Risk stratification of patients who present with chest pain and have normal troponins using a machine learning model.

BACKGROUND: Risk stratification tools exist for patients presenting with chest pain to the emergency room and have achieved the recommended negative predictive value (NPV) of 99%. However, due to low positive predictive value (PPV), current stratification tools result in unwarranted investigations such as serial laboratory tests and cardiac stress tests (CSTs). AIM: To create a machine learning model (MLM) for risk stratification of chest pain with a better PPV. METHODS: This retrospective cohort study used de-identified hospital data from January 2016 until November 2021. Inclusion criteria were patients aged > 21 years who presented to the ER, had at least two serum troponins measured, were subsequently admitted to the hospital, and had a CST within 4 d of presentation. Exclusion criteria were elevated troponin value (> 0.05 ng/mL) and missing values for body mass index. The primary outcome was abnormal CST. Demographics, coronary artery disease (CAD) history, hypertension, hyperlipidemia, diabetes mellitus, chronic kidney disease, obesity, and smoking were evaluated as potential risk factors for abnormal CST. Patients were also categorized into a high-risk group (CAD history or more than two risk factors) and a low-risk group (all other patients) for comparison. Bivariate analysis was performed using a χ 2 test or Fisher's exact test. Age was compared by t test. Binomial regression (BR), random forest, and XGBoost MLMs were used for prediction. Bootstrapping was used for the internal validation of prediction models. BR was also used for inference. Alpha criterion was set at 0.05 for all statistical tests. R software was used for statistical analysis. RESULTS: The final cohort of the study included 2328 patients, of which 245 (10.52%) patients had abnormal CST. When adjusted for covariates in the BR model, male sex [risk ratio (RR) = 1.52, 95% confidence interval (CI): 1.2-1.94, P < 0.001)], CAD history (RR = 4.46, 95%CI: 3.08-6.72, P < 0.001), and hyperlipidemia (RR = 3.87, 95%CI: 2.12-8.12, P < 0.001) remained statistically significant. Incidence of abnormal CST was 12.2% in the high-risk group and 2.3% in the low-risk group (RR = 5.31, 95%CI: 2.75-10.24, P < 0.001). The XGBoost model had the best PPV of 24.33%, with an NPV of 91.34% for abnormal CST. CONCLUSION: The XGBoost MLM achieved a PPV of 24.33% for an abnormal CST, which is better than current stratification tools (13.00%-17.50%). This highlights the beneficial potential of MLMs in clinical decision-making.

Comprehensive Assessment of Copy Number Alterations Uncovers Recurrent AIFM3 and DLK1 Copy Gain in Medullary Thyroid Carcinoma.

Medullary thyroid carcinoma (MTC) is a malignant tumor originating from thyroid C-cells that can occur either in sporadic (70-80%) or hereditary (20-30%) form. In this study we aimed to identify recurrent copy number alterations (CNA) that might be related to the pathogenesis or progression of MTC. We used Affymetrix SNP array 6.0 on MTC and paired-blood samples to identify CNA using PennCNV and Genotyping Console software. The algorithms identified recurrent copy number gains in chromosomes 15q, 10q, 14q and 22q in MTC, whereas 4q cumulated losses. Coding genes were identified within CNA regions. The quantitative PCR analysis performed in an independent series of MTCs (n = 51) confirmed focal recurrent copy number gains encompassing the DLK1 (14q32.2) and AIFM3 (22q11.21) genes. Immunohistochemistry confirmed AIFM3 and DLK1 expression in MTC cases, while no expression was found in normal thyroid tissues and few MTC samples were found with normal copy numbers. The functional relevance of CNA was also assessed by in silico analysis. CNA status correlated with protein expression (DLK1, p = 0.01), tumor size (DLK1, p = 0.04) and AJCC staging (AIFM3p = 0.01 and DLK1p = 0.05). These data provide a novel insight into MTC biology, and suggest a common CNA landscape, regardless of if it is sporadic or hereditary MTC.

Transcriptome Analysis of Mesenchymal Stem Cells from Multiple Myeloma Patients Reveals Downregulation of Genes Involved in Cell Cycle Progression, Immune Response, and Bone Metabolism.

