Isolation of cDNA Encoding 7H6-Reactive Polypeptide Defines a New Class of Protein with alpha-Helical Coiled-Coil Structure and DA-Box Similar to Yeast Chromosomal Segregation Proteins

7H6 monoclonal antibody was recently developed in our laboratory by im-munizing mice with a bile canaliculus-rich fraction of the rat liver. The anti-body reacted with a novel 155 Kd polypeptide designated 7H6 antigen that specifically localizes at tight junctions of various epithelia. Correlations of the paracellular barrier function of the tight junction with expression of the 7H6 antigen at the cell border have suggested important roles of this polypeptide for the maintenance of tight junctional functions. As the first step for the analysis of the antigen at the molecular level, we isolated a series of cDNA clones encod-ing 7H6-reactive polypeptides. Five clones were isolated by immunoscreening. Among them a clone designated RL5.3 which carries the largest 5.3Kb insert was characterized in this study. Both plaque screening and immunoblotting of the fusion protein produced by the RL5.3 clone with lysogen confirmed that the pro-tein specifically reacts with the 7H6 monoclonal antibody. Using DNA fragmentsof the RL5.3 clone, 21 clones were further identified. Studies with restriction enzymes and probe hybridization revealed that all the cDNA clones were derived from a single class of transcripts. A partial sequence identified one open reading frame with an α-helical coiled-coil structure and highly conserved aspartate (D)- alanine (A) residues with a helix-loop-helix structure corresponding to DA- box. Since this domain has been specifically found in yeast chromosomal segregation proteins (SMC1, CUT3 and CUT14), the polypeptide encoded by the RL5.3 clone provides the first rodent counterpart of these protein family. Yeast is known to be lethal when SMC and CUT proteins are deleted, suggesting essential roles of these proteins for cell cycle progression as a regulator for chromosomal segregation. Identification of a mammalian counterpart of this pro-tein family may give us some clues for a better understanding of fundamental regulatory mechanisms in the function of tigh junctions

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