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

Z-350, A Novel Compound with ␣ 1 -Adrenoceptor Antagonistic and Steroid 5␣-Reductase Inhibitory Actions: Pharmacological Properties In Vivo

ABSTRACT The ␣ 1 -adrenoceptor-antagonistic and steroid 5␣-reductaseinhibitory actions of Z-350 [(S)-4-{3-{4-{1-(4-methylphenyl)-3-[4-(2-methoxyphenyl)piperazine-1-yl]propoxy}benzoyl}indole-1-yl}butyric acid hydrochloride] were investigated in rabbits and rats in vivo. Z-350 (1-30 mg/kg), administered intraduodenally, dosedependently inhibited phenylephrine-induced increases in prostatic urethral pressure with an ED 50 value of 3.8 mg/kg in anesthetized male rabbits, whereas the effects on mean blood pressure and orthostatic hypotensive response were weaker when compared with other ␣ 1 -adrenoceptor antagonists, tamsulosin and prazosin. Z-350 (1-10 mg/kg p.o.) dose-dependently inhibited the prostatic steroid 5␣-reductase activity in rats with an ED 50 value of 2.8 mg/kg. The daily oral administration of Z-350, at м10 mg/kg for 7 days, significantly reduced the prostatic growth induced by testosterone in castrated rats, with no effect on dihydrotestosterone-induced prostatic growth. These results indicate that Z-350 exhibited ␣ 1 -adrenoceptor-antagonistic and 5␣-reductase inhibitory actions at almost equal doses in vivo, and was expected to improve the bladder outlet obstruction associated with benign prostatic hyperplasia with smaller cardiovascular adverse effect. Benign prostatic hyperplasia (BPH) is a frequent disorder in elderly men, characterized by the progressive enlargement of prostatic tissue, resulting in an obstruction of the proximal urethra and disturbance of urinary flow. Symptomatic BPH is generally considered to consist of the following two components: a static component related to prostatic tissue mass, and a dynamic component related to prostatic smooth muscle tone. The ability of an ␣ 1 -adrenoceptor antagonist to improve the clinical symptoms of BPH was first demonstrated by In contrast, other approaches to reduce prostatic enlargement had also been made previously. It is well known that the growth of the prostate gland is dependent on tissue androgen Simultaneous ␣ 1 -adrenoceptor-antagonistic and steroid 5␣-reductase inhibitory actions are thus expected to be more effective than each action alone

Artificial intelligence-based radiomics for the prediction of nodal metastasis in early-stage lung cancer

Abstract We aimed to investigate the value of computed tomography (CT)-based radiomics with artificial intelligence (AI) in predicting pathological lymph node metastasis (pN) in patients with clinical stage 0–IA non-small cell lung cancer (c-stage 0–IA NSCLC). This study enrolled 720 patients who underwent complete surgical resection for c-stage 0–IA NSCLC, and were assigned to the derivation and validation cohorts. Using the AI software Beta Version (Fujifilm Corporation, Japan), 39 AI imaging factors, including 17 factors from the AI ground-glass nodule analysis and 22 radiomics features from nodule characterization analysis, were extracted to identify factors associated with pN. Multivariate analysis showed that clinical stage IA3 (p = 0.028), solid-part size (p < 0.001), and average solid CT value (p = 0.033) were independently associated with pN. The receiver operating characteristic analysis showed that the area under the curve and optimal cut-off values of the average solid CT value relevant to pN were 0.761 and -103 Hounsfield units, and the threshold provided sensitivity, specificity, and negative predictive values of 69%, 65%, and 94% in the entire cohort, respectively. Measuring the average solid-CT value of tumors for pN may have broad applications such as guiding individualized surgical approaches and postoperative treatment

Derivation of Mesenchymal Stromal Cells from Pluripotent Stem Cells through a Neural Crest Lineage using Small Molecule Compounds with Defined Media

