APPLICATION OF QUANTILE DISCRETIZATION AND BAYESIAN NETWORK ANALYSIS TO PUBLICLY AVAILABLE CYSTIC FIBROSIS DATA SETS.

The availability of multiple publicly-available datasets studying the same phenomenon has the promise of accelerating scientific discovery. Meta-analysis can address issues of reproducibility and often increase power. The promise of meta-analysis is especially germane to rarer diseases like cystic fibrosis (CF), which affects roughly 100,000 people worldwide. A recent search of the National Institute of Health's Gene Expression Omnibus revealed 1.3 million data sets related to cancer compared to about 2,000 related to CF. These studies are highly diverse, involving different tissues, animal models, treatments, and clinical covariates. In our search for gene expression studies of primary human airway epithelial cells, we identified three studies with compatible methodologies and sufficient metadata: GSE139078, Sala Study, and PRJEB9292. Even so, experimental designs were not identical, and we identified significant batch effects that would have complicated functional analysis. Here we present quantile discretization and Bayesian network construction using the Hill climb method as a powerful tool to overcome experimental differences and reveal biologically relevant responses to the CF genotype itself, exposure to virus, bacteria, and drugs used to treat CF. Functional patterns revealed by cluster Profiler included interferon signaling, interferon gamma signaling, interleukins 4 and 13 signaling, interleukin 6 signaling, interleukin 21 signaling, and inactivation of CSF3/G-CSF signaling pathways showing significant alterations. These pathways were consistently associated with higher gene expression in CF epithelial cells compared to non-CF cells, suggesting that targeting these pathways could improve clinical outcomes. The success of quantile discretization and Bayesian network analysis in the context of CF suggests that these approaches might be applicable to other contexts where exactly comparable data sets are hard to find.

Obesity in Severe COVID-19 Patients Has a Distinct Innate Immune Phenotype.

Obesity alters the capacity of effective immune responses in infections. To further address this phenomenon in the context of COVID-19, this study investigated how the immunophenotype of leukocytes was altered in individuals with obesity in severe COVID-19. This cross-sectional study enrolled 27 ICU COVID-19 patients (67% women, 56.33 ± 19.55 years) that were assigned to obese (BMI ≥ 30 kg/m2, n = 9) or non-obese (BMI < 30kg/m2, n = 18) groups. Monocytes, NK, and both Low-Density (LD) and High-Density (HD) neutrophils were isolated from peripheral blood samples, and surface receptors' frequency and expression patterns were analyzed by flow cytometry. Clinical status and biochemical data were additionally evaluated. The frequency of monocytes was negatively correlated with BMI, while NK cells and HD neutrophils were positively associated (p < 0.05). Patients with obesity showed a significant reduction of monocytes, and these cells expressed high levels of PD-L1 (p < 0.05). A higher frequency of NK cells and increased expression of TREM-1+ on HD neutrophils were detected in obese patients (p < 0.05). The expression of receptors related to antigen-presentation, phagocytosis, chemotaxis, inflammation and suppression were strongly correlated with clinical markers only in obese patients (p < 0.05). Collectively, these outcomes revealed that obesity differentially affected, and largely depressed, innate immune response in severe COVID-19.

The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases.

SARS-CoV-2 has caused a high number of deaths in several countries. In Brazil, there were 37 million confirmed cases of COVID-19 and 700,000 deaths caused by the disease. The population size and heterogeneity of the Brazilian population should be considered in epidemiological surveillance due to the varied tropism of the virus. As such, municipalities and states must be factored in for their unique specificities, such as socioeconomic conditions and population distribution. Here, we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and their dynamics in each microregion from Sergipe state, northeastern Brazil, in the first 3 years of the pandemic. We analyzed 586 genomes sequenced between March 2020 and November 2022 extracted from the GISAID database. Phylogenetic analyses were carried out for each data set to reconstruct evolutionary history. Finally, the existence of a correlation between the number of lineages and infection cases by SARS-CoV-2 was evaluated. Aracaju, the largest city in northeastern Brazil, had the highest number of samples sequenced. This represented 54.6% (320) of the genomes, and consequently, the largest number of lineages identified. Studies also analyzed the relationship between mean lineage distributions and mean monthly infections, daily cases, daily deaths, and hospitalizations of vaccinated and unvaccinated patients. For this, a correlation matrix was created. Results revealed that the increase in the average number of SARS-CoV-2 variants was related to the average number of SARS-CoV-2 cases in both unvaccinated and vaccinated individuals. Thus, our data indicate that it is necessary to maintain epidemiological surveillance, especially in capital cities, since they have a high rate of circulation of resident and non-resident inhabitants, which contributes to the dynamics of the virus.

