Daily expression of a clock gene in the brain and pituitary of the Malabar grouper (Epinephelus malabaricus)

Recent studies have revealed that, in addition to regulating the circadian system, clock genes such as cryptochrome (Cry) genes are involved in seasonal and lunar rhythmicity in fish. This study clarified the transcriptional characteristics of a Cry subtype (mgCry2) in the brain of the Malabar grouper, Epinephelus malabaricus, which is an important aquaculture species that spawns around the new moon. The cDNA sequence of mgCry2 showed high identity (97-99%) with fish Cry2 and had an open reading frame encoding a protein with 170 amino acids. Phylogenetic analyses revealed that mgCRY2 had high identity with CRY in other fish species. Real-time quantitative polymerase chain reaction (qPCR) showed the widespread distribution of mgCry2 in neural (brain, pituitary, and retina) and peripheral (heart, liver, kidney, spleen, gill, intestine, and ovary) tissues. When immature Malabar groupers were reared under a light-dark cycle (LD=12:12) and the amounts of mgCry2 mRNA in the telencephalon and diencephalon were measured at 4-h intervals, the levels increased during photophase and decreased during scotophase. Day-night variation in mgCry2 mRNA abundance was also observed in the pituitary. These daily profiles suggest that mgCry2 is a light-responsive gene in neural tissues. In situ hybridization analyses showed that mgCry2 was strongly transcribed in the nucleus lateralis tuberis of the ventral hypothalamus, peripheral area of the proximal pars distalis, and the pars intermedia of the pituitary. We conclude that clock genes expressed in the pituitary and diencephalon play a role in entraining the endocrine network of the Malabar grouper to periodic changes in external cues

Melatonin influences reproduction in the sapphire devil Chrysiptera cyanea via regulation of dopamine 2b receptor transcription

Melatonin and dopamine participate in the regulation of reproduction-related hormone/peptide synthesis and secretion at the hypothalamic–pituitary–gonadal axis in fish. Here, we report a unique reproduction-related interaction of melatonin and dopamine in the brain of the sapphire devil Chrysiptera cyanea, a tropical damselfish with a long-day preference. We examined the expression of arylalkylamine N-acetyltransferase 2 (aanat2)—a rate-limiting enzyme of melatonin, dopamine 2b receptor (d2b), gonadotropin-releasing hormone (gnrh1), and β-subunit of follicle-stimulating hormone (fshβ) and luteinizing hormone (lhβ)—in the brain of the sapphire devil. During the reproductive season, mature females were divided into the early vitellogenesis (EV), late vitellogenesis (LV), and post-spawning (PS) stages; a day-low and night-high profile of aanat2 was observed during EV and LV but not during PS. There were nocturnal increases in gnrh1 during EV and LV as well as d2b during LV, suggesting that melatonin has a positive effect on the levels of gnrh1 and d2b transcripts in mature fish. When the brains of females in the non-breeding season were sampled at 4-h intervals, nocturnal increases in the levels of fshβ and lhβ transcripts were observed at 00:00 and 04:00, respectively. The immersion of immature fish in melatonin-containing seawater for 6 h resulted in the upregulation of fshβ and lhβ, as well as downregulation of d2b, in the brain. Additionally, in situ hybridization analysis showed that melatonin treatment lowered the signals of d2b transcripts in the ventral hypothalamus, rostral pars distalis, proximal pars distalis, and pars intermedia, suggesting that melatonin has a negative impact on the levels of d2b transcripts in the hypothalamus and pituitary of immature females; the opposite effect is likely concerning the levels of fshβ and lhβ transcripts in the pituitary. In conclusion, melatonin positively and negatively acted on the hypothalamus and pituitary in the sapphire devil; these opposite effects were related to differences in gonadal development status

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 selected light wavelengths on the transcript levels of photoreceptors and growth-related hormones and peptides in the Malabar grouper Epinephelus malabaricus

Fish growth is influenced by environmental cues, including light conditions. The duration of exposure (photoperiod), the intensity of exposure (illumination), and quality (light spectrum) play crucial roles in maximizing growth. This study aimed to clarify how selected light wavelengths are perceived and transduced as an internal signal to stimulate growth of the Malabar grouper Epinephelus malabaricus, an important aquaculture species in Asian countries. Four opsins (RH1, RH2, SWS2, and LWS) were selected from the database of photoreceptors of groupers, and reverse-transcription polymerase chain reaction revealed that these opsins were expressed in the eyes and brain. When fish were reared under conditions of long-day (light:dark = 14:10) with red (peak at 632 nm), green (519 nm), and blue (465 nm) LED and natural light, the specific growth rate was higher (P < 0.05) in fish exposed to blue LED light than to red LED light. Rearing fish under shorter light wavelengths (blue or green) resulted in high transcript levels (P < 0.05) of RH1 and RH2 in the eyes (retina) and of RH1 and SWS2 in the brain (diencephalon), suggesting that certain light wavelengths activate photoreceptors in light perceptive organs. The transcript levels of growth hormone (GH) and insulin-like growth factor (IGF-I) increased significantly (P < 0.05) in the pituitary and liver of fish reared under blue LED light, respectively. Moreover, similar increases (P < 0.05) in the transcripts of neuropeptide Y (NPY) and pro-opiomelanocortin were observed in the brain of fish reared under blue LED light. We concluded that blue light perceived by visual opsins in the eyes and brain activates the growth of the endocrine axis and its interaction with NPY. Consequently, rearing the Malabar grouper under specific light wavelengths helps maximize their growth

Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study

Abstract Background Although cases of respiratory bacterial infections associated with coronavirus disease 2019 (COVID-19) have often been reported, their impact on the clinical course remains unclear. Herein, we evaluated and analyzed the complication rates of bacterial infections, causative organisms, patient backgrounds, and clinical outcome in Japanese patients with COVID-19. Methods We performed a retrospective cohort study that included inpatients with COVID-19 from multiple centers participating in the Japan COVID-19 Taskforce (April 2020 to May 2021) and obtained demographic, epidemiological, and microbiological results and the clinical course and analyzed the cases of COVID-19 complicated by respiratory bacterial infections. Results Of the 1,863 patients with COVID-19 included in the analysis, 140 (7.5%) had respiratory bacterial infections. Community-acquired co-infection at COVID-19 diagnosis was uncommon (55/1,863, 3.0%) and was mainly caused by Staphylococcus aureus, Klebsiella pneumoniae and Streptococcus pneumoniae. Hospital-acquired bacterial secondary infections, mostly caused by Staphylococcus aureus, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia, were diagnosed in 86 patients (4.6%). Severity-associated comorbidities were frequently observed in hospital-acquired secondary infection cases, including hypertension, diabetes, and chronic kidney disease. The study results suggest that the neutrophil–lymphocyte ratio (> 5.28) may be useful in diagnosing complications of respiratory bacterial infections. COVID-19 patients with community-acquired or hospital-acquired secondary infections had significantly increased mortality. Conclusions Respiratory bacterial co-infections and secondary infections are uncommon in patients with COVID-19 but may worsen outcomes. Assessment of bacterial complications is important in hospitalized patients with COVID-19, and the study findings are meaningful for the appropriate use of antimicrobial agents and management strategies

Additional file 1 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study

Additional file 1. Identification of organisms in ventilator-associated pneumoniacase

Additional file 5 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study

Additional file 5. Association of anti-IL-6 receptor antibody use with incidence of secondary infection and death

Additional file 6 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study

Additional file 6. Admission to intensive care unitand use of invasive mechanical ventilationof bacterial respiratory infection with coronavirus disease 2019