TaqMan OpenArray Research Articles

Serum expression of mirnas in obese and lean patients with heart failure

Abstract Background Heart Failure (HF) is a progressive disease that results in increased morbidity and mortality, and clinical studies have demonstrated that body mass index (BMI) is an independent risk factor for the development of HF. Evidence has suggested that human obesity is associated with reduced mortality among patients with HF, a clinical phenomenon known as the "Obesity Paradox." MicroRNAs (miRNAs) have been underscored for their pivotal regulatory roles in numerous diseases, particularly in the context of HF. Nevertheless, our understanding of the impact of these miRNAs on obesity in conjunction with HF remains limited. Purpose The objective of this study was to evaluate the serum expression of miRNAs in obese and lean patients with HF and establish the relationship between these miRNAs and BMI. Additionally, we explored this association within two distinct phenotypes: HF with reduced ejection fraction (HFrEF) and HF with preserved ejection fraction (HFpEF). Methods Sixty-five patients with symptomatic HF (all NYHA >/=II, mean-LVFE 44.4 %), 29 lean (BMI= 25.87 ± 2.52 Kg/m2) and 36 obese (BMI= 34.52 ± 4.15 Kg/m2), were prospectively evaluated by clinical, laboratory and echocardiographic analyses. Serum expression of miRNAs was assessed by the TaqMan OpenArray Human MicroRNA system, a polymerase chain reaction-based quantitative platform that contains 754 microRNAs in a microfluidic platform. Results Among the studied miRNAs, seventeen were upregulated and one downregulated in obese HF patients compared to lean HF patients (Figure 1A). Ten miRNAs were differentially expressed in the serum of obese HFpEF patients compared to lean HFrEF patients (Figure 1B) and five were differentially expressed in the serum of obese HFpEF patients when compared to lean HFpEF patients (Figure 1C). miR-132 was upregulated in obese patients with HFrEF and HFpEF compared to lean patients, whereas miR-1291 was downregulated only in obese patients with HFpEF. Correlation analysis demonstrated a positive association between BMI and miR-132 (r=0.502; p=0.001), miR-148b (r=0.510; p<0.001), miR-103a-3p (r=0.373; p =0.011) and miR-374b-5p (r=0.325; p=0.034) in HF patients and gene set enrichment analysis identified seventy-nine potential target genes common to at least three of these four miRNAs, with the EIF4E3 and TRA2B genes common to the four miRNAs. Conclusions Our study reveals a profile of miRNAs that are differentially expressed in obese patients with HF when compared to lean patients with HF. Furthermore, four of these miRNAs showed a positive correlation with BMI in patients with HF. Although the literature indicates that miR-132 presents reduced expression in obesity models, our study identified increased serum expression of this miRNA, suggesting that it might be a potential "missing link" in the obesity paradox in patients with HF. Further studies with a larger sample are needed to confirm and explore the mechanisms linking these miRNAs to the obesity paradox.

Circulating Serum Micro-RNA as Non-Invasive Diagnostic Biomarkers of Endometriosis.

Endometriosis (END) is a painful gynecological condition. Clinical examination, imaging, and laparoscopy can provide a definitive diagnosis of END. Nonetheless, non-invasive biomarkers could help enhance and streamline the diagnostic process. Micro-RNAs (miRNAs), a family of small non-coding RNAs, could serve as useful non-invasive biomarkers for END. The aim of this study was to perform serum miRNA profiling in a retrospective cohort of women to identify miRNAs that are differentially expressed in END compared to control patients. RNA was isolated from serum samples of 67 END patients and 60 control women. The expression profile of a 754-miRNA panel was studied with RT-qPCR performed on a QuantStudio 12K Flex with the TaqMan OpenArray miRNA panel. A Censored Regression Model was used for miRNA differential expression analysis. Several gene-enrichment algorithms were employed to identify pathways related to the target genes of differentially expressed miRNAs. One hundred and thirty miRNAs were detected in at least 75% of samples from either the END or the control group. Sixteen miRNAs were significantly modulated between the END and control groups. Enrichment analysis identified targets significantly overrepresented in numerous pathways involved in biological processes related to END, including inflammation, angiogenesis, cellular invasion, cell-cycle/cell proliferation, and estrogen and progesterone hormonal signaling. Our study indicates that differentially expressed miRNAs between END patients and controls can be identified through liquid biopsy. Our findings also suggest a potential role for serum miRNAs in the pathophysiology of END, warranting further investigations for their use as non-invasive biomarkers.

