HIHISIV: a database of gene expression in HIV and SIV host immune response.

In the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the interaction with different viruses and their influence on disease progression. The simian immunodeficiency virus (SIV) infecting nonhuman primates (NHP) is widely used as a model for the study of the human immunodeficiency virus (HIV) both because they are evolutionarily linked and because they share physiological and anatomical similarities that are largely explored to understand the disease progression. The HIHISIV database was developed to support researchers to integrate and evaluate the large number of transcriptional data associated with the presence/absence of the pathogen (SIV or HIV) and the host response (NHP and human). The datasets are composed of microarray and RNA-Seq gene expression data that were selected, curated, analyzed, enriched, and stored in a relational database. Six query templates comprise the main data analysis functions and the resulting information can be downloaded. The HIHISIV database, available at  https://hihisiv.github.io , provides accurate resources for browsing and visualizing results and for more robust analyses of pre-existing data in transcriptome repositories.

Interleukin-27 Promotes Divergent Effects on HIV-1 Infection in Peripheral Blood Mononuclear Cells through BST-2/Tetherin.

Interleukin-27 (IL-27) is able to inhibit HIV-1 replication in peripheral blood mononuclear cells (PBMCs), macrophages, and dendritic cells. Here, we identify that IL-27 can produce opposing effects on HIV-1 replication in PBMCs and that the HIV-1 restriction factor BST-2/Tetherin is involved in both inhibitory and enhancing effects on HIV-1 infection induced by IL-27. IL-27 inhibited HIV-1 replication when added to cells 2 h after infection, promoting the prototypical BST-2/Tetherin-induced virion accumulation at the cell membrane of HIV-1-infected PBMCs. BST-2/Tetherin gene expression was significantly upregulated in the IL-27-treated PBMCs, with a simultaneous increase in the number of BST-2/Tetherin+ cells. The silencing of BST-2/Tetherin diminished the anti-HIV-1 effect of IL-27. In contrast, IL-27 increased HIV-1 production when added to infected cells 4 days after infection. This enhancing effect was prevented by BST-2/Tetherin gene knockdown, which also permitted IL-27 to function again as an HIV-1 inhibitory factor. These contrasting roles of IL-27 were associated with the dynamic of viral production, since the IL-27-mediated enhancement of virus replication was prevented by antiretroviral treatment of infected cells, as well as by keeping cells under agitation to avoid cell-to-cell contact. Likewise, inhibition of CD11a, an integrin associated with HIV-1 cell-to-cell transmission, abrogated the IL-27 enhancement of HIV-1 production. Our findings illustrate the complexity of the HIV-1-host interactions and may impact the potential therapeutic use of IL-27 and other soluble mediators that induce BST-2/Tetherin expression for HIV-1 infection. IMPORTANCE Here, we describe new findings related to the ability of the cytokine IL-27 to regulate the growth of HIV-1 in CD4+ T lymphocytes. IL-27 has long been considered a potent inhibitor of HIV-1 replication, a notion based on several reports showing that this cytokine controls HIV-1 infection in peripheral blood mononuclear cells (PBMCs), monocyte-derived macrophages, and dendritic cells. However, our present results are contrary to the current knowledge that IL-27 acts only as a powerful downregulator of HIV-1 replication. We observed that IL-27 can either prevent or enhance viral growth in PBMCs, an outcome dependent on when this cytokine is added to the infected cells. We detected that the increase of HIV-1 dissemination is due to enhanced cell-to-cell transmission with the involvement of the interferon-induced HIV-1 restriction factor BST-2/Tetherin and CD11a (LFA-1), an integrin that participates in formation of virological synapse.

Association between swallowing dynamics, tongue pressure and pulmonary function in patients with idiopathic pulmonary fibrosis.

