Unveiling the Significance of HLA and KIR Diversity in Underrepresented Populations.

Human leukocyte antigen (HLA) molecules and their relationships with natural killer (NK) cells, specifically through their interaction with killer-cell immunoglobulin-like receptors (KIRs), exhibit robust associations with the outcomes of diverse diseases. Moreover, genetic variations in HLA and KIR immune system genes offer limitless depths of complexity. In recent years, a surge of high-powered genome-wide association studies (GWASs) utilizing single nucleotide polymorphism (SNP) arrays has occurred, significantly advancing our understanding of disease pathogenesis. Additionally, advances in HLA reference panels have enabled higher resolution and more reliable imputation, allowing for finer-grained evaluation of the association between sequence variations and disease risk. However, it is essential to note that the majority of these GWASs have focused primarily on populations of Caucasian and Asian origins, neglecting underrepresented populations in Latin America and Africa. This omission not only leads to disparities in health care access but also restricts our knowledge of novel genetic variants involved in disease pathogenesis within these overlooked populations. Since the KIR and HLA haplotypes prevalent in each population are clearly modelled by the specific environment, the aim of this review is to encourage studies investigating HLA/KIR involvement in infection and autoimmune diseases, reproduction, and transplantation in underrepresented populations.

Acute internal medicine physicians' clinical intuition based on acute care telephone referral: A prospective study.

INTRODUCTION: In the Netherlands, most emergency department (ED) patients are referred by a general practitioner (GP) or a hospital specialist. Early risk stratification during telephone referral could allow the physician to assess the severity of the patients' illness in the prehospital setting. We aim to assess the discriminatory value of the acute internal medicine (AIM) physicians' clinical intuition based on telephone referral of ED patients to predict short-term adverse outcomes, and to investigate on which information their predictions are based. METHODS: In this prospective study, we included adult ED patients who were referred for internal medicine by a GP or a hospital specialist. Primary outcomes were hospital admission and triage category according to the Manchester Triage System (MTS). Secondary outcome was 31-day mortality. The discriminatory performance of the clinical intuition was assessed using an area under the receiver operating characteristics curve (AUC). To identify which information is important to predict adverse outcomes, we performed univariate regression analysis. Agreement between predicted and observed MTS triage category was assessed using intraclass and Spearman's correlation. RESULTS: We included 333 patients, of whom 172 (51.7%) were referred by a GP, 146 (43.8%) by a hospital specialist, and 12 (3.6%) by another health professional. The AIM physician's clinical intuition showed good discriminatory performance regarding hospital admission (AUC 0.72, 95% CI: 0.66-0.78) and 31-day mortality (AUC 0.73, 95% CI: 0.64-0.81). Univariate regression analysis showed that age ≥65 years and a sense of alarm were significant predictors. The predicted and observed triage category were similar in 45.2%, but in 92.5% the prediction did not deviate by more than one category. Intraclass and Spearman's correlation showed fair agreement between predicted and observed triage category (ICC 0.48, Spearman's 0.29). CONCLUSION: Clinical intuition based on relevant information during a telephone referral can be used to accurately predict short-term outcomes, allowing for early risk stratification in the prehospital setting and managing ED patient flow more effectively.

Cell-free DNA methylation profile potential in the diagnosis of lung squamous cell carcinoma.

Background: Aberrant methylation plays an essential role in early cancer development. In this study, we investigated methylation patterns in lung squamous cell carcinoma (LUSC) and matched non-tumor tissue and plasma samples to evaluate the potential of these patterns in the diagnosis of LUSC. Methods: The study group included 49 patients with stage I-III LUSC. We collected resected tumor tissue, paired peritumoral tissue, distant normal tissue, and corresponding plasma samples. A bespoke lung cancer bisulfite sequencing panel was used to profile the methylation level. Another 48 healthy volunteers provided control plasma samples. Results: Peritumoral and distant normal tissues presented similar methylation signatures, distinct from those in tumor tissue samples. A comparison of methylation profiles led to the identification of 871 tumor-specific differentially methylated blocks, including 847 hypermethylated and 24 hypomethylated blocks (adjusted P value <0.05). All top-ranked blocks were tumor-related. Tissue samples were analyzed for field cancerization to identify progressively aggravating aberrant methylations during tumor initiation and development. The analysis revealed that 221 blocks presented a stepwise increase in methylation levels, while seven blocks presented a stepwise decrease in methylation pattern as the sampling drew nearer to the tumor. The malignant contaminated ratio (MCR) confirmed the presence of distinct methylation patterns between tumor and peritumoral tissue samples. We then constructed a diagnostic panel using a combined diagnostic score of cell-free DNA (cfDNA) that showed high sensitivity and specificity. The healthy controls had a significantly lower combined diagnostic score (cd-score) than LUSC patients. Additionally, based on the methylation profiles, LUSC could be classified into two subgroups, C1 and C2. The methylation profile of the C2 group was not distinct from the healthy controls, which had a significantly lower cd-score than did the C1 group. Conclusions: LUSC-specific methylation patterns could potentially discriminate between peritumoral tissue, distant normal tumor tissue, and tumor tissues. This preliminary study also supported the potential utility of cfDNA methylation analysis in diagnosing LUSC.