Differential Expression of Circulating miRNAs and Carfilzomib-Related Cardiovascular Adverse Events in Patients with Multiple Myeloma.

This study investigates the association between circulating microRNA (miRNA) expression and cardiovascular adverse events (CVAE) in multiple myeloma (MM) patients treated with a carfilzomib (CFZ)-based regimen. A cohort of 60 MM patients from the Prospective Observation of Cardiac Safety with Proteasome Inhibitor (PROTECT) study was analyzed. Among these, 31 patients (51.6%) developed CVAE post-CFZ treatment. The Taqman OpenArray Human microRNA panels were used for miRNA profiling. We identified 13 differentially expressed miRNAs at baseline, with higher expressions of miR-125a-5p, miR-15a-5p, miR-18a-3p, and miR-152-3p and lower expression of miR-140-3p in patients who later developed CVAE compared to those free of CVAE, adjusting for age, gender, race, and higher B-type natriuretic peptide levels. We also identified three miRNAs, including miR-150-5p, that were differentially expressed in patients with and without CVAE post-treatment. Additionally, five miRNAs responded differently to CFZ treatment in CVAE vs. non-CVAE patients, including significantly elevated post-treatment expression of miR-140-3p and lower expressions of miR-598, miR-152, miR-21, and miR-323a in CVAE patients. Pathway enrichment analysis highlighted the involvement of these miRNAs in cardiovascular diseases and vascular processes. These findings suggest that specific miRNAs could serve as predictive biomarkers for CVAE and provide insights into the underlying mechanisms of CFZ-CVAE. Further investigation is warranted before these findings can be applied in clinical settings.

Caffeine, Lorazepam, and Morphine Use in Neonatal Intensive Care Unit Population and Potential Relevance of Pharmacogenomics

Abstract Medications are critical for managing acutely ill infants in neonatal intensive care unit (NICU). Tailoring therapies to individual differences in response and dose requirements might help improve outcomes. However, tools for optimizing pharmacotherapy remain limited. In this retrospective study, we explored the potential utility of pharmacogenetics for commonly prescribed NICU medications. All patients admitted to our local NICU March-December, 2022 were eligible for inclusion in the study. In infants who received at least three doses of one or more medications, we extracted DNA from residual EDTA blood collected for routine clinical care according to IRB-approved study protocols. Demographic, pharmacy, and clinical information was recorded retrospectively. Targeted pharmacogenetics testing was performed with a custom TaqMan OpenArray and a QuantStudio 12K Flex (ThermoFisher Scientific) with DNA normalized to 50 ng/mL. Results were analyzed using Genotyper Software version 1.3 and allele calls were made based on the combination of variants detected and consensus nomenclature. For drugs administered to at least 30 NICU patients, pharmacogenes were evaluated for variant allele frequency and potential clinical relevance. Of the 132 patients enrolled, 81 were male. Average length of stay was 47 days. Of the 64 different medications prescribed to at least one infant, for 15 of them are described clinical annotations with specific pharmacogenes by the PharmGKB and/or Clinical Pharmacogenetics Implementation Consortium. Of those 15 medications, three were administered at least three times to at least 30 infants: caffeine (n=102), morphine (n=56), and lorazepam (n=31). The associated pharmacogenes were CYP1A2 (caffeine); CYP3A4, OPRM1, COMT, ABCB1 (morphine); and UGT2B15 (lorazepam). Relevant to the rate of clearance of caffeine, rs2069514 (CYP1A2) was heterozygous in 18% of patients, and homozygous in 5%. Relevant to the rate of clearance of morphine, CYP3A4*22 was heterozygous in 5%. The common variants associated with response to morphine, c.472G>A (COMT) and c.118A>G (OPRM1) were heterozygous in 43% and 26%, and were homozygous in 22% and 8%, respectively. The transporter variant ABCB1*2 was heterozygous in 6% and homozygous in 11%. Relevant to the rate of clearance of lorazepam, UGT2B15*2 (rs1902023) was heterozygous in 45%, and homozygous in 31%. Correlation of pharmacogenetic results to specific clinical phenotypes is currently in progress. Pharmacogenetic variants relevant to commonly prescribed medications in the NICU are prevalent. Further clinical correlation of pharmacogenetic results may help inform selection and dosing of medications for critically ill NICU infants. This research may also facilitate detection and definition of new drug-gene associations unique to this patient population.