BACKGROUND: Swallowing is a complex process that requires the coordination of muscles in the mouth, pharynx, larynx, and esophagus. Dysphagia occurs when a person has difficulty swallowing. In the case of subjects with respiratory diseases, the presence of oropharyngeal dysphagia potentially increases lung disease exacerbations, which can lead to a rapid decline in lung function. This study aimed to analyze the swallowing of patients with idiopathic pulmonary fibrosis (IPF). METHODS: Patients with IPF were evaluated using the Eating Assessment Tool (EAT-10), tongue pressure, the Timed Water Swallow Test (TWST), and the Test of Mastication and Swallowing Solids (TOMASS). The findings were related to dyspnea severity assessed by the modified Medical Research Counsil (mMRC) score; the nutritional status screened with Mini Nutritional Assessment (MNA) tool; and pulmonary function tests, specifically spirometry and measurement of the diffusing capacity for carbon monoxide (DLCO), the maximal inspiratory pressure (PImax), and the maximal expiratory pressure (PEmax). RESULTS: The sample consisted of 34 individuals with IPF. Those who exhibited swallowing modifications scored lower on the MNA than those who did not (9.6 ± 0.76 vs. 11.64 ± 0.41 points; mean difference 1.98 ± 0.81 points; p = 0.02). They also showed poorer lung function when considering the predicted force vital capacity (FVC; 81.5% ± 4.61% vs. 61.87% ± 8.48%; mean difference 19.63% ± 9.02%; p = 0.03). The speed of liquid swallowing was altered in 31of 34 of the evaluated subjects (91.1%). The number of liquid swallows correlated significantly with the forced expiratory volume in 1 s (FEV1)/FVC ratio (r = 0.3; p = 0.02). Solid eating and swallowing assessed with the TOMASS score correlated with lung function. The number of chewing cycles correlated negatively with PImax% predicted (r = -0.4; p = 0.0008) and PEmax% predicted (r = -0.3; p = 0.02). FVC% predicted correlated with increased solid swallowing time (r = -0.3; p = 0.02; power = 0.6). Swallowing solids was also impacted by dyspnea. CONCLUSION: Patients with mild-to-moderate IPF can present feeding adaptations, which can be related to the nutritional status, lung function, and the severity of dyspnea.

Sulforaphane Supplementation Did Not Modulate NRF2 and NF-kB mRNA Expressions in Hemodialysis Patients.

BACKGROUND: Patients with chronic kidney disease (CKD) have reduced expression of erythroid nuclear factor-related factor 2 (NRF2) and increased nuclear factor κB (NF-κB). "Food as medicine" has been proposed as an adjuvant therapeutic alternative in modulating these factors. No studies have investigated the effects of sulforaphane (SFN) in cruciferous vegetables on the expression of these genes in patients with CKD. OBJECTIVE: The study aimed to evaluate the effects of SFN on the expression of NRF2 and NF-κB in patients on hemodialysis (HD). DESIGN AND METHODS: A randomized, double-blind, crossover study was performed on 30 patients on regular HD. Fourteen patients were randomly allocated to the intervention group (1 sachet/day of 2.5 g containing 1% SFN extract with 0.5% myrosinase) and 16 patients to the placebo group (1 sachet/day of 2.5 g containing corn starch colored with chlorophyll) for 2 months. After a washout period of 2 months, the groups were switched. NRF2 and NF-κB mRNA expression was evaluated by real-time quantitative polymerase chain reaction, and tumor necrosis factor alpha and interleukin-6 levels were quantified by enzyme-linked immunosorbent assay. Malondialdehyde was evaluated as a marker of lipid peroxidation. RESULTS: Twenty-five patients (17 women, 55 [interquartile range = 19] years and 55 [interquartile range = 74] months on HD) completed the study. There was no significant difference concerning the expression of mRNA NRF2 (P = .915) and mRNA NF-κB (P = .806) after supplementation with SFN. There was no difference in pro-inflammatory and oxidative stress biomarkers. CONCLUSION: 150 µmol of SFN for 2 months had no antioxidant and anti-inflammatory effect in patients with CKD undergoing HD.

Effects of Polydextrose Supplementation on Intestinal Function in Hemodialysis Patients: A Double-Blind, Randomized, Placebo-Controlled Trial.

OBJECTIVES: Intestinal constipation is a frequent complication in hemodialysis (HD) patients. Polydextrose (PDX), a nondigestible oligosaccharide, has been reported as a fermentable fiber with potential benefits. This study aimed to investigate the possible influence of PDX supplementation on intestinal function in HD patients. METHODS: This randomized, double-blind, placebo-controlled trial included 28 patients who received daily oral supplementation with 12 g of PDX or placebo (corn starch) for 2 months. ROME IV criteria were used to define constipation and questionnaires were applied to patient assessment of constipation symptoms (PAC-SYM) and their impact on the patient assessment of constipation quality of life. The Bristol scale was used to assess stool consistency. Commercial Enzyme-Linked Immuno Sorbent Assay kits were used to evaluate the interleukin-6 and tumor necrosis factor-α plasma levels. RESULTS: 25 patients completed the study; 16 in the PDX group [7 females, 48.5 years (IQR = 15.5)] and 9 in the control group [3 females, 44.0 years (IQR = 6.0)]. According to ROME IV criteria, 55% of patients were diagnosed with constipation. PAC-SYM faecal symptoms domain was reduced after 2 months of PDX supplementation (P = .004). We also observed a significant reduction in the PAC-QoL-concerns domain (P = .02). The average values for PAC-SYM and patient assessment of constipation quality of lifewere reduced significantly after intervention with PDX. There were no significant changes after the intervention period concerning biochemical variables, food intake, and inflammation markers. No adverse effects were observed during the supplementation period. CONCLUSIONS: The results of the present study suggest that short-term PDX supplementation may have favourable results on intestinal function and the quality of life of chronic kidney disease patients in HD.

