanese patients.</p> <h3>Methodology/Principal Findings</h3><p>We analyzed <em>HLA-DRB1</em> and <em>-DPB1</em> alleles, and IgG antibodies specific for <em>Helicobacter pylori</em>, <em>Chlamydia pneumoniae</em>, varicella zoster virus, and Epstein-Barr virus nuclear antigen (EBNA) in 145 MS patients and 367 healthy controls (HCs). Frequencies of <em>DRB1*0405</em> and <em>DPB1*0301</em> were significantly higher, and <em>DRB1*0901</em> and <em>DPB1*0401</em> significantly lower, in MS patients as compared with HCs. MS patients with <em>DRB1*0405</em> had a significantly earlier age of onset and lower Progression Index than patients without this allele. The proportion and absolute number of patients with <em>DRB1*0405</em> successively increased with advancing year of birth. In MS patients without <em>DRB1*0405</em>, the frequency of the <em>DRB1*1501</em> allele was significantly higher, while the <em>DRB1*0901</em> allele was significantly lower, compared with HCs. Furthermore, <em>DRB1*0405</em>-negative MS patients were significantly more likely to be positive for EBNA antibodies compared with HCs.</p> <h3>Conclusions</h3><p>Our study suggests that MS patients harboring <em>DRB1*0405</em>, a genetic risk factor for MS in the Japanese population, have a younger age at onset and a relatively benign disease course, while <em>DRB1*0405</em>-negative MS patients have features similar to Western-type MS in terms of association with Epstein-Barr virus infection and <em>DRB1*1501</em>. The recent increase of MS in young Japanese people may be caused, in part, by an increase in <em>DRB1*0405</em>-positive MS patients.</p> </div

Demographic features of patients.

<p>NA = not applicable; NMO = neuromyelitis optica; NMOSD = neuromyelitis optica spectrum disorder; OND = other non-inflammatory neurological diseases; PPMS = primary progressive multiple sclerosis; RRMS = relapsing remitting multiple sclerosis; CSF = cerebrospinal fluid; SD = standard deviation; EDSS = Expanded Disability Status Scale.</p>*, #<p>p<0.05.</p

Correlations of cytokines/chemokines in RRMS and NMO/NMOSD in the relapse phase.

<p>NMO = neuromyelitis optica; NMOSD = neuromyelitis optica spectrum disorder; OND = other non-inflammatory neurological diseases; RRMS = relapsing remitting multiple sclerosis. rho = Spearman's correlation coefficient, <i>^corrp</i> = corrected p value by Benjamini-Hochberg method.</p

Correlation of cytokine and chemokine levels in patients with RRMS and NMO/NMOSD in the relapse phase.

<p>Among the cytokines and chemokines analyzed, distances of each pair of cytokines/chemokines, based on Spearman's correlation coefficient, of RRMS and NMO/NMOSD in the relapse phase were shown as a heatmap. NMO = neuromyelitis optica; NMOSD = neuromyelitis optica spectrum disorder; RRMS = relapsing remitting multiple sclerosis.</p

Frequencies of <i>HLA-DRB1</i> alleles among MS patients and healthy controls.

<p>p^uncorr was corrected by multiplying the value by 18 to calculate p^corr.</p><p>X^a includes all observed alleles at the <i>HLA-DRB1</i> locus with frequencies of less than 1% in subjects; <i>DRB1*0301, DRB1*0401, DRB1*0404, DRB1*0407, DRB1*0410, DRB1*0701, DRB1*1001, DRB1*1106, DRB1*1301, DRB1*1601</i> and <i>DRB1*1602</i>.</p><p>CI, confidence interval; HCs, healthy controls; MS, multiple sclerosis; NA, not applicable; OR, odds ratio; p^corr, corrected p value.</p

Frequencies of antibodies against common infectious agents among MS patients with and without the <i>HLA-DRB1*0405</i> allele and healthy controls.

*a<p>p^corr = 0.0324, as compared with HCs.</p>*b<p>p^corr = 0.0033, as compared with <i>HLA-DRB1*0405</i> (+) MS.</p><p>The age of patients during examination was not significantly different among HCs and MS patients, regardless of the presence or absence of the <i>DRB1*0405</i> allele (mean ± SD in years; 35.22±12.18 in <i>DRB1*0405</i>-positive MS patients, 40.74±12.41 in <i>DRB1*0405</i>-negative MS patients, and 38.93±12.11 in HCs).</p><p>EBV, Epstein-Barr virus; HCs, healthy controls; MS, multiple sclerosis; VZV, varicella zoster virus.</p

Proportion of <i>HLA-DRB1*0405</i>-positive and -negative MS patients by year of birth.

<p>Among MS patients, the proportion and absolute number of patients with <i>DRB1*0405</i> successively increased with advancing year of birth. MS, multiple sclerosis.</p