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

Adaptive responses induced by 24S-hydroxycholesterol through liver X receptor pathway reduce 7-ketocholesterol-caused neuronal cell death

Lipid peroxidation products have been known to induce cellular adaptive responses and enhance tolerance against subsequent oxidative stress through up-regulation of antioxidant compounds and enzymes. 24S-hydroxycholesterol (24SOHC) which is endogenously produced oxysterol in the brain plays an important role in maintaining brain cholesterol homeostasis. In this study, we evaluated adaptive responses induced by brain-specific oxysterol 24SOHC in human neuroblastoma SH-SY5Y cells. Cells treated with 24SOHC at sub-lethal concentrations showed significant reduction in cell death induced by subsequent treatment with 7-ketocholesterol (7KC) in both undifferentiated and retinoic acid-differentiated SH-SY5Y cells. These adaptive responses were also induced by other oxysterols such as 25-hydroxycholesterol and 27-hydroxycholesterol which are known to be ligands of liver X receptor (LXR). Co-treatment of 24SOHC with 9-cis retinoic acid, a retinoid X receptor ligand, enhanced the adaptive responses. Knockdown of LXRβ by siRNA diminished the adaptive responses induced by 24SOHC almost completely. The treatment with 24SOHC induced the expression of LXR target genes, such as ATP-binding cassette transporter A1 (ABCA1) and G1 (ABCG1). The 24SOHC-induced adaptive responses were significantly attenuated by siRNA for ABCG1 but not by siRNA for ABCA1. Taken together, these results strongly suggest that 24SOHC at sub-lethal concentrations induces adaptive responses via transcriptional activation of LXR signaling pathway, thereby protecting neuronal cells from subsequent 7KC-induced cytotoxicity

Functional Synergy between Cholecystokinin Receptors CCKAR and CCKBR in Mammalian Brain Development

<div><p>Cholecystokinin (CCK), a peptide hormone and one of the most abundant neuropeptides in vertebrate brain, mediates its actions via two G-protein coupled receptors, CCKAR and CCKBR, respectively active in peripheral organs and the central nervous system. Here, we demonstrate that the CCK receptors have a dynamic and largely reciprocal expression in embryonic and postnatal brain. Using compound homozygous mutant mice lacking the activity of both CCK receptors, we uncover their additive, functionally synergistic effects in brain development and demonstrate that CCK receptor loss leads to abnormalities of cortical development, including defects in the formation of the midline and corpus callosum, and cortical interneuron migration. Using comparative transcriptome analysis of embryonic neocortex, we define the molecular mechanisms underlying these defects. Thus we demonstrate a developmental, hitherto unappreciated, role of the two CCK receptors in mammalian neocortical development.</p></div

International Trends in Adverse Drug Event-Related Mortality from 2001 to 2019: An Analysis of the World Health Organization Mortality Database from 54 Countries

Background and Objective Adverse drug events (ADEs) are becoming a significant public health issue. However, reports on ADE-related mortality are limited to national-level evaluations. Therefore, we aimed to reveal overall trends in ADE-related mortality across the 21st century on an international level. Methods This observational study analysed long-term trends in ADE-related mortality rates from 2001 to 2019 using the World Health Organization Mortality Database. The rates were analysed according to sex, age and region. North America, Latin America and the Caribbean, Western Europe, Eastern Europe and Western Pacific regions were assessed. Fifty-four countries were included with four-character International Statistical Classification of Disease and Related Health Problems, Tenth Revision codes in the database, population data in the World Population Prospects 2019 report, mortality data in more than half of the study period, and high-quality or medium-quality death registration data. A locally weighted regression curve was used to show international trends in age-standardised rates. Results The global ADE-related mortality rate per 100,000 population increased from 2.05 (95% confidence interval 0.92–3.18) in 2001 to 6.86 (95% confidence interval 5.76–7.95) in 2019. Mortality rates were higher among men than among women, especially in those aged 20–50 years. The population aged ≥ 75 years had higher ADE-related mortality rates than the younger population. North America had the highest mortality rate among the five regions. The global ADE-related mortality rate increased by approximately 3.3-fold from 2001 to 2019. Conclusions The burden of ADEs has increased internationally with rising mortality rates. Establishing pharmacovigilance systems can facilitate efforts to reduce ADE-related mortality rates globally

Pathway analysis (Ingenuity.com) of RNA-Seq data.

<p>Pathway analysis (Ingenuity.com) of RNA-Seq data.</p

Neuronal migration defects in <i>Cckar/br</i> mutants.

<p>(A-F) In situ hybridization with markers of cortical interneurons at P7: <i>Gad1</i> (A,B) (a general interneuron marker); <i>Lhx6</i> (C,D) (a marker of MGE-derived interneurons); and <i>reelin</i> (E,F) (a marker of CGE- and pre-optic area derived interneurons) indicates a significant overall reduction of interneurons in <i>Cckar/br</i> mutants, irrespective of their origin. Scale bar, 200 μm. (G) Quantification of <i>Lhx6-</i>expressing interneurons. <i>Cckar/br</i> mutants have a 26% reduction in MGE-derived cortical interneurons at P7 (p = 0.0160, n = 3). (H) Distribution of <i>Lhx6-</i>expressing interneurons. Despite the reduction in their number, cortical interneurons are distributed in a similar fashion in control and <i>Cckar/br</i> mutant neocortex, suggesting that interneurons that successfully completed tangential migration are able to respond to local cues in the neocortex and settle into their final position. The fraction of <i>Lhx6-</i>positive interneurons per bin is similar in control and <i>Cckar/br</i> mutant neocortices (p is at least > 0.15 for all comparisons, n = 3). (I) Quantification of <i>reelin</i>-expressing interneurons. <i>Cckar/br</i> mutants have a 15% reduction in CGE- and POA-derived cortical interneurons at P7 (p = 0.0226, n = 4). Error bars represent s.e.m.</p

Abnormal differentiation of the midline in <i>Cckar/br</i> mutant embryos.

<p>(A-F) In situ hybridization with <i>Gfap</i>, a marker of midline glia at perinatal stages, reveals that two midline cell populations, the induseum griseum (IG) and midline zipper glia (mzg), are reduced in <i>Cckar/br</i> double mutants (D-F) compared even with <i>Cckar^+/-;Cckbr^+/-</i> double heterozygous embryos (A-C) at E17.5. Expression of <i>Gfap</i> at the glial wedge (gw) does not appear to be affected to the same extent, suggesting defective differentiation of the midline. Scale bar, 200 μm. (G and H) In situ hybridization with <i>Tag1</i>, a marker of commissural neurons, which also marks the subcallosal sling (scs), demonstrates that a continuous sling is present in control <i>Cckbr^+/-</i> pups (G) at P0, but it fails to transverse the gap between the two hemispheres in <i>Cckar/br</i> mutants (H). Scale bar, 200 μm. (I-N) In situ hybridization demonstrates a modest increase in <i>Cckbr</i> transcripts in the ventral hypothalamus of <i>Cckar</i> single mutants (J,L,N) compared with wild type (I,K,M) at P14. The sections shown are at three different rostro-caudal levels. Scale bar, 0.5 mm.</p