Influence of killer immunoglobulin-like receptors genes on the recurrence rate of ocular toxoplasmosis in Brazil.

BACKGROUND: Recurrence is a hallmark of ocular toxoplasmosis (OT), and conditions that influence its occurrence remain a challenge. Natural killer cells (NK) are effectors cells whose primary is cytotoxic function against many parasites, including Toxoplasma gondii. Among the NK cell receptors, immunoglobulin-like receptors (KIR) deserve attention due to their high polymorphism. OBJECTIVES: This study aimed to analyse the influence of KIR gene polymorphism in the course of OT infection and its association with recurrences after an active episode. METHODS: Ninety-six patients from the Ophthalmologic Clinic of the National Institute of Infectology Evandro Chagas were followed for up to five years. After DNA extraction, genotyping of the patients was performed by polymerase chain reaction sequence-specific oligonucleotide (PCR-SSO) utilising Luminex equipment for reading. During follow-up, 60.4% had a recurrence. FINDINGS: We identified 25 KIR genotypes and found a higher frequency of genotype 1 (31.7%) with worldwide distribution. We note that the KIR2DL2 inhibitor gene and the gene activator KIR2DS2 were more frequent in patients without recurrence. Additionally, we observed that individuals who carry these genes progressed recurrence episodes slowly compared to individuals who do not carry these genes. MAIN CONCLUSIONS: The KIR2DL2 and KIR2DS2 are associated as possible protection markers against ocular toxoplasmosis recurrence (OTR).

Polymorphisms at CYP enzymes, NR1I2 and NR1I3 in association with virologic response to antiretroviral therapy in Brazilian HIV-positive individuals.

Virologic failure of antiretroviral therapy (ART) may be explained by single nucleotide polymorphisms (SNPs) in drug absorption and metabolism genes. Here, we characterized the associations between polymorphisms in cytochrome P450 enzymes' genes CYP2B6 and CYP3A4/A5, nuclear receptor genes NR1I2/3, and initial ART efficacy among 203 HIV-positive individuals from Rio de Janeiro. Association between SNPs and virologic control was evaluated after 6 and 12 months of follow-up using Cox regression models. The SNP rs2307424 (NR1I3) was associated with increased virologic response after 12 months of treatment, while rs1523127 (NR1I2), rs3003596, and rs2502815 (NR1I3) were associated with decreased response. Increased virologic response after 12 months (adjHR = 1.54; p = 0.02) was also observed among carriers of the NR1I3 haplotype rs2502815G-rs3003596A-rs2307424A versus the reference haplotype G-A-G. Our results suggest that NR1I2 and NR1I3 variants are associated with virologic responses to ART among Brazilians.

Naturally acquired antibody response to a Plasmodium falciparum chimeric vaccine candidate GMZ2.6c and its components (MSP-3, GLURP, and Pfs48/45) in individuals living in Brazilian malaria-endemic areas.

BACKGROUND: The GMZ2.6c malaria vaccine candidate is a multi-stage Plasmodium falciparum chimeric protein which contains a fragment of the sexual-stage Pfs48/45-6C protein genetically fused to GMZ2, a fusion protein of GLURP and MSP-3, that has been shown to be well tolerated, safe and immunogenic in clinical trials performed in a malaria-endemic area of Africa. However, there is no data available on the antigenicity or immunogenicity of GMZ2.6c in humans. Considering that circulating parasites can be genetically distinct in different malaria-endemic areas and that host genetic factors can influence the immune response to vaccine antigens, it is important to verify the antigenicity, immunogenicity and the possibility of associated protection in individuals living in malaria-endemic areas with different epidemiological scenarios. Herein, the profile of antibody response against GMZ2.6c and its components (MSP-3, GLURP and Pfs48/45) in residents of the Brazilian Amazon naturally exposed to malaria, in areas with different levels of transmission, was evaluated. METHODS: This study was performed using serum samples from 352 individuals from Cruzeiro do Sul and Mâncio Lima, in the state of Acre, and Guajará, in the state of Amazonas. Specific IgG, IgM, IgA and IgE antibodies and IgG subclasses were detected by Enzyme-Linked Immunosorbent Assay. RESULTS: The results showed that GMZ2.6c protein was widely recognized by naturally acquired antibodies from individuals of the Brazilian endemic areas with different levels of transmission. The higher prevalence of individuals with antibodies against GMZ2.6c when compared to its individual components may suggest an additive effect of GLURP, MSP-3, and Pfs48/45 when inserted in a same construct. Furthermore, naturally malaria-exposed individuals predominantly had IgG1 and IgG3 cytophilic anti-GMZ2.6c antibodies, an important fact considering that the acquisition of anti-malaria protective immunity results from a delicate balance between cytophilic/non-cytophilic antibodies. Interestingly, anti-GMZ2.6c antibodies seem to increase with exposure to malaria infection and may contribute to parasite immunity. CONCLUSIONS: The data showed that GMZ2.6c protein is widely recognized by naturally acquired antibodies from individuals living in malaria-endemic areas in Brazil and that these may contribute to parasite immunity. These data highlight the importance of GMZ2.6c as a candidate for an anti-malarial vaccine.