TREM-1 Expression on the Surface of Neutrophils in Patients With Visceral Leishmaniasis Is Associated With Immunopathogenesis.

Visceral leishmaniasis (VL) is a systemic chronic and potentially fatal disease for humans. Mechanisms related to the dysregulation of the inflammatory response may be involved in both the pathogenesis and prognosis of VL. Triggering Receptor Expressed on Myeloid Cells-1 (TREM-1) is a receptor constitutively expressed on neutrophils and monocyte subsets. The protein serves to regulate and amplify inflammatory responses. This study aimed to evaluate the expression profile of TREM-1 on the surface of neutrophils from patients with VL at varying time points during leishmanicidal treatment. For this purpose, neutrophils were isolated from the peripheral blood of patients with VL at different stages of treatment, which include 0, 7, and 30 days after treatment. Surface TREM-1 expression was assessed by immunophenotyping neutrophil populations. In addition, the association of TREM-1 expression on the surface of neutrophils with clinical and laboratory parameters and serum levels of inflammatory mediators was also evaluated. Results demonstrate a lower surface expression of TREM-1 in VL patients in the absence of treatment. However, increased levels of TREM-1 expression were observed 7 and 30 days after the start of treatment, with levels similar to those of healthy controls. TREM-1 expression was directly correlated with lymphocyte and erythrocyte count and indirectly correlated with spleen and liver size. Furthermore, elevated levels of TREM-1 expression were also correlated with lower serum levels of interleukin (IL)-22. Taken together, these results suggest that infection by Leishmania infantum leads to depressed TREM-1 expression on the neutrophil surface and may contribute to the inflammatory imbalance that characterizes active VL disease.

Polymorphism in the catalytic subunit of the PI3Kγ gene is associated with Trypanosoma cruzi-induced chronic chagasic cardiomyopathy.

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi. During the chronic phase of disease, while most infected people do not present symptoms, characterizing the asymptomatic form, some patients develop the cardiac form or chronic chagasic cardiomyopathy, which is considered the most severe manifestation of this disease. Considering that the activation of the PI3Kγ signaling pathway is essential for an efficient immune response against T. cruzi infection, we evaluated the PIK3CG C > T (rs1129293) polymorphism in exon 3 of this gene, which encodes the catalytic subunit of PI3Kγ. The PIK3CG CT and TT genotypes were found to be associated with an increased risk of developing the cardiac form of the disease rather than the asymptomatic or digestive forms. In conclusion, the presence of the T allele at single or double doses may differentiate the cardiac from other clinical manifestations of Chagas disease. This finding should help in further studies to evaluate the mechanisms underlying the differential association of PIK3CG in Chagas disease.

TLR4 abrogates the Th1 immune response through IRF1 and IFN-ß to prevent immunopathology during L. infantum infection.

