Molecular characterization, expression pattern and immunologic function of CD82a in large yellow croaker (Larimichthys crocea)

Visceral white spot disease (VWND) caused by Pseudomonas plecoglossicida poses a major threat to the sustainable development of large yellow croaker (Larimichthys crocea) aquaculture. Genome-wide association analysis (GWAS) and RNA-seq research indicated that LcCD82a play an important role in resistance to visceral white spot disease in L. crocea, but the molecular mechanism of LcCD82a response to P. plecoglossicida infection is still unclear. In this study, we cloned and validated the Open Reading Frame (ORF) sequence of LcCD82a and explored the expression profile of LcCD82a in various tissues of L.crocea. In addition, two different transcript variants (LcCD82a-L and LcCD82a-S) of LcCD82a were identified that exhibit alternative splicing patterns after P. plecoglossicida infection, which may be closely related to the immune regulation during pathogenetic process of VWND. In order to explore the function of LcCD82a, we purified the recombinant protein of LcCD82a-L and LcCD82a-S. The bacterial agglutination and apoptosis function analysis showed that LcCD82a may involve in extracellular bacterial recognition, agglutination, and at the same time participate in the process of antigen presentation and induction of cell apoptosis. Collectively, our studies demonstrate that LcCD82a plays a crucial role in regulating apoptosis and antimicrobial immunity

Machine learning-based identification of lower grade glioma stemness subtypes discriminates patient prognosis and drug response

Glioma stem cells (GSCs) remodel their tumor microenvironment to sustain a supportive niche. Identification and stratification of stemness related characteristics in patients with glioma might aid in the diagnosis and treatment of the disease. In this study, we calculated the mRNA stemness index in bulk and single-cell RNA-sequencing datasets using machine learning methods and investigated the correlation between stemness and clinicopathological characteristics. A glioma stemness-associated score (GSScore) was constructed using multivariate Cox regression analysis. We also generated a GSC cell line derived from a patient diagnosed with glioma and used glioma cell lines to validate the performance of the GSScore in predicting chemotherapeutic responses. Differentially expressed genes (DEGs) between GSCs with high and low GSScores were used to cluster lower-grade glioma (LGG) samples into three stemness subtypes. Differences in clinicopathological characteristics, including survival, copy number variations, mutations, tumor microenvironment, and immune and chemotherapeutic responses, among the three LGG stemness-associated subtypes were identified. Using machine learning methods, we further identified genes as subtype predictors and validated their performance using the CGGA datasets. In the current study, we identified a GSScore that correlated with LGG chemotherapeutic response. Through the score, we also identified a novel classification of the LGG subtype and associated subtype predictors, which might facilitate the development of precision therapy

Conventional dendritic cell 2 links the genetic causal association from allergic asthma to COVID-19: a Mendelian randomization and transcriptomic study

Abstract Recent evidence suggests that allergic asthma (AA) decreases the risk of Coronavirus Disease 2019 (COVID-19). However, the reasons remain unclear. Here, we systematically explored data from GWAS (18 cohorts with 11,071,744 samples), bulk transcriptomes (3 cohorts with 601 samples), and single-cell transcriptomes (2 cohorts with 29 samples) to reveal the immune mechanisms that connect AA and COVID-19. Two-sample Mendelian randomization (MR) analysis identified a negative causal correlation from AA to COVID-19 hospitalization (OR = 0.968, 95% CI 0.940–0.997, P = 0.031). This correlation was bridged through white cell count. Furthermore, machine learning identified dendritic cells (DCs) as the most discriminative immunocytes in AA and COVID-19. Among five DC subtypes, only conventional dendritic cell 2 (cDC2) exhibited differential expression between AA/COVID-19 and controls (P < 0.05). Subsequently, energy metabolism, intercellular communication, cellular stemness and differentiation, and molecular docking analyses were performed. cDC2s exhibited more differentiation, increased numbers, and enhanced activation in AA exacerbation, while they showed less differentiation, reduced number, and enhanced activation in severe COVID-19. The capacity of cDC2 for differentiation and SARS-CoV-2 antigen presentation may be enhanced through ZBTB46, EXOC4, TLR1, and TNFSF4 gene mutations in AA. Taken together, cDC2 links the genetic causality from AA to COVID-19. Future strategies for COVID-19 prevention, intervention, and treatment could be stratified according to AA and guided with DC-based therapies. Graphical Abstrac

Bioelectric characterization of epithelia from neonatal CFTR knockout ferrets

Cystic fibrosis (CF) is a life-shortening, recessive, multiorgan genetic disorder caused by the loss of CF transmembrane conductance regulator (CFTR) chloride channel function found in many types of epithelia. Animal models that recapitulate the human disease phenotype are critical to understanding pathophysiology in CF and developing therapies. CFTR knockout ferrets manifest many of the phenotypes observed in the human disease, including lung infections, pancreatic disease and diabetes, liver disease, malnutrition, and meconium ileus. In the present study, we have characterized abnormalities in the bioelectric properties of the trachea, stomach, intestine, and gallbladder of newborn CF ferrets. Short-circuit current (ISC) analysis of CF and wild-type (WT) tracheas revealed the following similarities anddifferences: (1) amiloride-sensitive sodium currents were similar between genotypes; (2) responses to 4,49- diisothiocyano-2,29-stilbene disulphonic acid were 3.3-fold greater in CF animals, suggesting elevated baseline chloride transport through non-CFTR channels in a subset of CF animals; and (3) a lack of 3-isobutyl-1-methylxanthine (IBMX)/forskolin-stimulated and N-(2-Naphthalenyl)- ((3,5-dibromo-2,4-dihydroxyphenyl)methylene) glycine hydrazide (GlyH-101)-inhibited currents in CF animals due to the lack of CFTR. CFTR mRNA was present throughout all levels of theWTferret and IBMX/forskolin-inducible ISC was only observed in WTanimals. However, despite the lack of CFTR function in the knockout ferret, the luminal pH of the CF ferret gallbladder, stomach, and intestines was not significantly changed relative to WT. The WT stomach and gallbladder exhibited significantly enhanced IBMX/ forskolin ISC responses and inhibition by GlyH-101 relative to CF samples. These findings demonstrate that multiple organs affected by disease in the CF ferret have bioelectric abnormalities consistent with the lack of cAMP-mediated chloride transport. Copyrigh

Disease phenotype of a ferret CFTR-knockout model of cystic fibrosis

Cystic fibrosis (CF) is a recessive disease that affects multiple organs. It is caused by mutations in CFTR. Animal modeling of this disease has been challenging, with species- and strain-specific differences in organ biology and CFTR function influencing the emergence of disease pathology. Here, we report the phenotype of a CFTR-knockout ferret model of CF. Neonatal CFTR-knockout ferrets demonstrated many of the characteristics of human CF disease, including defective airway chloride transport and submucosal gland fluid secretion; variably penetrant meconium ileus (MI); pancreatic, liver, and vas deferens disease; and a predisposition to lung infection in the early postnatal period. Severe malabsorption by the gastrointestinal (GI) tract was the primary cause of death in CFTR-knockout kits that escaped MI. Elevated liver function tests in CFTR-knockout kits were corrected by oral administration of ursodeoxycholic acid, and the addition of an oral proton-pump inhibitor improved weight gain and survival. To overcome the limitations imposed by the severe intestinal phenotype, we cloned 4 gut-corrected transgenic CFTR-knockout kits that expressed ferret CFTR specifically in the intestine. One clone passed feces normally and demonstrated no detectable ferret CFTR expression in the lung or liver. The animals described in this study are likely to be useful tools for dissecting CF disease pathogenesis and developing treatments