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

Effects of electronic stopping power on fast-ion-induced secondary ion emission from methanol microdroplets

The formation processes of secondary ions in liquid materials were studied for methanol microdroplets bombarded by carbon ions with incident energies of 0.4–4.0 MeV, where the corresponding electronic stopping power ranged 300–800 eV nm−1. Positive and negative secondary ions including molecular fragments, methanol clusters, and reaction products were investigated, and each ion yield was examined as a function of electronic stopping power Se. We observed different Se-dependence on the emission yields between positive and negative ions. For positive cluster ions [(CH3OH)n + H]+ (n = 2−10), the yield nonlinearly increases and follows the power-law Seα with α = 3. For negative secondary ions, the value of α varies according to secondary ion species or ion mass: α ≈ 0 for fragments with small mass (CH−, CH2−, and OH−), α = 0.5–1.5 for reaction products with medium mass(C2−, C2H−, C2HO−, and C2H5O−), and α = 1.2−1.5 for clusters with large mass [(CH3OH)n – H]− (n = 1−25). The latter finding implies that the value of α is a quantity related to the electronic energy density depending on the distance from the ion trajectory

Fast Heavy-Ion-Induced Anion–Molecule Reactions on the Methanol Droplet Surface

To gain insight into complex ion–molecule reactions induced by MeV-energy heavy ion irradiation of condensed matter, we performed a mass spectrometric study of secondary ions emitted from methanol microdroplet surfaces by 2.0 MeV C²⁺. We observed positive and negative secondary ions, including fragments, clusters, and reaction products. We found that a wider variety of negative ions than positive ions (such as C₂H⁻, C₂HO⁻, C₂H₅O⁻, and C₂H₃O₂⁻) were formed. We performed measurements for deuterated methanol (CH₃OD) droplets to identify the hydrogen elimination site of the intermediates involved in the reactions and to reveal the mechanism that generates various negative reaction product ions. Comparing the results of CH₃OD with CH₃OH droplets, we propose that the primary formation mechanism is association reactions of anion and neutral fragments, such as CH₃O⁻ + CO → C₂H₃O₂⁻. Quantum chemical calculations confirmed that the reactions can proceed with no barrier. This study provides new insights into the importance of rapid anion–molecule reactions among fragments as the mechanism that generates complex molecular species in fast heavy-ion-induced reactions

Effects of radical scavengers on aqueous solutions exposed to heavy-ion irradiation using the liquid microjet technique

The effects of the radical scavenger ascorbic acid on water radiolysis are studied by fast heavy-ion irradiation of aqueous solutions of ascorbic acid, using the liquid microjet technique under vacuum. To understand the reaction mechanisms of hydroxyl radicals in aqueous solutions, we directly measure secondary ions emitted from solutions with different ascorbic acid concentrations. The yield of hydronium secondary ions is strongly influenced by the reaction between ascorbic acid and hydroxyl radicals. From analysis using a simple model considering chemical equilibria, we determine that the upper concentration limit of ascorbic acid with a radical scavenger effect is approximately 70 μM

Brefeldin A-Inhibited Guanine Nucleotide-Exchange Factor 1 (BIG1) Governs the Recruitment of Tumor Necrosis Factor Receptor-Associated Factor 2 (TRAF2) to Tumor Necrosis Factor Receptor 1 (TNFR1) Signaling Complexes

Tumor necrosis factor receptor-associated factor 2 (TRAF2) is a critical mediator of tumor necrosis factor-α (TNF-α) signaling. However, the regulatory mechanisms of TRAF2 are not fully understood. Here we show evidence that TRAF2 requires brefeldin A-inhibited guanine nucleotide-exchange factor 1 (BIG1) to be recruited into TNF receptor 1 (TNFR1) signaling complexes. In BIG1 knockdown cells, TNF-α-induced c-Jun N-terminal kinase (JNK) activation was attenuated and the sensitivity to TNF-α-induced apoptosis was increased. Since these trends correlated well with those of TRAF2 deficient cells as previously demonstrated, we tested whether BIG1 functions as an upstream regulator of TRAF2 in TNFR1 signaling. As expected, we found that knockdown of BIG1 suppressed TNF-α-dependent ubiquitination of TRAF2 that is required for JNK activation, and impaired the recruitment of TRAF2 to the TNFR1 signaling complex (complex I). Moreover, we found that the recruitment of TRAF2 to the death-inducing signaling complex termed complex II was also impaired in BIG1 knockdown cells. These results suggest that BIG1 is a key component of the machinery that drives TRAF2 to the signaling complexes formed after TNFR1 activation. Thus, our data demonstrate a novel and unexpected function of BIG1 that regulates TNFR1 signaling by targeting TRAF2

Relation between biomolecular dissociation and energy of secondary electrons generated in liquid water by fast heavy ions

In this work, we measured and simulated the dissociation of biomolecules in liquid water induced by secondary electrons ejected from water molecules during fast heavy-ion irradiation. We calculated the energy spectra of secondary electrons generated along carbon ion tracks in liquid water in the Bragg peak region. The calculation was done using the Particle and Heavy Ion Transport code System (PHITS) in carbon track structure mode. This mode enables simulation of inelastic collisions along a carbon ion track based on the cross sections considered in the Monte Carlo code KURBUC. To understand the biomolecular dissociation processes in our previous MeV-SIMS experiments with microdroplet targets of glycine solution, we calculated the collision spectra of secondary electrons produced near liquid surfaces using PHITS. Furthermore, we examined the relationship between the secondary electron energy and formation of positive and negative glycine fragments. The results showed that the formation of methylene amine cations is caused by secondary electrons with energies of 13–100 eV. The formation of glycine-related negative ions such as cyanide anion, formate anion, and deprotonated glycine was found to be caused by low-energy (less than 13 eV) secondary electrons. These ions are known products of dissociative electron attachment

Effects of molecular axis orientation of MeV diatomic projectiles on secondary ion emission from biomolecular targets

We report first experimental results on the orientation effect of fast diatomic molecular projectiles on secondary ion emission processes for 3.6-MeV C2+ traversing a self-supporting target of phenylalanine (Phe) film evaporated on a carbon foil. Coincidence measurements were performed on the image of fragments resulting from the Coulomb explosion of C2+ projectiles and the time-of-flight mass spectrometry of secondary ions emitted from the Phe film. We compared the secondary ion yield for C2+ projectiles with parallel and perpendicular orientations to the beam direction. The parallel orientation was found to enhance the secondary ion yield by a factor of approximately 1.1 compared with that for the perpendicular orientation. This enhancement corresponds to an increase in the average charge of Coulomb-exploded fragments. This finding implies that there is a linear correlation between the electronic energy deposition causing secondary ion production and the effective charge number of the incident molecular ions which interact with biomolecular targets