A striking feature of human visceral leishmaniasis (VL) is chronic inflammation in the spleen and liver, and VL patients present increased production levels of multiple inflammatory mediators, which contribute to tissue damage and disease severity. Here, we combined an experimental model with the transcriptional profile of human VL to demonstrate that the TLR4-IFN-ß pathway regulates the chronic inflammatory process and is associated with the asymptomatic form of the disease. Tlr4-deficient mice harbored fewer parasites in their spleen and liver than wild-type mice. TLR4 deficiency enhanced the Th1 immune response against the parasite, which was correlated with an increased activation of dendritic cells (DCs). Gene expression analyses demonstrated that IRF1 and IFN-ß were expressed downstream of TLR4 after infection. Accordingly, IRF1- and IFNAR-deficient mice harbored fewer parasites in the target organs than wild-type mice due to having an increased Th1 immune response. However, the absence of TLR4 or IFNAR increased the serum transaminase levels in infected mice, indicating the presence of liver damage in these animals. In addition, IFN-ß limits IFN-γ production by acting directly on Th1 cells. Using RNA sequencing analysis of human samples, we demonstrated that the transcriptional signature for the TLR4 and type I IFN (IFN-I) pathways was positively modulated in asymptomatic subjects compared with VL patients and thus provide direct evidence demonstrating that the TLR4-IFN-I pathway is related to the nondevelopment of the disease. In conclusion, our results demonstrate that the TLR4-IRF1 pathway culminates in IFN-ß production as a mechanism for dampening the chronic inflammatory process and preventing immunopathology development.

Meta-Analysis of HTLV-1-Infected Patients Identifies CD40LG and GBP2 as Markers of ATLL and HAM/TSP Clinical Status: Two Genes Beat as One.

Human T-lymphotropic virus 1 (HTLV-1) was the first recognized human retrovirus. Infection can lead to two main symptomatologies: adult T-cell lymphoma/leukemia (ATLL) and HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). Each manifestation is associated with distinct characteristics, as ATLL presents as a leukemia-like disease, while HAM/TSP presents as severe inflammation in the central nervous system, leading to paraparesis. Previous studies have identified molecules associated with disease development, e.g., the downregulation of Foxp3 in Treg cells was associated with increased risk of HAM/TSP. In addition, elevated levels of CXCL10, CXCL9, and Neopterin in cerebrospinal fluid also present increased risk. However, these molecules were only associated with specific patient groups or viral strains. Furthermore, the majority of studies did not jointly compare all clinical manifestations, and robust analysis entails the inclusion of both ATLL and HAM/TSP. The low numbers of samples also pose difficulties in conducting gene expression analysis to identify specific molecular relationships. To address these limitations and increase the power of manifestation-specific gene associations, meta-analysis was performed using publicly available gene expression data. The application of supervised learning techniques identified alterations in two genes observed to act in tandem as potential biomarkers: GBP2 was associated with HAM/TSP, and CD40LG with ATLL. Together, both molecules demonstrated high sample-classification accuracy (AUC values: 0.88 and 1.0, respectively). Next, other genes with expression correlated to these genes were identified, and we attempted to relate the enriched pathways identified with the characteristic of each clinical manifestation. The present findings contribute to knowledge surrounding viral progression and suggest a potentially powerful new tool for the molecular classification of HTLV-associated diseases.

The impact of cancer campaigns in Brazil: a Google Trends analysis.

It is estimated that more than 600,000 new cases of cancer will be reported in Brazil during the 2018-2019 biennium, especially with regard to prostate, breast, lung and colorectal cancers. Due to the high prevalence, incidence and mortality rates of these diseases, cancer campaigns such as 'Pink October' and 'Blue November' were strongly promoted in the past decade throughout the country to raise awareness of breast and prostate cancer, respectively. Nevertheless, whether the implementation of these campaigns has been proven efficient is still unknown. In the present study, we analysed the effectiveness of these campaigns on eliciting population online interest for cancer information. The Google Trends database was evaluated for the relative Internet search popularity for the terms 'breast cancer' and 'prostate cancer' from 2014 to 2019. Aside from some regional differences, we found that there was a high demand for 'breast cancer' and, to a lesser extent, 'prostate cancer' searches in a seasonal fashion (during October and November, respectively). Despite the worldwide high incidence of lung and colorectal cancers, searches including these keywords did not show increases in any specific period of the year, demonstrating the efficiency of the 'Pink October' and 'Blue November' campaigns in engaging the interest of the Brazilian population on the subject. These results allow us to infer that campaigns are effective in mobilising the attention of the Brazilian population with regard to breast and prostate cancers, but the practical aspects in reducing incidence and mortality should still be discussed.

