Network vaccinology.

The structure and function of the immune system is governed by complex networks of interactions between cells and molecular components. Vaccination perturbs these networks, triggering specific pathways to induce cellular and humoral immunity. Systems vaccinology studies have generated vast data sets describing the genes related to vaccination, motivating the use of new approaches to identify patterns within the data. Here, we describe a framework called Network Vaccinology to explore the structure and function of biological networks responsible for vaccine-induced immunity. We demonstrate how the principles of graph theory can be used to identify modules of genes, proteins, and metabolites that are associated with innate and adaptive immune responses. Network vaccinology can be used to assess specific and shared molecular mechanisms of different types of vaccines, adjuvants, and routes of administration to direct rational design of the next generation of vaccines.

Amino acid starvation sensing dampens IL-1ß production by activating riboclustering and autophagy.

Activation of the amino acid starvation response (AAR) increases lifespan and acute stress resistance as well as regulates inflammation. However, the underlying mechanisms remain unclear. Here, we show that activation of AAR pharmacologically by Halofuginone (HF) significantly inhibits production of the proinflammatory cytokine interleukin 1ß (IL-1ß) and provides protection from intestinal inflammation in mice. HF inhibits IL-1ß through general control nonderepressible 2 kinase (GCN2)-dependent activation of the cytoprotective integrated stress response (ISR) pathway, resulting in rerouting of IL-1ß mRNA from translationally active polysomes to inactive ribocluster complexes-such as stress granules (SGs)-via recruitment of RNA-binding proteins (RBPs) T cell-restricted intracellular antigen-1(TIA-1)/TIA-1-related (TIAR), which are further cleared through induction of autophagy. GCN2 ablation resulted in reduced autophagy and SG formation, which is inversely correlated with IL-1ß production. Furthermore, HF diminishes inflammasome activation through suppression of reactive oxygen species (ROS) production. Our study unveils a novel mechanism by which IL-1ß is regulated by AAR and further suggests that administration of HF might offer an effective therapeutic intervention against inflammatory diseases.

OUTBREAK: a user-friendly georeferencing online tool for disease surveillance.

The current COVID-19 pandemic has already claimed more than 3.7 million victims and it will cause more deaths in the coming months. Tools that track the number and locations of cases are critical for surveillance and help in making policy decisions for controlling the outbreak. However, the current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We developed a user-friendly web tool, named OUTBREAK, that facilitates epidemic surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. We applied our tool to visualize the SARS 2003, MERS, and COVID19 epidemics, and provided them as examples on the website. Through the zoom feature, it is also possible to visualize cases at city and even neighborhood levels. We made the tool freely available at https://outbreak.sysbio.tools/ . OUTBREAK has the potential to guide and help health authorities to intervene and minimize the effects of outbreaks.

Activation of integrated stress response pathway regulates IL-1ß production through posttranscriptional and translational reprogramming in macrophages.

Immune cells sense and programme its cellular machinery appropriately to the environmental changes through the activation of cytoprotective adaptive pathway so-called the "integrated stress response (ISR)". However, the mechanisms implicated in ISR-induced protective responses are poorly understood. Here, we show that ISR activation by arsenite (Ar) results in suppression of IL-1ß production in macrophages and inhibition of DSS-induced colitis in a murine model through a novel posttranscriptional and translation regulatory (PTR) mechanism. Ar triggers PTR events through eIF2α-phosphorylation, which results in the attenuation of active polysome formation leading to the accumulation of translationally stalled IL-1ß mRNAs. Translationally stalled IL-1ß mRNAs recruit RNA-binding proteins (TIA-1/TIAR), resulting in the formation of RBP-RNA complexes known as stress granules (SGs). The SGs bound IL-1ß mRNAs might undergo degradation through induction of autophagy. Also, we show that Ar posttranslationally impairs processing and secretion of IL-1ß by diminishing inflammasome activation. Altogether, this study unveils a novel mechanism of IL-1ß regulation and further suggests that pharmacological activation of cytoprotective ISR pathway might provide an effective therapeutic intervention against inflammatory diseases.

Transcriptome meta-analysis identifies immune signature comprising of RNA binding proteins in ulcerative colitis patients.