<div><p>Neural crest cells (NCCs) are an embryonic migratory cell population with the ability to differentiate into a wide variety of cell types that contribute to the craniofacial skeleton, cornea, peripheral nervous system, and skin pigmentation. This ability suggests the promising role of NCCs as a source for cell-based therapy. Although several methods have been used to induce human NCCs (hNCCs) from human pluripotent stem cells (hPSCs), such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), further modifications are required to improve the robustness, efficacy, and simplicity of these methods. Chemically defined medium (CDM) was used as the basal medium in the induction and maintenance steps. By optimizing the culture conditions, the combination of the GSK3β inhibitor and TGFβ inhibitor with a minimum growth factor (insulin) very efficiently induced hNCCs (70–80%) from hPSCs. The induced hNCCs expressed cranial NCC-related genes and stably proliferated in CDM supplemented with EGF and FGF2 up to at least 10 passages without changes being observed in the major gene expression profiles. Differentiation properties were confirmed for peripheral neurons, glia, melanocytes, and corneal endothelial cells. In addition, cells with differentiation characteristics similar to multipotent mesenchymal stromal cells (MSCs) were induced from hNCCs using CDM specific for human MSCs. Our simple and robust induction protocol using small molecule compounds with defined media enabled the generation of hNCCs as an intermediate material producing terminally differentiated cells for cell-based innovative medicine.</p></div

Derivation of hMSCs from hNCCs.

<p>A) Schematic protocol for the induction of hMSCs. B) Phase contrast images of cells before (D8) and after (D21) the induction. Scale bar, 200 µm. C) Expression of surface markers in hBM-MSCs (hBM90) and 201B7-derived MSCs (201B7-MSC). D) Hierarchical clustering analyses by genome-wide gene expression profiles. RNAs were extracted from hBM-MSCs (BM90, BM91 and BM94), induced-MSCs, and the corresponding hNCCs and hiPSCs. E) Differentiation properties of induced-MSCs. The induction for osteogenic (OI), chondrogenic (CI), and adipogenic (AI) lineages was performed as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112291#s2" target="_blank">Materials and Methods</a> section and evaluated by Alizarin Red staining (OI), Alcian Blue staining (CI), and Oil Red O staining (AI), respectively. Scale bar, 100 µm. F) Population of SSEA4-positive cells. G) The expression levels of pluripotent markers (<i>OCT3/4</i>, <i>NANOG</i> and <i>SOX2</i>) in hPSCs, hNCCs, and hMSCs. Average ± SD. N = 3, biological triplicates.</p

Induction of p75^high cells from hPSCs.

<p>A) Schematic representation of the protocol. B) Morphology of colonies during the induction. Phase contrast images were taken on days 0, 3, and 7. Scale bar, 200 µm. C) The fraction of p75-positive cells in 201B7 cells was treated with SB431542 (SB) (10 µM) and CHIR99021 (CHIR) (indicated concentration) for seven days, stained with an anti-p75 antibody, and analyzed by FACS. D) Fraction of the p75^high population induced by SB (10 µM) and CHIR (1 µM) from hESCs (KhES1, KhES3, H9) and hiPSCs (414C2, 201B7). Average ± SD. N = 3, biological triplicate. E) Immunocytochemical analyses of colonies on day 7 (201B7). Cells were stained with antibodies against PAX6, TFAP2A, and p75. Scale bar, 100 µm.</p

Expression profiles of sorted p75^high cells.

<p>A) The expression of marker genes in sorted p75^high and p75^low cells. The mRNA expression of each gene was analyzed by RT-qPCR in undifferentiated 201B7 (hiPSCs) and sorted p75^low and p75^high cells, and was shown as a relative value using the level in sorted p75^high cells as 1.0. Average ± SD. N = 3, biological triplicates. B) Clustering analyses of NCC markers in p75^high populations from several hESC and hiPSC lines. Marker genes for each sub-population of NCCs were labeled using the indicated colors.</p