Homozygotes NAT2*5B slow acetylators are highly associated with hepatotoxicity induced by anti-tuberculosis drugs.

BACKGROUND: Distinct N-acetyltransferase 2 (NAT2) slow acetylators genotypes have been associated with a higher risk to develop anti-tuberculosis drug-induced hepatotoxicity (DIH). However, studies have not pointed the relevance of different acetylation phenotypes presented by homozygotes and compound heterozygotes slow acetylators on a clinical basis. OBJECTIVES: This study aimed to investigate the association between NAT2 genotypes and the risk of developing DIH in Brazilian patients undergoing tuberculosis treatment, focusing on the discrimination of homozygotes and compound heterozygotes slow acetylators. METHODS/FINDINGS: The frequency of NAT2 genotypes was analysed by DNA sequencing in 162 patients undergoing tuberculosis therapy. The mutation analyses revealed 15 variants, plus two new NAT2 mutations, that computational simulations predicted to cause structural perturbations in the protein. The multivariate statistical analysis revealed that carriers of NAT2*5/*5 slow acetylator genotype presented a higher risk of developing anti-tuberculosis DIH, on a clinical basis, when compared to the compound heterozygotes presenting NAT2*5 and any other slow acetylator haplotype [aOR 4.97, 95% confidence interval (CI) 1.47-16.82, p = 0.01]. CONCLUSION: These findings suggest that patients with TB diagnosis who present the NAT2*5B/*5B genotype should be properly identified and more carefully monitored until treatment outcome in order to prevent the occurrence of anti-tuberculosis DIH.

Can Resveratrol Supplementation Reduce Uremic Toxin Plasma Levels From the Gut Microbiota in Nondialyzed Patients With Chronic Kidney Disease?

OBJECTIVES: Uremic toxins such as indoxyl sulfate (IS), p-cresyl sulfate (pCS), and indole-3-acetic acid (IAA) produced by the gut microbiota are recognized as risk factors for many comorbidities, including cardiovascular diseases. Patients with chronic kidney disease (CKD) have an accumulation of these toxins, and nutritional strategies have been proposed to mitigate gut dysbiosis and, consequently, reduce these toxins. This study aimed to evaluate the effects of resveratrol supplementation on the plasma levels of IS, pCS, and IAA in nondialyzed patients with CKD. METHODS: In this placebo-controlled crossover study, twenty nondialyzed patients were randomly divided into two groups: they received either one capsule/day containing 500 mg of trans-resveratrol (63 ± 7.5 years, glomerular filtration rate [GFR]: 34 ± 14 mL/min, body mass index: 26.8 ± 5.6 kg/m2) or a placebo containing 500 mg wheat flour (62 ± 8.4 years, GFR: 34 ± 13 mL/min, body mass index: 28.6 ± 4.4 kg/m2) during 4 weeks. After 8 weeks of washout (no supplementation), another 4 weeks of supplementation with crossover was initiated. IS, IAA, and pCS plasma levels were quantified by the reverse phase high-efficiency liquid chromatography method with fluorescent detection. The mRNA expression of nuclear factor erythroid 2-related factor 2 and nuclear factor kappa B in peripheral blood mononuclear cells was evaluated by polymerase chain reaction. C-reactive protein plasma levels were also evaluated. RESULTS: As expected, the uremic toxin levels were negatively correlated with the GFR, but no effect of trans-resveratrol supplementation was found on levels of IS, IAA, and pCS. There was a positive correlation between IS and nuclear factor erythroid 2-related factor 2 (r = 0.24, P = .03) and also between IS and C-reactive protein (r = 0.21, P = .05). CONCLUSION: Supplementation with trans-resveratrol did not reduce the plasma levels of IS, pCS, and IAA in nondialyzed patients with CKD. The interactions among uremic toxins and anti-inflammatory and proinflammatory pathways deserve more studies.