Ulcerative colitis (UC) is a persistent inflammatory illness, which is clinically categorised as Inflammatory bowel disease (IBD), affecting millions of people worldwide. The precise cause behind the pathology of the disease remains unknown. However, the involvement of multiple factors including genetic predisposition, immunological deregulations, microbiota imbalance, and environmental triggers has been suggested. Amongst all these factors, the over-active immunological response reported in UC patients seems to be a promising target for therapy. Moreover, identification of gene signatures associated with disease onset and progression would help in better understanding of the molecular mechanisms involved in the disease pathogenesis. Here, we have conducted meta-analysis of gene expression profiles of UC patient microarray datasets accessible in public databases and further validated the in-silico findings in UC patients' blood samples. Our study reveals that UC pathogenesis perturbs expression of several inflammatory genes. In addition, we report a novel gene signature comprising of TIA1 (T cell restricted intracellular antigen) and TIAR (TIA1 related protein; also known as TIAL1), which were found to be significantly downregulated in UC patients. TIA1 and TIAR are RNA-binding proteins (RBPs), which function as a translational represser by binding to ARE sequences in the 3' UTR of mRNAs encoding inflammatory mediators including cytokines. Our findings demonstrate that deletion of TIAR using gene specific siRNAs in-vitro results in enhanced production of inflammatory cytokine IL-1ß. In conclusion, the findings of this study reveal that down regulation of TIA1/TIAR genes could be responsible for UC associated inflammation. This study highlights the usefulness of the meta-analysis approach in the identification of unique gene signatures that might deliver mechanistic insights into UC pathogenesis and possibly assist in discovery of prognostic markers and therapeutic interventions.

Temporal and spatial analysis of over 7,000 measles cases outbreak from 2018 to 2019 in the Brazilian Amazon.

OBJECTIVE: This study aimed to present a temporal and spatial analysis of the 2018 measles outbreak in Brazil, particularly in the metropolitan city of Manaus in the Amazon region, and further introduce a new tool for spatial analysis. METHODS: We analyzed the geographical data of the residences of over 7,000 individuals with measles in Manaus during 2018 and 2019. Spatial and temporal analyses were conducted to characterize various aspects of the outbreak, including the onset and prevalence of symptoms, demographics, and vaccination status. A visualization tool was also constructed to display the geographical and temporal distribution of the reported measles cases. RESULTS: Approximately 95% of the included participants had not received vaccination within the past decade. Heterogeneity was observed across all facets of the outbreak, including variations in the incubation period and symptom presentation. Age distribution exhibited two peaks, occurring at one year and 18 years of age, and the potential implications of this distribution on predictive analysis were discussed. Additionally, spatial analysis revealed that areas with the highest case densities tended to have the lowest standard of living. CONCLUSION: Understanding the spatial and temporal spread of measles outbreaks provides insights for decision-making regarding measures to mitigate future epidemics.

Tucuxi-BLAST: Enabling fast and accurate record linkage of large-scale health-related administrative databases through a DNA-encoded approach.

Background: Public health research frequently requires the integration of information from different data sources. However, errors in the records and the high computational costs involved make linking large administrative databases using record linkage (RL) methodologies a major challenge. Methods: We present Tucuxi-BLAST, a versatile tool for probabilistic RL that utilizes a DNA-encoded approach to encrypt, analyze and link massive administrative databases. Tucuxi-BLAST encodes the identification records into DNA. BLASTn algorithm is then used to align the sequences between databases. We tested and benchmarked on a simulated database containing records for 300 million individuals and also on four large administrative databases containing real data on Brazilian patients. Results: Our method was able to overcome misspellings and typographical errors in administrative databases. In processing the RL of the largest simulated dataset (200k records), the state-of-the-art method took 5 days and 7 h to perform the RL, while Tucuxi-BLAST only took 23 h. When compared with five existing RL tools applied to a gold-standard dataset from real health-related databases, Tucuxi-BLAST had the highest accuracy and speed. By repurposing genomic tools, Tucuxi-BLAST can improve data-driven medical research and provide a fast and accurate way to link individual information across several administrative databases.

Gene signatures of autopsy lungs from obese patients with COVID-19.

BACKGROUND & AIMS: Obesity is associated with low grade systemic inflammation and insulin resistance. Although metabolic and immunological changes may contribute to the increased risk for COVID-19 mortality in obese, little is known about the impact of obesity in the lungs of patients with COVID-19. METHODS: We analyzed gene expression profiles of autopsy lungs of a cohort of 14 COVID-19 patients and 4 control individuals. Patients were divided into 3 groups according to their comorbidities: hypertension, type 2 diabetes (T2D) and obesity. We then identified the molecular alterations associated with these comorbidities in COVID-19 patients. RESULTS: Patients with only hypertension showed higher levels of inflammatory genes and B-cell related genes when compared to those with T2D and obesity. However, the levels of IFN-gamma, IL22, and CD274 (a ligand that binds to receptor PD1) were higher in COVID-19 patients with T2D and obesity. Several metabolic- and immune-associated genes such as G6PD, LCK and IL10 were significantly induced in the lungs of the obese group. CONCLUSION: Our findings suggest that SARS-CoV-2 infection in the lungs may exacerbate the immune response and chronic condition in obese COVID-19 patients.