A growing body of evidence suggests a key role of tumor microenvironment, especially for bone marrow mesenchymal stem cells (MSC), in the maintenance and progression of multiple myeloma (MM), through direct and indirect interactions with tumor plasma cells. Thus, this study aimed to investigate the gene expression and functional alterations of MSC from MM patients (MM-MSC) in comparison with their normal counterparts from normal donors (ND-MSC). Gene expression analysis (Affymetrix) was performed in MM-MSC and ND-MSC after in vitro expansion. To validate these findings, some genes were selected to be evaluated by quantitative real time PCR (RT-qPCR), and also functional in vitro analyses were performed. We demonstrated that MM-MSC have a distinct gene expression profile than ND-MSC, with 485 differentially expressed genes (DEG) - 280 upregulated and 205 downregulated. Bioinformatics analyses revealed that the main enriched functions among downregulated DEG were related to cell cycle progression, immune response activation and bone metabolism. Four genes were validated by qPCR - ZNF521 and SEMA3A, which are involved in bone metabolism, and HLA-DRA and CHIRL1, which are implicated in the activation of immune response. Taken together, our results suggest that MM-MSC have constitutive abnormalities that remain present even in the absence of tumors cells. The alterations found in cell cycle progression, immune system activation, and osteoblastogenesis suggest, respectively, that MM-MSC are permanently dependent of tumor cells, might contribute to immune evasion and play an essential role in bone lesions frequently found in MM patients.

Genes related to maintenance of autophagy and successful aging / Genes relacionados à manutenção da autofagia e envelhecimento bem-sucedido

ABSTRACT Considering aging as a phenomenon in which there is a decline in essential processes for cell survival, we investigated the autophagic and proteasome pathways in three different groups: young, older and oldest old male adults. The expression profile of autophagic pathway-related genes was carried out in peripheral blood, and the proteasome quantification was performed in plasma. No significant changes were found in plasma proteasome concentrations or in correlations between proteasome concentrations and ages. However, some autophagy- and/or apoptosis-related genes were differentially expressed. In addition, the network and enrichment analysis showed an interaction between four of the five differentially expressed genes and an association of these genes with the transcriptional process. Considering that the oldest old individuals maintained both the expression of genes linked to the autophagic machinery, and the proteasome levels, when compared with the older group, we concluded that these factors could be considered crucial for successful aging.

RESUMO Considerando o envelhecimento como um fenômeno em que há um declínio nos processos essenciais a sobrevivência celular, investigamos as vias autofágica e proteassômica em três grupos: jovens, idosos e longevos. O perfil de expressão dos genes relacionados à via autofágica foi analisado em sangue periférico, e a quantificação do proteassoma realizada em plasma. Não foram encontradas alterações significativas nas concentrações plasmáticas de proteassoma ou na correlação entre as concentrações de proteassoma e as idades. No entanto, alguns genes relacionados a autofagia e / ou apoptose foram expressos diferencialmente. Além disso, as análises de rede e de enriquecimento mostraram uma interação entre quatro dos cinco genes diferencialmente expressos e a associação desses ao processo transcricional. Considerando que os indivíduos longevos mantiveram tanto a expressão de genes ligados à maquinaria autofágica, quanto os níveis de proteassoma quando comparados aos idosos, concluímos que esses fatores poderiam ser considerados cruciais para o envelhecimento bem-sucedido.

The association between caffeine consumption and objective sleep variables is dependent on ADORA2A c.1083T>C genotypes.

OBJECTIVE: To verify the association between c.1083T>C polymorphism in the adenosine receptor A2A gene (ADORA2A) and objective sleep, as well as the correlation between caffeine consumption, sleep parameters, and electroencephalographic spectral power in a large, population-based sample from São Paulo, Brazil. METHODS: This study was conducted in participants of the São Paulo Epidemiologic Sleep Study (EPISONO), a large, population-based survey consisting of a representative sample of the inhabitants of the city from São Paulo, Brazil, according to sex, age (20-80 years), and socioeconomic status in the year 2007. Questionnaires, polysomnography, spectral analysis of sleep electroencephalogram, and c.1083T>C polymorphism genotyping were performed in this study. RESULTS: We found that caffeine consumption was positively correlated with sleep latency and α spectral power, as well as negatively correlated with percentage of N3 stage and δ spectral power in this stage. However, this association was identified only in T allele carriers and not in CC genotype. CONCLUSION: Our data support an important aspect of this polymorphism in ADORA2A gene, showing that the variant affects the association between caffeine consumption and objective sleep parameters in a large population-based cohort. CLINICAL TRIAL INFORMATION: Name: Epidemiology of sleep disturbances among adult population of the Sao Paulo City. URL: http://www.clinicaltrials.gov/ct2/show/NCT00596713?term = NCT00596713&rank = 1. Number: NCT00596713.