Identification of genomic regions, genetic variants and gene networks regulating candidate genes for lipid metabolism in pig muscle

The intramuscular fat content and fatty acid composition of porcine meat have a significant impact on its quality and nutritional value. This research aimed to investigate the expression of 45 genes involved in lipid metabolism in the longissimus dorsi muscle of three experimental pig backcrosses, with a 25% of Iberian background. To achieve this objective, we conducted an expression Genome-Wide Association Study (eGWAS) using gene expression levels in muscle measured by high-throughput real-time qPCR for 45 target genes and genotypes from the PorcineSNP60 BeadChip or Axiom Porcine Genotyping Array and 65 single nucleotide polymorphisms (SNPs) located in 20 genes genotyped by a custom-designed Taqman OpenArray in a cohort of 354 animals. The eGWAS analysis identified 301 eSNPs associated with 18 candidate genes (ANK2, APOE, ARNT, CIITA, CPT1A, EGF, ELOVL6, ELOVL7, FADS3, FASN, GPAT3, NR1D2, NR1H2, PLIN1, PPAP2A, RORA, RXRA and UCP3). Three cis-eQTL (expression quantitative trait loci) were identified for GPAT3, RXRA, and UCP3 genes, which indicates that a genetic polymorphism proximal to the same gene is affecting its expression. Furthermore, 24 trans-eQTLs were detected, and eight candidate regulatory genes were located in these genomic regions. Additionally, two trans-regulatory hotspots in Sus scrofa chromosomes 13 and 15 were identified. Moreover, a co-expression analysis performed on 89 candidate genes and the fatty acid composition revealed the regulatory role of four genes (FABP5, PPARG, SCD, and SREBF1). These genes modulate the levels of α-linolenic, arachidonic, and oleic acids, as well as regulating the expression of other candidate genes associated with lipid metabolism. The findings of this study offer novel insights into the functional regulatory mechanism of genes involved in lipid metabolism, thereby enhancing our understanding of this complex biological process.

Implication of myddosome complex genetic variants in outcome severity of COVID-19 patients.

During a viral infection, the immune response is mediated by the toll-like receptors and myeloid differentiation Factor 88 (MyD88) that play an important role sensing infections such as SARS-CoV-2 which has claimed the lives of more than 6.8 million people around the world. We carried out a cross-sectional with a population of 618 SARS-CoV-2-positive unvaccinated subjects and further classified based on severity: 22% were mild, 34% were severe, 26% were critical, and 18% were deceased. Toll Like Receptor 7 (TLR7) single-nucleotide polymorphisms (rs3853839, rs179008, rs179009, and rs2302267) and MyD88 (rs7744) were genotyped using TaqMan OpenArray. The association of polymorphisms with disease outcomes was performed by logistic regression analysis adjusted by covariates. A significant association of rs3853839 and rs7744 of the TLR7 and MyD88 genes, respectively, was found with COVID-19 severity. The G/G genotype of the rs3853839 TLR7 was associated with the critical outcome showing an Odd Ratio=1.98 (95% IC=1.04-3.77). The results highlighted an association of the G allele of MyD88 gene with severe, critical and deceased outcomes. Furthermore, in the dominant model (AG+GG vs. AA), we observed an Odd Ratio=1.70 (95% CI=1.02-2.86) with severe, Odd Ratio=1.82 (95% CI=1.04-3.21) with critical, and Odd Ratio=2.44 (95% CI=1.21-4.9) with deceased outcomes. To our knowledge this work represents an innovative report that highlights the significant association of TLR7 and MyD88 gene polymorphisms with COVID-19 outcomes and the possible implication of the MyD88 variant with D-dimer and IFN-α concentrations.