The cumulative effect of multiple dimensions of lifestyle on risky drinking during the Covid-19 pandemic.

Lifestyle impacts morbidity and mortality worldwide. Herein, we evaluated the association of a multidimensional lifestyle measure and its domains (diet/nutrition, substance use, physical activity, social, stress management, sleep, environmental exposure) with risky drinking. Also, we analyzed the cumulative effect of unhealthy domains in the likelihood of presenting risky drinking. To reach these objectives, data from a web survey conducted in Brazil and Spain was analyzed. The main outcome was risky drinking assessed by the AUDIT-C. Lifestyle was measured using the Short Multidimensional Inventory Lifestyle Evaluation (SMILE). Fixed logistic models were used to evaluate associations between lifestyle and risky drinking. Between April and May 2020, 22,785 individuals answered the survey. The prevalence of risky drinking was 45.6% in Brazil and 30.8% in Spain. The SMILE score was lower (unhealthier lifestyle) among at-risk drinkers. Worse scores on Diet, Substance use, Stress management and Environment were associated with an increased likelihood of risky drinking. The higher the number of unhealthy domains, the higher the likelihood of presenting risky drinking: adjusted odds ratio (aOR) for risky drinking was 1.15 (IC95% 0.98-1.35) and 23.42 (IC95% 3.08-178.02) for those presenting worse lifestyle in 1 and 5 domains, respectively. Finally, interactions suggest that improvement in lifestyle domains would have a larger effect in Spain than in Brazil. Our results suggest that future interventions aiming at reducing Risky drinking may benefit from strategies targeting multiple domains of lifestyle.

Natural variation of the cardiac transcriptome in humans.

We investigated the gene-expression variation among humans by analysing previously published mRNA-seq and ribosome footprint profiling of heart left-ventricles from healthy donors. We ranked the genes according to their coefficient of variation values and found that the top 5% most variable genes had special features compared to the rest of the genome, such as lower mRNA levels and shorter half-lives coupled to increased translation efficiency. We observed that these genes are mostly involved with immune response and have a pleiotropic effect on disease phenotypes, indicating that asymptomatic conditions contribute to the gene expression diversity of healthy individuals.

Increased expression of CDKN1A/p21 in HIV-1 controllers is correlated with upregulation of ZC3H12A/MCPIP1.

BACKGROUND: Some multifunctional cellular proteins, as the monocyte chemotactic protein-induced protein 1 (ZC3H12A/MCPIP1) and the cyclin-dependent kinase inhibitor CDKN1A/p21, are able to modulate the cellular susceptibility to the human immunodeficiency virus type 1 (HIV-1). Several studies showed that CDKN1A/p21 is expressed at high levels ex vivo in cells from individuals who naturally control HIV-1 replication (HIC) and a recent study supports a coordinate regulation of ZC3H12A/MCPIP1 and CDKN1A/p21 transcripts in a model of renal carcinoma cells. Here, we explored the potential associations between mRNA expression of ZC3H12A/MCPIP1 and CDKN1A/p21 in HIC sustaining undetectable (elite controllers-EC) or low (viremic controllers-VC) viral loads. RESULTS: We found a selective upregulation of ZC3H12A/MCPIP1 and CDKN1A/p21 mRNA levels in PBMC from HIC compared with both ART-suppressed and HIV-negative control groups (P≤ 0.02) and higher MCPIP1 and p21 proteins levels in HIC than in HIV-1 negative subjects. There was a moderate positive correlation (r ≥ 0.57; P ≤ 0.014) between expressions of both transcripts in HIC and in HIC combined with control groups. We found positive correlations between the mRNA level of CDKN1A/p21 with activated CD4+ T cells levels in HIC (r ≥ 0.53; P ≤ 0.017) and between the mRNA levels of both CDKN1A/p21 (r = 0.74; P = 0.005) and ZC3H12A/MCPIP1 (r = 0.58; P = 0.040) with plasmatic levels of sCD14 in EC. Reanalysis of published transcriptomic data confirmed the positive association between ZC3H12A/MCPIP1 and CDKN1A/p21 mRNA levels in CD4+ T cells and monocytes from disparate cohorts of HIC and other HIV-positive control groups. CONCLUSIONS: These data show for the first time the simultaneous upregulation of ZC3H12A/MCPIP1 and CDKN1A/p21 transcripts in the setting of natural suppression of HIV-1 replication in vivo and the positive correlation of the expression of these cellular factors in disparate cohorts of HIV-positive individuals. The existence of a common regulatory pathway connecting ZC3H12A/MCPIP1 and CDKN1A/p21 could have a synergistic effect on HIV-1 replication control and pharmacological manipulation of these multifunctional host factors may open novel therapeutic perspectives to prevent HIV-1 replication and disease progression.