A Coordinated School Health Program Effect on Cardiorespiratory Fitness of South Texas Preschool Children: A Cluster Randomized Trial.

BACKGROUND: The purpose of this study was to assess the effects of the Bienestar/NEEMA Coordinated School Health Program (BN CSHP) on cardiorespiratory fitness (CRF) of preschool children. METHODS: A cluster randomized trial was conducted of preschools in South Texas. Of 48 eligible schools, 28 were randomly assigned (14 intervention, 14 control). Family demographics and household health characteristics were collected from parents and CRF from children. Generalized linear mixed model (GLMM) was used to analyze the data. RESULTS: Family demographics, household health characteristics, and children's weight, obesity prevalence, and sedentary activity of the control group were similar to the intervention group at baseline. After adjusting for covariates, the number of laps ran by children in the control group increased by 23% (CI: -5% to 60%) per each data collection period compared with 53% (CI: 7% to 119%) in the intervention group. IMPLICATIONS FOR SCHOOL HEALTH POLICY, PRACTICE, AND EQUITY: State mandates, parent engagement, and funding are key for designing effective health and Physical Education (PE) programs. CONCLUSION: Children in the BN CSHP, compared to those in the control group, had a significantly higher increase in their CRF. This finding is important because of the health benefits of CRF in children. CLINICALTRIALS: gov Identifier: NCT05501392.

HLA alleles: important pieces to the COVID-19 puzzle.

Research on human leukocyte antigen (HLA) molecules in coronavirus disease 2019 (COVID-19) raised high expectations but has yielded limited results. Augusto et al.'s recent study in Nature unveils a strong association of HLA-B*15:01 with asymptomatic COVID-19, representing an important contribution to genetics in COVID-19.

HLA-A*11:01 and HLA-C*04:01 are associated with severe COVID-19.

We analyzed the association between HLA polymorphisms and susceptibility to SARS-CoV-2 infection and disease severity. Genotyping data from a total of 9373 COVID-19-positive cases from the Spanish Coalition to Unlock Research on Host Genetics on COVID-19 (SCOURGE) consortium and 5943 population controls were included in the study. We found an association of the alleles HLA-B*14:02 and HLA-C*08:02 with a lower risk to COVID-19 infection (p = 0.006, OR = 0.84, 95% CI = [0.75-0.95], p = 0.024, OR = 0.86, 95% CI = [0.78-0.95], respectively). We also found the alleles HLA-A*11:01 and HLA-C*04:01 associated with disease severity (p = 0.033, OR = 1.16, 95% CI = [1.04-1.31], p = 0.045, OR = 1.14, 95% CI = [1.05-1.25], respectively). These results suggest that an effective presentation of viral peptides by HLA class I alleles involve a faster infection clearance, decreasing the susceptibility and severity of COVID-19.

Bioinformatics analysis and single-cell RNA sequencing: elucidating the ubiquitination pathways and key enzymes in lung adenocarcinoma.

Background: Lung adenocarcinoma (LUAD) is a prevalent subtype of lung cancer associated with high mortality rates. We aimed to utilize single-cell multiomics analysis to identify the key molecules involved in ubiquitination modification, which plays a role in LUAD development and progression. Methods: We use a systematic approach to analyze LUAD-related single-cell and bulk transcriptome datasets from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Single-cell RNA sequencing (scRNA-seq) data were normalized, clustered, and annotated with the Seurat package in R. InferCNV was used to distinguish malignant from epithelial cells, and AUCell evaluated the area under the curve (AUC) score of ubiquitination-related enzymes. Survival and differential analyses identified significant molecular markers associated with ubiquitination. PSMD14 expression was confirmed using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot assays, and its knockdown cell lines were assessed for effects on cellular processes and tumor formation in mice. PSMD14's interacting proteins were predicted, and its impact on AGR2 protein half-life and ubiquitination was evaluated. Rescue experiments involving PSMD14 overexpression and AGR2 silencing assessed their impact on malignant behaviors. Results: By means of single-cell sequencing analysis, we probed the ubiquitination modification landscape in the LUAD microenvironment. Malignant cells had elevated scores for enzymes and ubiquitin-binding domains compared to normal epithelial cells, with 53 ubiquitination-related molecules showing prognostic disparities. FGR, PSMD14, and ZBTB16 were identified as genes with prognostic significance, with PSMD14 showing higher expression in epithelial and malignant cells. Two missense mutation sites were identified in PSMD14, which had a high copy number amplification ratio and positive correlation with messenger RNA (mRNA) expression. PSMD14 expression and tumor stage were found to be independent prognostic factors, and interfering with PSMD14 expression reduced the malignant behavior of LUAD cells. PSMD14 was found to bind to AGR2 protein and reduce its ubiquitination, leading to increased AGR2 stability. Knockdown of AGR2 inhibited the enhancement of cell viability, invasion, and migration resulting from PSMD14 overexpression. Conclusions: This study examined ubiquitination modifications in LUAD using sequencing data, identifying PSMD14's critical role in malignancy regulation and its potential as a prognostic and therapeutic biomarker. These insights enhance understanding of LUAD mechanisms and treatment.

