Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.

The clinical outcome and disease severity in coronavirus disease 2019 (COVID-19) are heterogeneous, and the progression or fatality of the disease cannot be explained by a single factor like age or comorbidities. In this study, we used system-wide network-based system biology analysis using whole blood RNA sequencing, immunophenotyping by flow cytometry, plasma metabolomics, and single-cell-type metabolomics of monocytes to identify the potential determinants of COVID-19 severity at personalized and group levels. Digital cell quantification and immunophenotyping of the mononuclear phagocytes indicated a substantial role in coordinating the immune cells that mediate COVID-19 severity. Stratum-specific and personalized genome-scale metabolic modeling indicated monocarboxylate transporter family genes (e.g., SLC16A6), nucleoside transporter genes (e.g., SLC29A1), and metabolites such as α-ketoglutarate, succinate, malate, and butyrate could play a crucial role in COVID-19 severity. Metabolic perturbations targeting the central metabolic pathway (TCA cycle) can be an alternate treatment strategy in severe COVID-19.

Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication.

Viruses hijack host metabolic pathways for their replicative advantage. In this study, using patient-derived multiomics data and in vitro infection assays, we aimed to understand the role of key metabolic pathways that can regulate severe acute respiratory syndrome coronavirus-2 reproduction and their association with disease severity. We used multiomics platforms (targeted and untargeted proteomics and untargeted metabolomics) on patient samples and cell-line models along with immune phenotyping of metabolite transporters in patient blood cells to understand viral-induced metabolic modulations. We also modulated key metabolic pathways that were identified using multiomics data to regulate the viral reproduction in vitro. Coronavirus disease 2019 disease severity was characterized by increased plasma glucose and mannose levels. Immune phenotyping identified altered expression patterns of carbohydrate transporter, glucose transporter 1, in CD8+ T cells, intermediate and nonclassical monocytes, and amino acid transporter, xCT, in classical, intermediate, and nonclassical monocytes. In in vitro lung epithelial cell (Calu-3) infection model, we found that glycolysis and glutaminolysis are essential for virus replication, and blocking these metabolic pathways caused significant reduction in virus production. Taken together, we therefore hypothesized that severe acute respiratory syndrome coronavirus-2 utilizes and rewires pathways governing central carbon metabolism leading to the efflux of toxic metabolites and associated with disease severity. Thus, the host metabolic perturbation could be an attractive strategy to limit the viral replication and disease severity.

Role of Circulating T Follicular Helper Cells and Stem-Like Memory CD4+ T Cells in the Pathogenesis of HIV-2 Infection and Disease Progression.

CD4+ T cells are critical players in the host adaptive immune response. Emerging evidence suggests that certain CD4+ T cell subsets contribute significantly to the production of neutralizing antibodies and help in the control of virus replication. Circulating T follicular helper cells (Tfh) constitute a key T cell subset that triggers the adaptive immune response and stimulates the production of neutralizing antibodies (NAbs). T cells having stem cell-like property, called stem-like memory T cells (Tscm), constitute another important subset of T cells that play a critical role in slowing the rate of disease progression through the differentiation and expansion of different types of memory cell subsets. However, the role of these immune cell subsets in T cell homeostasis, CD4+ T cell proliferation, and progression of disease, particularly in HIV-2 infection, has not yet been elucidated. The present study involved a detailed evaluation of the different CD4+ T cell subsets in HIV-2 infected persons with a view to understanding the role of these immune cell subsets in the better control of virus replication and delayed disease progression that is characteristic of HIV-2 infection. We observed elevated levels of CD4+ Tfh and CD4+ Tscm cells along with memory and effector T cell abundance in HIV-2 infected individuals. We also found increased frequencies of CXCR5+ CD8+ T cells and CD8+ Tscm cells, as well as memory B cells that are responsible for NAb development in HIV-2 infected persons. Interestingly, we found that the frequency of memory CD4+ T cells as well as memory B cells correlated significantly with neutralizing antibody titers in HIV-2 infected persons. These observations point to a more robust CD4+ T cell response that supports B cell differentiation, antibody production, and CD8+ T cell development in HIV-2 infected persons and contributes to better control of the virus and slower rate of disease progression in these individuals.

Distinct lipid profile, low-level inflammation, and increased antioxidant defense signature in HIV-1 elite control status.

HIV-1 elite controllers (EC) are a rare but heterogeneous group of HIV-1-infected individuals who can suppress viral replication in the absence of antiretroviral therapy. The mechanisms of how EC achieve undetectable viral loads remain unclear. This study aimed to investigate host plasma metabolomics and targeted plasma proteomics in a Swedish HIV-1 cohort including EC and treatment-naïve viremic progressors (VP) as well as HIV-negative individuals (HC) to get insights into EC phenotype. Metabolites belonging to antioxidant defense had higher levels in EC relative to VP, whereas inflammation markers were increased in VP compared with EC. Only four plasma proteins (CCL4, CCL7, CCL20, and NOS3) were increased in EC compared with HC, and CCL20/CCR6 axis can play an essential role in EC status. Our study suggests that low-level inflammation and oxidative stress at physiological levels could be important factors contributing to elite control phenotype.

Molecular characterization of Enterococcus faecalis isolates from urinary tract infection and interaction between Enterococcus faecalis encountered Dendritic and Natural Killer cells.

PURPOSE: Enterococcus faecalis is an emerging nosocomial pathogen. The study investigates the E. faecalis specific innate immune cells interplay between Natural Killer cells (NK) and Dendritic cells (DCs) in vitro. The present study also determines the prevalence, phenotype, and genotype of Enterococcus faecalis isolated from paediatric patients with urinary tract infection. MATERIALS AND METHODS: A total of 14 clinical isolates of Enterococcus spp were characterized using standard phenotypic tests and virulence factors were determined by polymerase chain reaction (PCR). Immature monocyte-derived DCs were cultured in the presence of six pathogenic E. faecalis isolates infected DCs were co-cultured with NK cells. Bacteria induced matured DCs and activated NK cells were evaluated by polychromatic flow cytometry. RESULTS: Out of 14 isolates, 13 were identified as E. faecalis. E. faecalis infected DCs differentiated into inflammatory and CD141 + DCs that promote NK cell activation. Activated NK cells significantly elevated the secretion of cytokines and chemokines in infected DCs during E. faecalis. This suggests that DC induced NK cell activation is effectively enhanced by the presence of E. faecalis. CONCLUSIONS: Studies on virulence determinants are necessary to understand the pathogenesis of E. faecalis. DC/NK cross-talk is of particular importance at mucosal surfaces such as the intestine, urinary tract where the immune system exists in intimate association with commensal bacteria. We found E. faecalis specific NK cells activation by infected DC-derived effector signals may involve in the killing of transformed or infected cells, thus coordinating innate and adaptive immune responses. E. faecalis specific DC/NK interaction is necessary for DC maturation and modulation of innate effector functions. Similarly, activated NK cells that induce- maturation of DC by pattern recognition receptors are also required for the generation of bacterial specific adaptive immunity.