Local Regulation of Adrenal Steroidogenesis: Subtle in vitro Effects of IL-1ß on the Human Cell Line NCI-H295R Steroid Production along with Changes in MicroRNA Profile and Orphan Nuclear Receptors NR4As.

INTRODUCTION: IL-1ß, a cytokine from the innate immune response, is well known for its proinflammatory effects and stimulating activity on the hypothalamus-pituitary-adrenal axis, leading to the pituitary synthesis of adrenocorticotropic hormone followed by cortisol (and dehydroepiandrosterone - DHEA) release by the adrenal gland. While IL-1ß modulates the adrenal steroidogenesis at the central level, it is unclear whether it also exerts an effect on the adrenal gland. METHOD: We studied the effect of IL-1ß on adrenal steroid production and steroidogenic enzyme RNA expression in the human cell line NCI-H295R. We also explored eventual changes in the microRNA (miRNA) profile from IL-1ß-treated NCI-H295R cells. RESULTS: Transcripts encoding IL-1ß receptors 1 and 2 were noticeable in the cell line, with cortisol and DHEA production showing a subtle increase after cytokine treatment. Transcripts from key enzymes in the steroidogenic pathway were analyzed, with no noticeable changes on them. The miRNA profile was modified by IL-1ß treatment to an extent which bears some relationship with the regulatory mechanisms underlying adrenal steroid production. Since orphan nuclear receptors NR4As have emerged as potential key factors for coordinating inflammatory and metabolic responses, cell expression studies were also carried out to show an NR4As transcript augmentation following IL-1ß treatment. DISCUSSION/CONCLUSIONS: The subtle increase in adrenal steroid production in response to IL-1ß stimulation without any modification in the transcription of the steroidogenic enzymes analyzed suggests an additional inflammatory/anti-inflammatory loop, wherein NR4As receptors may participate. Besides its physiological role, this process might be implied in pathological states accompanied by an unbalanced immune-endocrine relationship.

Clinical and genetic markers associated with tuberculosis, HIV-1 infection, and TB/HIV-immune reconstitution inflammatory syndrome outcomes.

BACKGROUND: Tuberculosis (TB) and AIDS are the leading causes of infectious disease death worldwide. In some TB-HIV co-infected individuals treated for both diseases simultaneously, a pathological inflammatory reaction termed immune reconstitution inflammatory syndrome (IRIS) may occur. The risk factors for IRIS are not fully defined. We investigated the association of HLA-B, HLA-C, and KIR genotypes with TB, HIV-1 infection, and IRIS onset. METHODS: Patients were divided into four groups: Group 1- TB+/HIV+ (n = 88; 11 of them with IRIS), Group 2- HIV+ (n = 24), Group 3- TB+ (n = 24) and Group 4- healthy volunteers (n = 26). Patients were followed up at INI/FIOCRUZ and HGNI (Rio de Janeiro/Brazil) from 2006 to 2016. The HLA-B and HLA-C loci were typed using SBT, NGS, and KIR genes by PCR-SSP. Unconditional logistic regression models were performed for Protection/risk estimation. RESULTS: Among the individuals with TB as the outcome, KIR2DS2 was associated with increased risk for TB onset (aOR = 2.39, P = 0.04), whereas HLA-B*08 and female gender were associated with protection against TB onset (aOR = 0.23, P = 0.03, and aOR = 0.33, P = 0.01, respectively). Not carrying KIR2DL3 (aOR = 0.18, P = 0.03) and carrying HLA-C*07 (aOR = 0.32, P = 0.04) were associated with protection against TB onset among HIV-infected patients. An increased risk for IRIS onset was associated with having a CD8 count ≤500 cells/mm3 (aOR = 18.23, P = 0.016); carrying the KIR2DS2 gene (aOR = 27.22, P = 0.032), the HLA-B*41 allele (aOR = 68.84, P = 0.033), the KIR2DS1 + HLA-C2 pair (aOR = 28.58, P = 0.024); and not carrying the KIR2DL3 + HLA-C1/C2 pair (aOR = 43.04, P = 0.034), and the KIR2DL1 + HLA-C1/C2 pair (aOR = 43.04, P = 0.034), CONCLUSIONS: These results suggest the participation of these genes in the immunopathogenic mechanisms related to the conditions studied. This is the first study demonstrating an association of HLA-B*41, KIR2DS2, and KIR + HLA-C pairs with IRIS onset among TB-HIV co-infected individuals.