In-depth analysis of laboratory parameters reveals the interplay between sex, age, and systemic inflammation in individuals with COVID-19.

BACKGROUND: The progression and severity of COVID-19 vary significantly in the population. While the hallmarks of SARS-CoV-2 and severe COVID-19 within routine laboratory parameters are emerging, the impact of sex and age on these profiles is still unknown. METHODS: A multidimensional analysis was performed involving millions of records of laboratory parameters and diagnostic tests for 178 887 individuals from Brazil, of whom 33 266 tested positive for SARS-CoV-2. Analyzed data included those relating to complete blood cell count, electrolytes, metabolites, arterial blood gases, enzymes, hormones, cancer biomarkers, and others. FINDINGS: COVID-19 induced similar alterations in laboratory parameters in males and females. CRP and ferritin were increased, especially in older men with COVID-19, whereas abnormal liver function tests were common across several age groups, except for young women. Low peripheral blood basophils and eosinophils were more common in the elderly with COVID-19. Both male and female COVID-19 patients admitted to intensive care units displayed alterations in the coagulation system, and higher values for neutrophils, CRP, and lactate dehydrogenase. CONCLUSIONS: Our study uncovered the laboratory profiles of a large cohort of COVID-19 patients, which formed the basis of discrepancies influenced by aging and biological sex. These profiles directly linked COVID-19 disease presentation to an intricate interplay between sex, age, and immune activation.

Dengue Virus Induced COX-2 Signaling Is Regulated Through Nutrient Sensor GCN2.

Nutrient sensor GCN2 plays a crucial role in the maintenance of cellular homeostasis during the condition of amino acid deprivation. Dysfunction in the GCN2 signaling underlies several chronic metabolic diseases. Recent studies highlight the anti-viral potential of GCN2 against RNA viruses such as Sindbis and HIV. However, its effect on dengue virus (DENV) pathogenesis remains poorly understood. Herein, we report that GCN2 deficient cells show increased DENV replication and viral yield in the culture supernatants compared to WT cells infected with DENV. Notably, enhanced DENV replication in GCN2-/- cells is associated with increased COX-2/PGE2 signaling. Conversely, GCN2 overexpression/activation effectively contains DENV infection by inhibiting COX-2/PGE2 signaling. Mechanistically, deletion of GCN2 triggers enhanced production of COX-2/PGE2 through profound activation of Iκκ-NF-κB signaling pathway. Altogether our results unveil a hitherto unrecognized role of GCN2 in DENV pathogenesis, thereby suggesting that targeting the GCN2 pathway might offer a novel therapeutic intervention against DENV infection.

Temporal and spatial analysis of over 7,000 measles cases outbreak from 2018 to 2019 in the Brazilian Amazon

ABSTRACT Objective: This study aimed to present a temporal and spatial analysis of the 2018 measles outbreak in Brazil, particularly in the metropolitan city of Manaus in the Amazon region, and further introduce a new tool for spatial analysis. Methods: We analyzed the geographical data of the residences of over 7,000 individuals with measles in Manaus during 2018 and 2019. Spatial and temporal analyses were conducted to characterize various aspects of the outbreak, including the onset and prevalence of symptoms, demographics, and vaccination status. A visualization tool was also constructed to display the geographical and temporal distribution of the reported measles cases. Results: Approximately 95% of the included participants had not received vaccination within the past decade. Heterogeneity was observed across all facets of the outbreak, including variations in the incubation period and symptom presentation. Age distribution exhibited two peaks, occurring at one year and 18 years of age, and the potential implications of this distribution on predictive analysis were discussed. Additionally, spatial analysis revealed that areas with the highest case densities tended to have the lowest standard of living. Conclusion: Understanding the spatial and temporal spread of measles outbreaks provides insights for decision-making regarding measures to mitigate future epidemics.

A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients.