Somatic mutations in tumor and plasma of locoregional recurrent and/or metastatic head and neck cancer using a next-generation sequencing panel: A preliminary study.

BACKGROUND: We explore the utility of TruSight Tumor 170 panel (TST170) for detecting somatic mutations in tumor and cfDNA from locoregional recurrent and/or metastatic head and neck squamous cell carcinoma (HNSCC). METHODS: Targeted NGS of tumor DNA and plasma cfDNA was performed using TST170 panel. In addition, a set of somatic mutations previously described in HNSCC were selected for validating in tumor, plasma, and saliva by digital droplet PCR. RESULTS: The TST170 panel identified 13 non-synonymous somatic mutations, of which five were detected in tumoral tissue, other five in plasma cfDNA, and three in both tissue and plasma cfDNA. Of the eight somatic mutations identified in tissue, three were also identified in plasma cfDNA, showing an overall concordance rate of 37.5%. CONCLUSIONS: This preliminary study shows the possibility to detect somatic mutations in tumor and plasma of HNSCC patients using a single assay that would facilitate the clinical implementation of personalized medicine in the clinic.

Plasma cell-free DNA and circulating tumor cells as prognostic biomarkers in small cell lung cancer patients.

Background: Lack of biomarkers for treatment selection and monitoring in small cell lung cancer (SCLC) patients with the limited therapeutic options, result in poor outcomes. Therefore, new prognostic biomarkers are needed to improve their management. The prognostic value of cell-free DNA (cfDNA) and circulating tumor cells (CTCs) have been less explored in SCLC. Methods: We quantified cfDNA in 46 SCLC patients at different times during first-line of chemotherapy or chemo-immunotherapy. Moreover, CTCs were analyzed in 21 patients before therapy onset using CellSearch® system. The possible association between both biomarkers and patients' outcomes was investigated in order to develop a prognostic model. Results: High cfDNA levels before therapy were associated with shorter progression-free survival (PFS) and overall survival (OS). Furthermore, cfDNA levels at 3 weeks and at progression disease were also associated with patients' outcomes. Multivariate analyses confirmed the independence of cfDNA levels as a prognostic biomarker. Finally, the three-risk category prognostic model developed included Eastern Cooperative Oncology Group Performance Status (ECOG PS), gender and baseline cfDNA levels was associated with a higher risk of progression and death. Conclusions: We confirmed the prognostic utility of cfDNA quantitative analysis in SCLC patients before and during therapy. Our novel risk prognostic model in clinical practice will allow to identify patients who could benefit with actual therapies.

Pharmacogenetic Variation and Its Clinical Relevance in a Latin American Rural Population.

Latin-American populations have been largely underrepresented in genomic studies of drug response and disease susceptibility. In this paper, we present a genome-wide Chilean dataset from Talca based on the Illumina Global Screening Array. This let us to compare the frequency of gene variants involved in response to drugs among our population and others, taking data from the 1000 Genomes Project. We found four single-nucleotide polymorphisms with low prevalence in Chileans when compared with African, Amerindian, East and South Asian, and European populations: rs2819742 (RYR2), rs2631367 (SLC22A5), rs1063320 (HLA-G), and rs1042522 (TP53). Moreover, two markers showed significant differences between lower and higher proportion of Mapuche ancestry groups: rs1719247 (located in an intergenic region in chromosome 15; p-value = 6.17 × 10-5, Bonferroni corrected p-value = 0.02) and rs738409 (A nonsynonymous gene variant in the PNPLA3 gene; p-value = 9.02 × 10-5, Bonferroni corrected p-value = 0.04). All of these polymorphisms have been shown to be associated with diverse pathologies, such as asthma, cancer, or chronic hepatitis B, or to be involved in a different response to drugs, such as metformin, HMG-CoA reductase inhibitors, or simvastatin. The present work provides a pharmacogenetic landscape of an understudied Latin American rural population and supports the notion that pharmacogenetic studies in admixed populations should consider ancestry for a higher accuracy of the results. Our study stresses the relevance of the pharmacogenomic research to provide guidance for a better choice of the best treatment for each individual in a population with admixed ancestry.