Oxidized Low-Density Lipoprotein (Ox-LDL) and Triggering Receptor-Expressed Myeloid Cell (TREM-1) Levels Are Associated with Cardiometabolic Risk in Nonobese, Clinically Healthy, and Young Adults.

Oxidative and inflammatory substances play an important role in the genesis of processes related to cardiometabolic risk. High levels of oxidized low-density lipoprotein (Ox-LDL) and of triggering receptor-expressed myeloid cells (TREM-1) are associated with cardiovascular and inflammatory diseases. In this study, we evaluate the association of the plasma concentrations of Ox-LDL and serum levels of circulating TREM-1 (sTREM-1) with the components of cardiometabolic risk (CMR) and other associated risk parameters. Although the individuals in this study were young, nonobese, and did not have signs, symptoms, and diagnosis of diseases, they already presented components of CMR. Ox-LDL lipid fraction correlated positively with CMR-related markers: body mass index (BMI), waist circumference (WC), body fat percentage, total cholesterol, LDL-c, VLDL-c, triglycerides, atherogenic cholesterol, and atherogenic index. Among these parameters, atherogenic cholesterol had a greater predictive effect for Ox-LDL alterations. Individuals with higher serum concentrations of sTREM-1 presented higher values for BMI, WC, triglycerides, VLDL-c, and atherogenic cholesterol. WC showed an effect on the association between the sTREM-1's inflammatory response and the components of CMR. The association of oxidative and inflammatory markers with anthropometric parameters and atherogenic cholesterol in nonobese, clinically healthy, and young individuals suggests the importance of early evaluation of these markers in order to prevent future cardiac events.

Follow up of a robust meta-signature to identify Zika virus infection in Aedes aegypti: another brick in the wall.

The mosquito Aedes aegypti is the main vector of several arthropod-borne diseases that have global impacts. In a previous meta-analysis, our group identified a vector gene set containing 110 genes strongly associated with infections of dengue, West Nile and yellow fever viruses. Of these 110 genes, four genes allowed a highly accurate classification of infected status. More recently, a new study of Ae. aegypti infected with Zika virus (ZIKV) was published, providing new data to investigate whether this "infection" gene set is also altered during a ZIKV infection. Our hypothesis is that the infection-associated signature may also serve as a proxy to classify the ZIKV infection in the vector. Raw data associated with the NCBI/BioProject were downloaded and re-analysed. A total of 18 paired-end replicates corresponding to three ZIKV-infected samples and three controls were included in this study. The nMDS technique with a logistic regression was used to obtain the probabilities of belonging to a given class. Thus, to compare both gene sets, we used the area under the curve and performed a comparison using the bootstrap method. Our meta-signature was able to separate the infected mosquitoes from the controls with good predictive power to classify the Zika-infected mosquitoes.

Follow up of a robust meta-signature to identify Zika virus infection in Aedes aegypti: another brick in the wall

The mosquito Aedes aegypti is the main vector of several arthropod-borne diseases that have global impacts. In a previous meta-analysis, our group identified a vector gene set containing 110 genes strongly associated with infections of dengue, West Nile and yellow fever viruses. Of these 110 genes, four genes allowed a highly accurate classification of infected status. More recently, a new study of Ae. aegypti infected with Zika virus (ZIKV) was published, providing new data to investigate whether this "infection" gene set is also altered during a ZIKV infection. Our hypothesis is that the infection-associated signature may also serve as a proxy to classify the ZIKV infection in the vector. Raw data associated with the NCBI/BioProject were downloaded and re-analysed. A total of 18 paired-end replicates corresponding to three ZIKV-infected samples and three controls were included in this study. The nMDS technique with a logistic regression was used to obtain the probabilities of belonging to a given class. Thus, to compare both gene sets, we used the area under the curve and performed a comparison using the bootstrap method. Our meta-signature was able to separate the infected mosquitoes from the controls with good predictive power to classify the Zika-infected mosquitoes.

