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

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

Differences in the Rates of Ethylene Production and Growth between the Calluses Derived from Rice (Oryza sativa L.) and Soybean (Glycine max (L.) Merr.)

The differences in the rates of ethylene production and growth between the calluses derived from the seeds of rice (16 cultivars of Oryza sativa L., Japonica and Indica types) and soybean (10 cultivars of Glycine max (L.) Merr.) were investigated. On the medium containing 2,4-dichlorophenoxyacetic acid (2,4-D) and benzylaminopurine (BAP), soybean calluses produced a larger amount of ethylene (208-1541 nLg–1 FW 24 h–1) than rice calluses (8-37 nLg–1 FW 24 h–1) and the rate of ethylene production from the calluses of both species greatly varied with the cultivar. The combined application of 2,4-D and BAP greatly increased the ethylene production rate and the growth of calluses in soybean, but not in rice. Moreover, the addition of BAP to the medium strikingly promoted ethylene production in soybean calluses cultured on the medium containing 2,4-D, but not in those cultured on the medium containing indolebutyric acid (IBA). The rate of ethylene production in both soybean and rice negatively correlated with the growth of calluses. The ethylene production and growth of calluses cultured under various conditions greatly differed between soybean and rice, and also varied with the cultivar of each species. The different aspects of the growth and ethylene production between soybean and rice calluses may represent the difference between dicots and monocots

Effect of Brassinolide Applied at the Meiosis and Flowering Stages on the Levels of Endogenous Plant Hormones during Grain-Filling in Rice Plant (Oryza salivaL.)

Brassinolide (BL), a brassinosteroid, applied to rice plants in pots promotes panicle ripening. In this study, we examined the effect of BL applied at the meiosis and flowering stages on endogenous levels of various plant hormones in the panicles of the rice plant (cv. Nipponbare) grown in a field-temperature (F-temp; 25°G on average ranging from 22 to 33°C during ripening periods) condition and low-temperature (L-temp; in phytotron kept at 22°C/ 17°C) condition in rice cultivation season in Japan. The content of either free- or bound-IAA in the rice spikelet at the milk-ripe stage (10 - 15 days after heading) was higher in the F-temp condition than in the L-temp condition. BL applied twice, 10 days before and on the day of heading, slightly increased the free-IAA content and greatly increased the bound-IAA content at the milk-ripe stage in both condition. BL slightly decreased the ABA content of the spikelet at the milk-ripe stage in the F-temp condition, and slightly increased it in the L-temp condition. The rate of ethylene production was measured only in the F-temp condition. It was markedly high at the milk-ripe stage and low at the dough-ripe stage (21 days after heading). BL treatment clearly increased the rate of ethylene production from the panicles under both light and dark conditions at the milk-ripe stage. These results suggest that BL, which promotes rice ripening, influences in the levels of endogenous plant hormones to play an important role in controlling the sink function during grain-filling

The Alpha/Beta Interferon Response Controls Tissue Tropism and Pathogenicity of Poliovirus

Poliovirus selectively replicates in neurons in the spinal cord and brainstem, although poliovirus receptor (PVR) expression is observed in both the target and nontarget tissues in humans and transgenic mice expressing human PVR (PVR-transgenic mice). We assessed the role of alpha/beta interferon (IFN) in determining tissue tropism by comparing the pathogenesis of the virulent Mahoney strain in PVR-transgenic mice and PVR-transgenic mice deficient in the alpha/beta IFN receptor gene (PVR-transgenic/Ifnar knockout mice). PVR-transgenic/Ifnar knockout mice showed increased susceptibility to poliovirus. After intravenous inoculation, severe lesions positive for the poliovirus antigen were detected in the liver, spleen, and pancreas in addition to the central nervous system. These results suggest that the alpha/beta IFN system plays an important role in determining tissue tropism by protecting nontarget tissues that are potentially susceptible to infection. We subsequently examined the expression of IFN and IFN-stimulated genes (ISGs) in the PVR-transgenic mice. In the nontarget tissues, ISGs were expressed even in the noninfected state, and the expression level increased soon after poliovirus infection. On the contrary, in the target tissues, ISG expression was low in the noninfected state and sufficient response after poliovirus infection was not observed. The results suggest that the unequal IFN response is one of the important determinants for the differential susceptibility of tissues to poliovirus. We consider that poliovirus replication was observed in the nontarget tissues of PVR-transgenic/Ifnar knockout mice because the IFN response was null in all tissues

Pathogenesis of Hepatitis C Virus Infection in Tupaia belangeri▿†

The lack of a small-animal model has hampered the analysis of hepatitis C virus (HCV) pathogenesis. The tupaia (Tupaia belangeri), a tree shrew, has shown susceptibility to HCV infection and has been considered a possible candidate for a small experimental model of HCV infection. However, a longitudinal analysis of HCV-infected tupaias has yet to be described. Here, we provide an analysis of HCV pathogenesis during the course of infection in tupaias over a 3-year period. The animals were inoculated with hepatitis C patient serum HCR6 or viral particles reconstituted from full-length cDNA. In either case, inoculation caused mild hepatitis and intermittent viremia during the acute phase of infection. Histological analysis of infected livers revealed that HCV caused chronic hepatitis that worsened in a time-dependent manner. Liver steatosis, cirrhotic nodules, and accompanying tumorigenesis were also detected. To examine whether infectious virus particles were produced in tupaia livers, naive animals were inoculated with sera from HCV-infected tupaias, which had been confirmed positive for HCV RNA. As a result, the recipient animals also displayed mild hepatitis and intermittent viremia. Quasispecies were also observed in the NS5A region, signaling phylogenic lineage from the original inoculating sequence. Taken together, these data suggest that the tupaia is a practical animal model for experimental studies of HCV infection