Interleukin-1ß and interleukin-6 gene polymorphisms are associated with manifestations of sickle cell anemia.

Sickle cell anemia (SCA), a disorder characterized by both acute and chronic inflammation, exhibits substantial phenotypic variability. Interleukin-1 beta (IL-1ß) and IL-6 are important in acute and chronic diseases, and their single nucleotide polymorphisms (SNPs) have been considered as predictors of prognosis in several inflammatory conditions. This study aims at exploring possible association of IL-1ß and IL-6 SNPs as potential genetic modifiers and or predictors of SCA clinical and laboratory phenotypes. This cross-sectional study involved 107 SCA patients and 110 age, sex and ethnicity-matched healthy individuals. The SNPs were identified by PCR-RFLP for IL-1ß (-511C>T and +3954C>T) and IL-6 (-597G>A and -174G>C) genes. Associations between these SNPs and the clinical and laboratory profiles of patients with SCA were then determined. Allelic and genotypic frequencies of IL-1ß and IL-6 SNPs between patients with SCA and controls were similar and followed HWE. IL-1ß +3954C>T SNP was associated with increased risk of osteonecrosis, elevated pulmonary arterial pressure and lower absolute reticulocyte count, while IL-6 -597G>A was associated with higher likelihood of retinopathy and leg ulcer. These data indicate that IL-1ß and IL-6 gene SNPs are associated with SCA complications among Brazilian patients and may act as genetic predictors of SCA clinical heterogeneity.

Multiple myeloma cell lines and primary tumors proteoma: protein biosynthesis and immune system as potential therapeutic targets.

Despite great advance in multiple myeloma (MM) treatment since 2000s, it is still an incurable disease and novel therapies are welcome. Therefore, the purpose of this study was to explore MM plasma cells' (MM-PC) proteome, in comparison with their normal counterparts (derived from palatine tonsils of normal donors, ND-PC), in order to find potential therapeutic targets expressed on the surface of these cells. We also aimed to evaluate the proteome of MM cell lines with different genetic alterations, to confirm findings obtained with primary tumor cells. Bone marrow (BM) samples from eight new cases of MM and palatine tonsils from seven unmatched controls were submitted to PC separation and, in addition to two MM cell lines (U266, RPMI-8226), were submitted to protein extraction for mass spectrometry analyses. A total of 81 proteins were differentially expressed between MM-PC and ND-PC - 72 upregulated and nine downregulated; U266 vs. RPMI 8226 cell lines presented 61 differentially expressed proteins - 51 upregulated and 10 downregulated. On primary tumors, bioinformatics analyses highlighted upregulation of protein biosynthesis machinery, as well as downregulation of immune response components, such as MHC class I and II, and complement receptors. We also provided comprehensive information about U266 and RPMI-8226 cell lines' proteome and could confirm some patients' findings.

Adenosine deaminase polymorphism affects sleep EEG spectral power in a large epidemiological sample.

Slow wave oscillations in the electroencephalogram (EEG) during sleep may reflect both sleep need and intensity, which are implied in homeostatic regulation. Adenosine is strongly implicated in sleep homeostasis, and a single nucleotide polymorphism in the adenosine deaminase gene (ADA G22A) has been associated with deeper and more efficient sleep. The present study verified the association between the ADA G22A polymorphism and changes in sleep EEG spectral power (from C3-A2, C4-A1, O1-A2, and O2-A1 derivations) in the Epidemiologic Sleep Study (EPISONO) sample from São Paulo, Brazil. Eight-hundred individuals were subjected to full-night polysomnography and ADA G22A genotyping. Spectral analysis of the EEG was carried out in all individuals using fast Fourier transformation of the signals from each EEG electrode. The genotype groups were compared in the whole sample and in a subsample of 120 individuals matched according to ADA genotype for age, gender, body mass index, caffeine intake status, presence of sleep disturbance, and sleep-disturbing medication. When compared with homozygous GG genotype carriers, A allele carriers showed higher delta spectral power in Stage 1 and Stages 3+4 of sleep, and increased theta spectral power in Stages 1, 2 and REM sleep. These changes were seen both in the whole sample and in the matched subset. The higher EEG spectral power indicates that the sleep of individuals carrying the A allele may be more intense. Therefore, this polymorphism may be an important source of variation in sleep homeostasis in humans, through modulation of specific components of the sleep EEG.

