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

川崎医科大学附属病院におけるバルーン小腸内視鏡検査の現状 : 325症例の解析結果を含めて

バルーン小腸内視鏡(balloon assisted endoscopy; BAE)は,従来困難であった小腸の検査・治療に有用な検査法である.当院では,2004年にダブルバルーン小腸内視鏡(double balloon endoscopy; DBE)を導入し,2012年6月現在,234症例(延べ325症例;シングルバルーン小腸内視鏡[single balloon endoscopy; SBE]2例を含む)経験した.症例の内訳は,男性127例,女性107例で,平均年齢は62.6歳であった.主訴は,原因不明の消化管出血(obscure gastrointestinal bleeding; OGIB)症例が143例(61.1%)と最多であった.基礎疾患は心血管障害47例(20.1%)が最多で,抗血小板・抗凝固療法を施行している症例は53例(22.6%)にみられた.経口的アプローチは325症例中158例で,経肛門的アプローチは167例,経口的,経肛門的アプローチを両方施行された症例は56例あった.病変は78例(24.0%)に検出され,その内訳は,びらん及び潰瘍性病変23例(29.5%),腫瘍性病変22例(28.2%),血管性病変21例(26.9%)であった.また,外科的切除,内視鏡的止血術等の治療を58例(74.4%)に施行した.BAE により小腸疾患の診断・治療が大きく進歩した.しかしながら,一方で手技が煩雑な点,患者の身体的侵襲も少なくなく合併症を有する点が欠点として挙げられる.そのため,各種小腸疾患の診断,治療に対しては,個々の患者の状況により,BAEとカプセル内視鏡(capsule endoscopy; CA)とを使い分けていくことが重要である.Balloon assisted endoscopy (BAE) is a novel endoscopic technique developed to investigate small bowel diseases (SBDs). BAE has been installed from 2004 in Kawasaki Medical School Hospital. Since then, 234 patients (107 female, 117 male; mean age 62.6 years) with suspected or known SBDs underwent BAE, and we have performed a total of 325 consecutive BAE procedures. The most common indication for BAE was an obscure gastrointestinal bleeding. Cardiovascular disease was the most major coexisting disease (47 patients, 20.1%), and 53 patients (22.6%) were prescribed anti-platelet and/or anticoagulant therapy. One hundred and fifty eight patients were treated BAE via the oral approach, 167 patients were performed via the anal approach, and 56 patients were treated via the dual approach. The overall diagnostic yield was 24.0% (78/325 cases). Among the 78 cases, there were 23 erosions/ulcerations, 22 tumors, 21 angiovascular lesions, and other SBDs. The subsequent treatments, such as endoscopic therapy and surgical therapy were performed following the BAE procedure in 74.4% (58/78) of cases. BAE is a useful tool that not only allows diagnostic workup of SBDs, but also makes it possible to carry out therapeutic intervention. On the other hand, we should make careful decisions of indications for BAE, because it\u27s an invasive and complex procedure and the examination requires substantial time to complete

7-Ketocholesterol enhances leukocyte adhesion to endothelial cells via p38MAPK pathway.

7-Ketocholesterol is a major dietary cholesterol oxidation product found in high concentrations in atherosclerotic plaques, which contribute to the development of atherosclerosis. This study aimed to investigate the effects of 7-ketocholesterol on endothelial inflammation, as well as the underlying mechanisms. Pretreatment of human umbilical vein endothelial cells (HUVEC) with 7-ketocholesterol significantly enhanced the total interactions between human monocytic cells (THP-1 cell line) and TNFα-activated HUVECs under physiological flow conditions, compared to pretreatment with cholesterol (TNFα+50 μM cholesterol: 13.1 ± 0.54 cells/CPF, TNFα+50 μM 7-ketocholesterol: 18.9 ± 0.35 cells/CPF, p < 0.01). 7-Ketocholesterol enhanced the expression of E-selectin, ICAM-1, and VCAM-1 proteins. It also activated p38 mitogen-activated protein kinase (MAPK), and treatment with a p38 MAPK inhibitor inhibited both E-selectin expression via ATF-2 activation and 7-ketocholesterol-induced THP-1 adhesion to HUVECs. These findings suggest that 7-ketocholesterol enhances leukocyte-endothelial interactions by upregulating the expression of adhesion molecules, presumably via the p38 MAPK-dependent pathway

Importin-α Promotes Passage through the Nuclear Pore Complex of Human Immunodeficiency Virus Type 1 Vpr

Viral protein R (Vpr) of human immunodeficiency virus type 1 has potent karyophilic properties, but details of the mechanism by which it enters the nucleus remain to be clarified. We reported previously that two regions, located between residues 17 and 34 (αH1) and between residues 46 and 74 (αH2), are indispensable for the nuclear localization of Vpr. Here, we reveal that a chimeric protein composed of the nuclear localization signal of Vpr, glutathione S-transferase, and green fluorescent protein was localized at the nuclear envelope and then entered the nucleus upon addition of importin-α. An in vitro transport assay using a series of derivatives of importin-α demonstrated that the carboxyl terminus was required for this nuclear import process. We also showed that Vpr interacts with importin-α through αH1 and αH2; only the interaction via αH1 is indispensable for the nuclear entry of Vpr. These observations indicate that importin-α functions as a mediator for the nuclear entry of Vpr