Altered Extracellular Vesicle miRNA Profile in Prodromal Alzheimer's Disease.

Extracellular vesicles (EVs) are nanosized vesicles released by almost all body tissues, representing important mediators of cellular communication, and are thus promising candidate biomarkers for neurodegenerative diseases like Alzheimer's disease (AD). The aim of the present study was to isolate total EVs from plasma and characterize their microRNA (miRNA) contents in AD patients. We isolated total EVs from the plasma of all recruited subjects using ExoQuickULTRA exosome precipitation solution (SBI). Subsequently, circulating total EVs were characterized using Nanosight nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and Western blotting. A panel of 754 miRNAs was determined with RT-qPCR using TaqMan OpenArray technology in a QuantStudio 12K System (Thermo Fisher Scientific). The results demonstrated that plasma EVs showed widespread deregulation of specific miRNAs (miR-106a-5p, miR-16-5p, miR-17-5p, miR-195-5p, miR-19b-3p, miR-20a-5p, miR-223-3p, miR-25-3p, miR-296-5p, miR-30b-5p, miR-532-3p, miR-92a-3p, and miR-451a), some of which were already known to be associated with neurological pathologies. A further validation analysis also confirmed a significant upregulation of miR-16-5p, miR-25-3p, miR-92a-3p, and miR-451a in prodromal AD patients, suggesting these dysregulated miRNAs are involved in the early progression of AD.

MicroRNAs as novel biomarkers and potential therapeutic options for inflammatory cardiomyopathy.

Inflammation of the heart is a complex biological and pathophysiological response of the immune system to a variety of injuries leading to tissue damage and heart failure. MicroRNAs (miRNAs) emerge as pivotal players in the development of numerous diseases, suggesting their potential utility as biomarkers for inflammation and as viable candidates for therapeutic interventions. The primary aim of this investigation was to pinpoint and assess particular miRNAs in individuals afflicted by virus-negative inflammatory dilated cardiomyopathy (DCMi). The study involved the analysis of 152 serum samples sourced from patients diagnosed with unexplained heart failure through endomyocardial biopsy. Among these samples, 38 belonged to DCMi patients, 24 to DCM patients, 44 to patients displaying inflammation alongside diverse viral infections, and 46 to patients solely affected by viral infections without concurrent inflammation. Additionally, serum samples from 10 healthy donors were included. The expression levels of 754 distinct miRNAs were evaluated using TaqMan OpenArray. MiR-1, miR-23, miR-142-5p, miR-155, miR-193, and miR-195 exhibited exclusive down-regulation solely in DCMi patients (P<0.005). These miRNAs enabled effective differentiation between individuals with inflammation unlinked to viruses (DCMi) and all other participant groups (P<0.005), boasting a specificity surpassing 86%. The identification of specific miRNAs offers a novel diagnostic perspective for recognizing intramyocardial inflammation within virus-negative DCMi patients. Furthermore, these miRNAs hold promise as potential candidates for tailored therapeutic strategies in the context of virus-negative DCMi.