Development of algorithms to estimate EQ-5D and derive health utilities from WHOQOL-HIV Bref: a mapping study.

PURPOSE: This study aimed to develop and evaluate different families of applicable models available for utility mapping between World Health Organization Quality of Life for HIV-abbreviated version (WHOQOL-HIV Bref) and EQ-5D-3L and to propose an optimised algorithm to estimate health utilities of people living with HIV. METHODS: Estimation dataset was collected between July 2014 and September 2016 in a cross-sectional study including 1526 people living with HIV/Aids (PLWH) under care at the Instituto Nacional de Infectologia Evandro Chagas-FIOCRUZ, in Brazil. Data of WHOQOL-HIV Bref and EQ-5D-3L questionnaires were collected. Fisher's exact tests were used for testing WHOQOL-HIV Bref response frequencies among groups of responses to each of the five EQ-5D-3L domains. Multiple correspondence analyses (MCA) were used to inspect the relationships between both instrument responses. Different families of applicable models available for utility mapping between WHOQOL-HIV Bref and EQ-5D-3L were adjusted for the prediction of disutility. RESULTS: Candidate models' performances using mean absolute error (MAE), mean squared error (MSE), and root mean squared error (RMSE) were similarly good, which was evidenced by the overlapping of its 95% confidence intervals of the mean tenfold cross-validation or estimated generalisation errors. However, the Hurdle Logistic-Log-Normal model was better on average according to generalisation errors both in the prediction of Brazilian utility values (MAE = 0.1037, MSE = 0.0178, and RMSE = 0.1332) and for those of the UK (MAE = 0.1476, MSE = 0.0443, and RMSE = 0.2099). CONCLUSIONS: Mapping EQ-5D-3L responses or deriving health utilities directly from WHOQOL-HIV Bref responses can be a valid alternative for settings with no preference-based health utility data.

Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis, two fungi species that share the same host.

BACKGROUND: Citrus are among the most important crops in the world. However, there are many diseases that affect Citrus caused by different pathogens. Citrus also hosts many symbiotic microorganisms in a relationship that may be advantageous for both organisms. The fungi Phyllosticta citricarpa, responsible for citrus black spot, and Phyllosticta capitalensis, an endophytic species, are examples of closely related species with different behavior in citrus. Both species are always biologically associated and are morphologically very similar, and comparing their genomes could help understanding the different lifestyles. In this study, a comparison was carried to identify genetic differences that could help us to understand the biology of P. citricarpa and P. capitalensis. RESULTS: Drafts genomes were assembled with sizes close to 33 Mb for both fungi, carrying 15,206 and 14,797 coding sequences for P. citricarpa and P. capitalensis, respectively. Even though the functional categories of these coding sequences is similar, enrichment analysis showed that the pathogenic species presents growth and development genes that may be necessary for the pathogenicity of P. citricarpa. On the other hand, family expansion analyses showed the plasticity of the genome of these species. Particular families are expanded in the genome of an ancestor of P. capitalensis and a recent expansion can also be detected among this species. Additionally, evolution could be driven by environmental cues in P. citricarpa. CONCLUSIONS: This work demonstrated genomic differences between P. citricarpa and P. capitalensis. Although the idea that these differences could explain the different lifestyles of these fungi, we were not able to confirm this hypothesis. Genome evolution seems to be of real importance among the Phyllosticta isolates and it is leading to different biological characteristics of these species.

Predominance of Th1 Immune Response in Pleural Effusion of Patients with Tuberculosis among Other Exudative Etiologies.