Rheumatoid arthritis (RA), a symmetric polyarticular arthritis, has long been feared as one of the most disabling forms of arthritis. Identification of gene signatures associated with RA onset and progression would lead toward development of novel diagnostics and therapeutic interventions. This study was undertaken to identify unique gene signatures of RA patients through large-scale meta-profiling of a diverse collection of gene expression data sets. We carried out a meta-analysis of 8 publicly available RA patients' (107 RA patients and 76 healthy controls) gene expression data sets and further validated a few meta-signatures in RA patients through quantitative real-time PCR (RT-qPCR). We identified a robust meta-profile comprising 33 differentially expressed genes, which were consistently and significantly expressed across all the data sets. Our meta-analysis unearthed upregulation of a few novel gene signatures including PLCG2, HLA-DOB, HLA-F, EIF4E2, and CYFIP2, which were validated in peripheral blood mononuclear cell samples of RA patients. Further, functional and pathway enrichment analysis reveals perturbation of several meta-genes involved in signaling pathways pertaining to inflammation, antigen presentation, hypoxia, and apoptosis during RA. Additionally, PLCG2 (phospholipase Cγ2) popped out as a novel meta-gene involved in most of the pathways relevant to RA including inflammasome activation, platelet aggregation, and activation, thereby suggesting PLCG2 as a potential therapeutic target for controlling excessive inflammation during RA. In conclusion, these findings highlight the utility of meta-analysis approach in identifying novel gene signatures that might provide mechanistic insights into disease onset, progression and possibly lead toward the development of better diagnostic and therapeutic interventions against RA.

Mesoporous ZnO nanocapsules for the induction of enhanced antigen-specific immunological responses.

The application of nanotechnology in vaccinology has fuelled rapid advancement towards the design and development of nanovaccines. Nanoparticles have been found to enhance vaccine efficacy through the spatiotemporal orchestration of antigen delivery to secondary lymphoid organs and antigen-presentation by Antigen Presenting Cells (APCs) synchronized with stimulation of innate and adaptive immune responses. Metal based nanoparticles (MNPs) have been extensively engineered for the generation of nanovaccines owing to their intrinsic adjuvant-like properties and immunomodulatory functions. Furthermore, mesoporous nanocapsules of late have attracted researchers due to their precise size and exclusive capacity to encapsulate a wide range of biomolecules and their sustained release at the targeted sites. Herein, we have designed a novel mesoporous ZnO nanocapsule (mZnO) having a size of ∼12 nm with an average pore diameter of 2.5 nm, using a surfactant-free sonochemical method and investigated its immunomodulatory properties by using Ova loaded mZnO nanocapsules [mZnO(Ova)] in a mice model. Our findings show that mZnO(Ova) administration steered the enhanced expansion of antigen-specific T-cells and induction of IFN-γ producing effector CD4+ and CD8+ T-cells. Also, antigen-specific IgG levels were enriched in both the serum and lymph nodes of mZnO(Ova) immunized mice. Further, we noticed a substantial increase in serum IgG2a or IgG2b levels and IFN-γ secretion in Ova restimulated splenocytes from mZnO(Ova) immunized mice, indicating that mZnO(Ova) skew Th1 type immune response. Overall, the uniqueness of mZnO nanocapsules in terms of the defined particle to pore numbers ratio (maximum of three cavities per particle) allows loading antigens efficiently. Given these features in combination with its immunomodulatory characteristics reinforces the idea that mZnO could be used as an effective antigen-adjuvant platform for the development of novel nano-based vaccines against multiple diseases.

Transcriptome meta-analysis reveals a dysregulation in extra cellular matrix and cell junction associated gene signatures during Dengue virus infection.

Dengue Viruses (DENVs) cause one of the most prevalent arthropod-borne viral diseases affecting millions of people worldwide. Identification of genes involved in DENV pathogenesis would help in deciphering molecular mechanisms responsible for the disease progression. Here, we carried out a meta-analysis of publicly available gene expression data of dengue patients and further validated the meta-profile using in-vitro infection in THP-1 cells. Our findings reveal that DENV infection modulates expression of several genes and signalling pathways including interferons, detoxification of ROS and viral assembly. Interestingly, we have identified novel gene signatures comprising of INADL/PATJ and CRTAP (Cartilage Associated Protein), which were significantly down-regulated across all patient data sets as well as in DENV infected THP-1 cells. PATJ and CRTAP genes are involved in maintaining cell junction integrity and collagen assembly (extracellular matrix component) respectively, which together play a crucial role in cell-cell adhesion. Our results categorically reveal that overexpression of CRTAP and PATJ genes restrict DENV infection, thereby suggesting a critical role of these genes in DENV pathogenesis. Conclusively, these findings emphasize the utility of meta-analysis approach in identifying novel gene signatures that might provide mechanistic insights into disease pathogenesis and possibly lead towards the development of better therapeutic interventions.

Post-transcriptional Regulation of Immunological Responses through Riboclustering.