Meta-Analysis of Aedes aegypti Expression Datasets: Comparing Virus Infection and Blood-Fed Transcriptomes to Identify Markers of Virus Presence.

The mosquito Aedes aegypti (L.) is vector of several arboviruses including dengue, yellow fever, chikungunya, and more recently zika. Previous transcriptomic studies have been performed to elucidate altered pathways in response to viral infection. However, the intrinsic coupling between alimentation and infection were unappreciated in these studies. Feeding is required for the initial mosquito contact with the virus and these events are highly dependent. Addressing this relationship, we reinterrogated datasets of virus-infected mosquitoes with two different diet schemes (fed and unfed mosquitoes), evaluating the metabolic cross-talk during both processes. We constructed coexpression networks with the differentially expressed genes of these comparison: virus-infected versus blood-fed mosquitoes and virus-infected versus unfed mosquitoes. Our analysis identified one module with 110 genes that correlated with infection status (representing ~0.7% of the A. aegypti genome). Furthermore, we performed a machine-learning approach and summarized the infection status using only four genes (AAEL012128, AAEL014210, AAEL002477, and AAEL005350). While three of the four genes were annotated as hypothetical proteins, AAEL012128 gene is a membrane amino acid transporter correlated with viral envelope binding. This gene alone is able to discriminate all infected samples and thus should have a key role to discriminate viral infection in the A. aegypti mosquito. Moreover, validation using external datasets found this gene as differentially expressed in four transcriptomic experiments. Therefore, these genes may serve as a proxy of viral infection in the mosquito and the others 106 identified genes provides a framework to future studies.

Hairless mice as an experimental model of infection with Leishmania (Leishmania) amazonensis.

HRS/J Hairless mice have been investigated as an experimental model in cutaneous leishmaniasis induced by Leishmania (Leishmania) amazonensis. The animals were inoculated with 10(6) promastigotes into the right hind footpad and the course of infection was followed up for 30, 60 and 90 days. BALB/c mice were infected and used as control. Hairless mice were susceptible to L. (L.) amazonensis infection and a progressive increase in number of parasites and footpad thickness was detected over time. Signals of dissemination and visceralization were confirmed by the presence of parasite in the draining lymph node of lesion and spleen, at different times post infection. IL-10 gene expression evaluated by RT-PCR was significantly higher in Hairless mice at 60 days post infection, corroborating the pattern of susceptibility. These results point this inbred strain as a promising susceptible model for the study of experimental infection induced by L. (L.) amazonensis. This model would allow the use of other infection sites that minimize secondary interference and best monitoring the skin lesion, as in the case of in vivo assays of potential drugs for LT.

Evaluation of the implementation of a quality system in a basic research laboratory: viability and impacts / Avaliação da implementação de um sistema de qualidade em um laboratório de pesquisa básica: viabilidade e impactos

OBJECTIVE: To evaluate the process of implementing a quality management system in a basic research laboratory of a public institution, particularly considering the feasibility and impacts of this improvement. METHODS: This was a prospective and qualitative study. We employed the norm "NIT DICLA 035 - Princípios das Boas Práticas de Laboratório (BPL)" and auxiliary documents of Organisation for Economic Co-operation and Development to complement the planning and implementation of a Quality System, in a basic research laboratory. In parallel, we used the PDCA tool to define the goals of each phase of the implementation process. RESULTS: This study enabled the laboratory to comply with the NIT DICLA 035 norm and to implement this norm during execution of a research study. Accordingly, documents were prepared and routines were established such as the registration of non-conformities, traceability of research data and equipment calibration. CONCLUSION: The implementation of a quality system, the setting of a laboratory focused on basic research is feasible once certain structural changes are made. Importantly, impacts were noticed during the process, which could be related to several improvements in the laboratory routine.