#4434 IMPACT OF GENETIC FACTORS FOR SALT-SENSITIVE HYPERTENSION AND RENAL DAMAGE ON HOSPITALIZED COVID-19 PATIENTS

Abstract Background and Aims The coronavirus SARS-CoV-2 infects patients by binding human angiotensin-converting enzyme 2. Also, the ATP1A1 subunit of the plasma membrane Na-K-pump is critical in supporting the entry of SARS-CoV-2 into cells. Targeting of the ouabain binding site on the Na-K-pump by gene silencing or low concentrations of ouabain blocks viral infection in murine model. A recent finding demonstrated a more effective antiviral activity of digoxin and ouabain against SARS-CoV-2 infection in vitro than previously approved antiviral agents such as chloroquine and remdesivir. Moreover, cardiotonic steroids can promote renal inflammation and oxidative stress through the Na-K-pump α-1 and Src kinase signaling complex in both renal epithelial and immune cells. Arterial hypertension is one of the most common comorbidities associated with COVID-19, especially in patients with severe clinical involvement and at risk of death. The aim of this study is to evaluate the genetic aspects of pathways related to hypertension and renal failure, and to Na-K-pump activity such as endogenous ouabain and RAAS system, in order to partly dissect the wide clinical spectrum of the disease in hospitalized patients infected by SARS-CoV-2, with various degrees of symptoms. Method We investigated the relationship between three outcomes and genetic determinants in the COVID-BioB study (ClincalTrials.gov NCT04318366), a characterization of an Italian cohort of about 500 patients, a SARS-CoV-2 positive population recruited during the first wave of pandemic at San Raffaele Scientific Institute with biological samples and clinical assessment data available in an internal biobank. Targeted DNA genotyping was performed by custom arrays on TaqMan OpenArray system (ThermoFisher) for single nucleotide polymorphisms (SNPs). The genetic variants were selected as candidate for salt-sensitive hypertension and renal failure. Associations with genetic markers and outcomes were carried out with logistic regression analysis for outcome absence/presence comparison. Results COVID-19 patients were all hospitalized, with mean age 67.4±13.5 (30.2% female), pneumonia 96.9%, hypertension 51.8%, coronary arterial disease 26.8%, emergency department AKI stage 1- 11.1%, AKI stage 2- 0.4%, CKD stage&amp;gt;3 11.5%, Chronic Obstructive Pulmonary Disease 8.2%, creatinine 1.19±0.70, all at emergency department admission, in-hospital AKI 37.8%, Intensive Care unit admission 18.3%, and in-hospital death 20.6%. The main outcomes for the analysis of SNPs were in-hospital death, AKI and onset of proteinuria. The main findings for the SNP analysis concerned different genetic markers, each specific for different outcomes. A SNP in renin gene (REN), rs10900555, was associated with the in-hospital death (OR 3.84 [95%CI 1.15;12.85], P = .029). PRKG1 gene coding for the protein kinase cGMP-Dependent reported association with AKI for two different SNPs (rs1904694, OR 2.78 [95%CI 1.63;4.72], P = .0002; rs7905063, OR 2.71 [95%CI 1.72;4.23], P = .00002), with the same risk alleles previously linked to salt-sensitive hypertension. TT genotype (at risk for salt-sensitivity) in uromodulin gene (UMOD, SNP rs4293393) increases the risk of proteinuria development (OR 1.86 [95%CI 1.02;3.40], P = .044). Conclusion This genetic analysis, firstly reported on the COVID-BioB cohort, showed an intriguing relation between some polymorphisms previously associated with salt-sensitive hypertension and worst outcome or renal damage, during COVID-19. This genetic stratification may help to identify patients at risk AKI, and (directly or not) for death and renal damage (proteinuria) during COVID-19. Moreover, it may explain, at least in part, the debated relationship between hypertension and severity of COVID-19.

Circulating microRNA signatures in patients with chronic Urticaria.

Background: Chronic Urticaria (CU) is a complex skin disease that appears as recurrent raised itchy rash/angioedema or both for more than six weeks. The pathophysiology of CU is complex and has yet to be understood entirely. It is predominantly a mast cell-driven disease with the possible involvement of type 2 inflammation. Current evidence largely favors mast cell activation by an IgE-mediated autoallergic mechanism or an autoimmune mechanism by IgG autoantibodies to IgE/ high-affinity receptor of IgE. MicroRNAs (miRNA) are small coding RNAs regulating gene expression at the post-transcription level. This study aimed to investigate the circulating miRNA as potential biomarkers in CU patients compared to healthy controls. Methods: The miRNA gene expression was done in seven patients with CU and seven healthy controls. The expression of miRNA is done using TaqMan openArray human advanced miRNA Panel. ExpressionSuite Software (Thermo Fischer Scientific, Waltham, MA, USA) is used for data analysis to quantify the miRNA expressions. P<0.05 is considered to be statistically significant. Results: A significant upregulation (p<0.05) in the miR-451a, miR-9-5p, miR-150-5p, miR-296-5p, and miR-182-5p was observed in CU compared to controls. Dysregulation of miR-451a is identified as an early biomarker in allergic diseases. Functional enrichment analysis with the KEGG pathway and disease ontology databases showed that these miRNAs were associated with skin diseases and inflammation. The differentially expressed miRNAs contribute to determining the genes regulated in CU. miRNA-based therapies that target different genes in a given pathway might be a potential candidate for treating CU. Conclusion: miRNA field has grown steadily over the past few years, but the role of circulating miRNAs in CU remains relatively unexplored. This study showed that the upregulated circulating miRNA might play an essential role in CU pathogenesis and inflammation. Also, our study highlights the importance of miRNAs as a future biomarker and potential therapeutic target to be investigated.