Pleural tuberculosis (PlTB), a common form of extrapulmonary TB, remains a challenge in the diagnosis among many causes of pleural effusion. We recently reported that the combinatorial analysis of interferon gamma (IFN-γ), IFN-γ-inducible protein 10 (IP-10), and adenosine deaminase (ADA) from the pleural microenvironment was useful to distinguish pleural effusion caused by TB (microbiologically confirmed or not) among other etiologies. In this cross-sectional cohort study, a set of inflammatory mediators was quantified in blood and pleural fluid (PF) from exudative pleural effusion cases, including PlTB (n = 27) and non-PlTB (nTB) (n = 25) patients. The levels of interleukin-2 (IL-2), IL-4, IL-6, IL-10, IL-17A, IFN-γ, tumor necrosis factor (TNF), IP-10, transforming growth factor ß1 (TGF-ß), and ADA were determined using cytometric bead assay, enzyme-linked immunosorbent assay (ELISA), or biochemical tests. IFN-γ, IP-10, TNF, TGF-ß, and ADA quantified in PF showed significantly higher concentrations in PlTB patients than in nTB patients. When blood and PF were compared, significantly higher concentrations of IL-6 and IL-10 in PF were identified in both groups. TGF-ß, solely, showed significantly increased levels in PF and blood from PlTB patients when both clinical specimens were compared to those from nTB patients. Principal-component analysis (PCA) revealed a T helper type 1 (Th1) pattern attributed mainly to higher levels of IP-10, IFN-γ, TGF-ß, and TNF in the pleural cavity, which was distinct between PlTB and nTB. In conclusion, our findings showed a predominantly cellular immune response in PF from TB cases, rather than other causes of exudative effusion commonly considered in the differential diagnosis of PlTB.

Superiority of Interferon Gamma Assay Over Tuberculin Skin Test for Latent Tuberculosis in Inflammatory Bowel Disease Patients in Brazil.

BACKGROUND AND AIMS: To compare tuberculin skin test (TST) and interferon gamma release assay (IGRA) in the screening of LTBI among patients with inflammatory bowel disease (IBD) in an endemic area for tuberculosis, to evaluate the need for repeating tests during anti-TNFα, therapy, and to check whether the results may be affected by immunosuppression. METHODS: A cross-sectional study of 110 IBD patients and 64 controls was conducted in Rio de Janeiro, Brazil. The TST was administered after the Quantiferon(®)-TB Gold In-tube test was performed. RESULTS: TST and IGRA agreement was poor regarding diagnosis (kappa: control = 0.318; UC = 0.202; and CD = - 0.093), anti-TNFα therapy (kappa: with anti-TNFα = 0.150; w/o anti-TNFα = - 0.123), and immunosuppressive therapy (IST) (kappa: with IS = - 0.088; w/o IS = 0.146). Indeterminate IGRA was reported in four CD patients on IST. Follow-up tests after anti-TNFα identified conversion in 8.62% using TST and 20.0% using IGRA. Considering IGRA as a criterion standard, TST showed low sensitivity (19.05%) and positive predictive value (PPV) (21.05%). LTBI detection remarkably improved when IGRA was added to TST (sensitivity of 80.95% and PPV of 53.13%). Results were particularly relevant among CD patients where rates started from zero to reach sensitivity and PPV of more than 60%. CONCLUSION: IGRA alone was more effective to detect LTBI than TST alone and had an overall remarkable added value as an add-on sequential test, particularly in CD patients. While cost-effectiveness of these strategies remains to be evaluated, IGRA appears to be justified in CD prior to and during anti-TNFα therapy, where tuberculosis is endemic.

Identification of Active Sarcoidosis Using Chitotriosidase and Angiotensin-Converting Enzyme.

PURPOSE: Activity/remission differentiation is a great challenge in the follow-up and treatment of sarcoidosis patients. Angiotensin-converting enzyme (ACE) and high sensitivity C-reactive protein (hs-CRP) were proposed as sarcoidosis biomarkers. More recently, chitotriosidase (CHITO) has been described as a better alternative. This study has the aim to evaluate the association of CHITO activity, ACE, hs-CRP or a combination of these biomarkers and to construct a clinical algorithm to differentiate between sarcoidosis activity/remission status. METHODS: Forty-six patients with either active sarcoidosis or sarcoidosis in remission and 21 healthy individuals were included. ACE, hs-CRP, and CHITO were evaluated in serum samples. Comparisons of the laboratory variable means among groups were performed by linear models. The cutoff points of the biomarkers for activity/remission differentiation were calculated using the Youden's index. Biomarker cutoff points and decision tree classifier (DTC) performance were estimated by their leave-one-out cross-validation (LOOCV) accuracy (Acc), sensitivity (Se), and specificity (Sp). RESULTS: A 55% mean Se and a 100% mean Sp were found for CHITO, while an 88% Se and a 47% Sp were found for ACE, and a 66% Se and a 68% Sp for hs-CRP cutoff points for activity/remission differentiation. The DTC algorithm with CHITO, hs-CRP, and ACE information had an LOOCV mean Acc of 82%, Se of 78%, and Sp of 89% for sarcoidosis activity/remission differentiation. CONCLUSIONS: The algorithm involving CHITO, hs-CRP, and ACE could be a suitable strategy for differentiation between sarcoidosis activity/remission status.