Polimorfismos en el gen FRMD4A se asocian a riesgo de enfermedad pulmonar obstructiva crónica en población latinoamericana / Polymorphisms in the FRMD4A Gene Are Associated With Chronic Obstructive Pulmonary Disease Susceptibility in a Latin American Population

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[Translated article] Polymorphisms in the FRMD4A Gene Are Associated With Chronic Obstructive Pulmonary Disease Susceptibility in a Latin American Population / Polimorfismos en el gen FRMD4A se asocian a riesgo de enfermedad pulmonar obstructiva crónica en población latinoamericana

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Efecto de las temperaturas extremas en la incidencia de enfermedades cardiovasculares: revisión bibliográfica 2016-2022 / Effect of extreme temperatures on the incidence of diseases cardiovascular: bibliographic review 2016-2022

Resumen: El panel intergubernamental sobre cambio climático estima que para el año 2100 74% de la población estará expuesta a olas de calor en el peor escenario (definido como 3 días consecutivos con temperaturas igual o sobre el percentil 95 de un periodo de tiempo), abarcando en Santiago hasta 40% de los días de verano con temperaturas extremas. Producto de la crisis climática también pueden ocurrir eventos de frío extremo. Ambos fenómenos constituyen un riesgo para la salud, particularmente para las enfermedades cardiovasculares. Objetivo: Estudiar la asociación entre temperaturas extremas y enfermedades cardiovasculares (mortalidad por enfermedades cardiovasculares, infarto agudo al miocardio, accidente cerebrovascular, hipertensión y paro cardíaco extra hospitalario). Métodos: Se realizó una revisión bibliográfica en los buscadores ISI-Web of Science, Scopus y Nature utilizando los términos de búsqueda heatwave, cardiovascular disease y extreme heat entre los años 2016-2021 incluyendo trabajos que presenten medidas de asociación entre temperaturas extremas (percentil 5 para temperaturas bajas y percentil 90 para temperaturas altas) y enfermedades cardiovasculares, arrojando 130 resultados de los cuales se seleccionaron 19. Resultados: Tanto las temperaturas altas como bajas aumentaron el riesgo de muerte por infarto agudo al miocardio (IAM) (RR: 2,29 [2,18-2,40] y RR: 2,3 [1,2-4,6], respectivamente) y paro cardíaco (OR 3,34 [1,90-3,58] y OR: 1,75 [1,23-2,49], respectivamente). La mortalidad por hipertensión arterial se asoció a temperaturas altas (OR 1,91 [1,2-3,1]), mientras que la mortalidad por enfermedades cardiovasculares (ECV) en general a bajas (RR: 1,79 [1,64 - 1,95]). En hospitalizaciones por ECV el riesgo por temperaturas altas (P99) fue RR: 1,74 [IC95%: 1,30-2,32]. Se identificaron diferencias por sexo y mayor riesgo en los mayores de 75 años y quienes presentaron exposiciones prolongadas. Conclusión: Hay una fuerte asociación entre hospitalizaciones y muerte por ECV y temperaturas extremas. Las mujeres y los adultos mayores son los más afectados.

Abstract: The Inter governmental panel estimates that in a worst case scenario, by 2100 74% of people will be exposed to heat waves (3 consecutive days with temperatures at or above the 95% percentile). This might be the case in up to 40% of days in Santiago. As a consequence of climate change there will also be periods with extremely low temperatures. Both conditions increase the risk of cardiovascular disease. Aim: to study the association of extreme temperatures with the incidence of cardiovascular disease (death, myocardial infarction, stroke and out of hospital sudden death). Method: The ISI-Web of Science, Scopus and Nature databases were searched using the terms "heat wave", "cardiovascular disease" and "extreme heat" for articles published between 2016 and 2021.

Specific miRNA Profile in Chronic Obstructive Pulmonary Disease Related to Biomass Smoke Exposure / Perfil específico de miRNAs en enfermedad pulmonar obstructiva crónica asociada a exposición a humo de biomasa

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Advances of Genomic Medicine in Psoriatic Arthritis.

Psoriatic arthritis (PsA) is a common type of inflammatory arthritis found in up to 40% of patients with psoriasis. Although early diagnosis is important for reducing the risk of irreversible structural damage, there are no adequate screening tools for this purpose, and there are no clear markers of predisposition to the disease. Much evidence indicates that PsA disorder is complex and heterogeneous, where genetic and environmental factors converge to trigger inflammatory events and the development of the disease. Nevertheless, the etiologic events that underlie PsA are complex and not completely understood. In this review, we describe the existing data in PsA in order to highlight the need for further research in this disease to progress in the knowledge of its pathobiology and to obtain early diagnosis tools for these patients.