Effects of the adenosine deaminase polymorphism and caffeine intake on sleep parameters in a large population sample.

STUDY OBJECTIVES: To evaluate the association between the adenosine deaminase polymorphism, sleep architecture, and caffeine consumption. DESIGNS: Genetic association study. SETTING: NA. PATIENTS OR PARTICIPANTS: 958 participants who underwent polysomnography and genotyping. INTERVENTIONS: NA. MEASUREMENTS AND RESULTS: Individuals carrying the A allele who consumed caffeine in the day prior to polysomnography demonstrated higher sleep efficiency and REM sleep percentage, after adjustment for potential confounders. No effect was observed in the absence of caffeine. CONCLUSIONS: Our data support the role of the ADA G22A polymorphism in sleep, and demonstrate for the first time that caffeine may act as a modulator of its functional effects. CLINICAL TRIAL INFORMATION: Name: Epidemiology of sleep disturbances among adult population of the Sao Paulo City. URL: http://www.clinicaltrials.gov/ct2/show/NCT00596713?term=NCT00596713&rank=1. Number: NCT00596713

Interleukin- 8- 251T > a, interleukin -1α -889C > t and apolipoprotein e polymorphisms in Alzheimer's disease

An inflammatory process has been involved in numerous neurodegenerative disorders such as Parkinson's disease, stroke and Alzheimer's disease (AD). In AD, the inflammatory response is mainly located in the vicinity of amyloid plaques. Cytokines, such as interleukin-8 (IL-8) and interleukin-1α (IL-1α), have been clearly involved in this inflammatory process. Polymorphisms of several interleukin genes have been correlated to the risk of developing AD. The present study investigated the association of AD with polymorphisms IL-8 -251T > A (rs4073) and IL-1α-889C > T (rs1800587) and the interactive effect of both, adjusted by the Apolipoprotein E genotype. 199 blood samples from patients with AD, 146 healthy elderly controls and 95 healthy young controls were obtained. DNA samples were isolated from blood cells, and the PCR-RFLP method was used for genotyping. The genotype distributions of polymorphisms IL-8, IL-1α and APOE were as expected under Hardy-Weinberg equilibrium. The allele frequencies did not differ significantly among the three groups tested. As expected, the APOE4 allele was strongly associated with AD (p < 0.001). No association of AD with either the IL-1α or the IL-8 polymorphism was observed, nor was any interactive effect between both polymorphisms. These results confirm previous studies in other populations, in which polymorphisms IL-8 -251T > A and IL-1α-889C > T were not found to be risk factors for AD.

Association of PPARalpha gene polymorphisms and lipid serum levels in a Brazilian elderly population.

Peroxisome proliferator-activated receptor alpha (PPARalpha) is a nuclear transcription factor strictly involved in lipid and lipoprotein metabolisms. Thus, PPARalpha gene polymorphisms have been investigated as cardiovascular risk factors. We aimed to investigate associations of L162V and intron 7G>C polymorphisms with common morbidities affecting a Brazilian elderly cohort as well as with lipid and protein serum levels. Genotyping was performed by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP), and allele frequencies were determined. In addition, we performed the linkage disequilibrium analysis. Descriptive statistics, logistic regression analysis, and Student's t-test were used. Rare alleles for L162V and intron 7 G>C polymorphisms showed frequencies of 0.047 and 0.199, respectively. Our data showed that these polymorphisms were in linkage disequilibrium (p=0.0002). Intron 7 G>C polymorphism presented a tendency of association with neoplasia (p=0.053), and C allele was associated with higher HDL (p=0.010), lower triglycerides (p=0.001), and VLDL levels (p=0.003) compared to G allele. These data might suggest a protective role of intron 7 G>C polymorphism in the development of cardiovascular diseases and will help to clarify the importance of PPARalpha polymorphisms as key modulators of lipid metabolism in Brazilian population.