OBJETIVO: Avaliar o processo de implantação de um sistema de qualidade em um laboratório de pesquisa básica, avaliando a viabilidade e os impactos dessa melhoria. MÉTODOS: Tratou-se de um estudo qualitativo prospectivo. Utilizou-se a norma NIT DICLA 035 - Princípios das Boas Práticas de Laboratório (BPL) e documentos da Organisation for Economic Co-operation and Development para complementar o planejamento e a implantação de um Sistema de Gestão da Qualidade, em um laboratório de pesquisa básica. Em paralelo, utilizou-se a ferramenta PDCA para definir os objetivos de cada etapa de implantação do sistema de qualidade. RESULTADOS: Este trabalho possibilitou ao laboratório atender requisitos solicitados pela norma NT DICLA 035 e implementá-los durante a execução de um projeto, dentre eles a elaboração de documentos, bem como estabelecer rotinas importantes para o andamento do mesmo, como a identificação de não conformidades, rastreabilidade de dados e calibração de equipamentos. CONCLUSÃO: A implantação do Sistema da Qualidade BPL, nesse cenário, é viável, gerando impactos positivos na rotina do laboratório.

Evaluation of the implementation of a quality system in a basic research laboratory: viability and impacts.

OBJECTIVE: To evaluate the process of implementing a quality management system in a basic research laboratory of a public institution, particularly considering the feasibility and impacts of this improvement. METHODS: This was a prospective and qualitative study. We employed the norm "NIT DICLA 035--Princípios das Boas Práticas de Laboratório (BPL)" and auxiliary documents of Organisation for Economic Co-operation and Development to complement the planning and implementation of a Quality System, in a basic research laboratory. In parallel, we used the PDCA tool to define the goals of each phase of the implementation process. RESULTS: This study enabled the laboratory to comply with the NIT DICLA 035 norm and to implement this norm during execution of a research study. Accordingly, documents were prepared and routines were established such as the registration of non-conformities, traceability of research data and equipment calibration. CONCLUSION: The implementation of a quality system, the setting of a laboratory focused on basic research is feasible once certain structural changes are made. Importantly, impacts were noticed during the process, which could be related to several improvements in the laboratory routine.

Aplicação de técnica sorológicas e moleculares na detecção de leishmania em doadores de sangue na cidade de Salvador, Bahia / Application of serological and molecular technique in the detection of Leishmania in blood donors in Salvador, Bahia

A leishmaniose é causada por protozoários do gênero Leishmania e constitui um problema grave de saúde pública na Bahia. A transmissão do protozoário pela transfusão de sangue já foi relatada e existe a possibilidade dos hemoderivados serem um potencial risco para a manutenção da doença. O presente trabalho teve como objetivo avaliar positividade sorológica contra Leishmania e a presença deste parasita no sangue periférico de doadores, na cidade de Salvador, BA. Para estipulando a soroprevalência de leishmaniose em doadores de sangue, foram coletadas amostras de sangue periférico de 700 indivíduos, no Hemocentro da Bahia (HEMOBA/SESAB), de janeiro a setembro de 2010. As amostras foram processadas para a obtenção de plasma e de DNA. A sorologia anti-Leishmania foi feita por ELISA, empregando antígeno solúvel de Leishmania chagasi (SLA). A presença de parasitas foi determinada por PCR qualitativo e por PCR quantitativo (qPCR). A população amostral foi composta por 74.5% de indivíduos masculinos, com média de idade de 34 anos. A partir de uma curva ROC, empregando soros de pacientes com leishmaniose visceral e soros de pacientes residentes em área não endêmica, o ponto de corte para o teste sorológico foi estabelecido em 0,0167 (DO em 405nm). A sorologia anti-Leishmania foi positiva em 5.4% (38/700) das amostras. Destes indivíduos, 73% (28/38) apresentaram amplificação para uma região repetitiva do genoma de Leishmania, empregando-se o PCR qualitativo. Empregando o qPCR, foi possível determinar a presença de parasitas em 0.4% (3/700) amostras e, nestas, a quantificação foi inferior a 10 parasitas. Nossos resultados mostram a prevalência de sorologia anti-Leishmania é de 5.4%, em doadores do HEMOBA/SESAB, similar ao encontrado em outras área onde ocorre a leishmania.