Immunological programing of immune cells varies in response to changing environmental signals. This process is facilitated by modifiers that regulate the translational fate of mRNAs encoding various immune mediators, including cytokines and chemokines, which in turn determine the rapid activation, tolerance, and plasticity of the immune system. RNA-binding proteins (RBPs) recruited by the specific sequence elements in mRNA transcripts are one such modifiers. These RBPs form RBP-RNA complexes known as "riboclusters." These riboclusters serve as RNA sorting machinery, where depending upon the composition of the ribocluster, translation, degradation, or storage of mRNA is controlled. Recent findings suggest that this regulation of mRNA homeostasis is critical for controlling the immune response. Here, we present the current knowledge of the ribocluster-mediated post-transcriptional regulation of immune mediators and highlight recent findings regarding their implications for the pathogenesis of acute or chronic inflammatory diseases.

OUTBREAK: a user-friendly georeferencing online tool for disease surveillance

The current COVID-19 pandemic has already claimed more than 3.7 million victims and it will cause more deaths in the coming months. Tools that track the number and locations of cases are critical for surveillance and help in making policy decisions for controlling the outbreak. However, the current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We developed a user-friendly web tool, named OUTBREAK, that facilitates epidemic surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. We applied our tool to visualize the SARS 2003, MERS, and COVID19 epidemics, and provided them as examples on the website. Through the zoom feature, it is also possible to visualize cases at city and even neighborhood levels. We made the tool freely available at https://outbreak.sysbio.tools/. OUTBREAK has the potential to guide and help health authorities to intervene and minimize the effects of outbreaks.

Using location history data from cell phones of infectious patients for disease surveillance / Usando dados do histórico de localização de telefones celulares de pacientes infecciosos para vigilância de doenças

Infectious diseases significantly contribute to global morbidity and mortality, highlighting the critical need for robust disease surveillance systems. The rapid and accurate identification of infection hotspots is crucial for effective disease control and eliminating vector reservoirs. Traditional methods, reliant on patient-reported data, are vague, slow, and non-integrative, presenting substantial barriers to fully understanding the underlying causes of infection transmission. The widespread usage of smartphones presents a unique opportunity to access, analyze, and monitor digital data. Particularly, location data can offer potential insights into infectious disease dynamics, which has remained largely unexplored. Firstly, the present study leverages location history data from smartphones of malaria patients in Manaus, Amazonas region, to pinpoint mosquito-breeding sites. Upon quantifying the location data, the primary transmission hotspots were identified to be concentrated on the outskirts of the city of Manaus. Additionally, the quantification and hotspot validation confirmed that newly visited locations during the exposure period were potential sources of infection transmission. Secondly, the current study also employs a novel digital contact investigation method for a human-to-human transmission infection such as tuberculosis to measure the exposure risk between the active index cases and their close contacts. The digital contact investigation revealed varied exposure durations between the recruited paired index and close contact participants based on the outcome of close contact. To summarize, the present study determines distinct mobility patterns associated with both these infectious diseases, potentially aiding in drafting targeted public health strategies and policies for digital epidemiological surveillance

As doenças infecciosas são um dos principais contribuintes para a morbidade e a mortalidade globais, enfatizando a necessidade crítica de sistemas robustos de vigilância de doenças. A identificação rápida e precisa dos pontos críticos de infecção é fundamental para o controle eficaz de doenças e a eliminação de reservatórios de vetores. Os métodos tradicionais, que dependem de dados relatados por pacientes, são vagos, lentos e não integrativos, apresentando barreiras significativas para a compreensão total das causas subjacentes da transmissão de infecções. O uso generalizado de dispositivos móveis apresenta uma oportunidade única de acessar, analisar e monitorar dados digitais. Especialmente, dados de localização podem oferecer informações úteis sobre a dinâmica de doenças infecciosas, que permanecem em grande parte inexploradas. Primeiramente, o presente estudo utiliza dados de histórico de localização de smartphones de pacientes com malária em Manaus, na região do Amazonas, para identificar locais de reprodução de mosquitos. Ao quantificar os dados de localização, identificaram-se os principais pontos de transmissão concentrados nos arredores da cidade de Manaus. Além do mais, a quantificação e a validação em campo confirmaram que os locais recém-visitados durante o período de exposição eram potenciais fontes de transmissão da infecção. Em segundo lugar, o estudo atual também emprega um inovador método de investigação digital de contato para uma infecção por transmissão de humano para humano, como a tuberculose, a fim de medir o risco por exposição entre os casos índice ativos e seus contatos próximos. A investigação digital de contato revelou períodos de exposição variados entre os participantes recrutados em pares de casos índice e contatos próximos, com base no resultado do contato próximo. Em resumo, o presente estudo identifica padrões distintos de mobilidade associados a ambas essas doenças infecciosas, auxiliando potencialmente na elaboração de estratégias e políticas de saúde pública direcionadas para a vigilância epidemiológica digital