MicroRNA Expression Signatures in Clear Cell Renal Cell Carcinoma: High-Throughput Searching for Key miRNA Markers in Patients from the Volga-Ural Region of Eurasian Continent.

Clear cell renal cell carcinoma (ccRCC) is characterized by high molecular genetic heterogeneity, metastatic activity and unfavorable prognosis. MicroRNAs (miRNA) are 22-nucleotide noncoding RNAs that are aberrantly expressed in cancer cells and have gained serious consideration as non-invasive cancer biomarkers. We investigated possible differential miRNA signatures that may differentiate high-grade ccRCC from primary disease stages. High-throughput miRNAs expression profiling, using TaqMan OpenArray Human MicroRNA panel, was performed in a group of 21 ccRCC patients. The obtained data was validated in 47 ccRCC patients. We identified nine dysregulated miRNAs (miRNA-210, -642, -18a, -483-5p, -455-3p, -487b, -582-3p, -199b and -200c) in tumor ccRCC tissue compared to normal renal parenchyma. Our results show that the combination of miRNA-210, miRNA-483-5p, miRNA-455 and miRNA-200c is able to distinguish low and high TNM ccRCC stages. Additionally, miRNA-18a, -210, -483-5p and -642 showed statistically significant differences between the low stage tumor ccRCC tissue and normal renal tissue. Contrariwise, the high stages of the tumor process were accompanied by alteration in the expression levels of miRNA-200c, -455-3p and -582-3p. Although the biological roles of these miRNAs in ccRCC are not totally clear, our findings need additional investigations into their involvement in the pathogenesis of ccRCC. Prospective studies with large study cohorts of ccRCC patients are important to further establish the clinical validity of our miRNA markers to predict ccRCC.

Recombinant human chorionic gonadotropin and gonadotropin-releasing hormone agonist differently affect the profile of extracellular vesicle microRNAs in human follicular fluid.

To compare the expression profile of extracellular vesicle microRNAs (EV-miRNAs) derived from follicular fluid after a trigger with recombinant human chorionic gonadotropin (r-hCG) or with a gonadotropin-releasing hormone GnRH agonist (GnRH-a) for final oocyte maturation. A retrospective analysis of a prospective cohort. Women undergoing in vitro fertilization at a tertiary university-affiliated hospital were recruited between 2014 and 2016. EV-miRNAs were extracted from the follicular fluid of a single follicle, and their expression was assessed using TaqMan Open Array®. Genes regulated by EV-miRNAs were analyzed using miRWalk2.0 Targetscan database, DAVID Bioinformatics Resources, Kyoto-Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). Eighty-two women were included in the r-hCG trigger group and 9 in the GnRH-a group. Of 754 EV-miRNAs screened, 135 were detected in at least 50% of the samples and expressed in both groups and were further analyzed. After adjusting for multiple testing, 41 EV-miRNAs whose expression levels significantly differed between the two trigger groups were identified. Bioinformatics analysis of the genes regulated by these EV-miRNAs showed distinct pathways between the two triggers, including TGF-beta signaling, cell cycle, and Wnt signaling pathways. Most of these pathways regulate cascades associated with apoptosis, embryo development, implantation, decidualization, and placental development. Trigger with GnRH-a or r-hCG leads to distinct EV-miRNAs expression profiles and to downstream biological effects in ovarian follicles. These findings may provide an insight for the increased apoptosis and the lower implantation rates following GnRH-a trigger vs. r-hCG in cases lacking intensive luteal phase support.

Rapid Detection of Uropathogens and Antibiotic-resistant Genes Using Open Array Multiplex PCR Technology

Abstract Introduction/Objective Introduction: Standard diagnostic practices for Urinary Tract Infection (UTI) take 2–3 days for pathogen identification and antibiotic susceptibility testing leading to delayed diagnosis and an increase in healthcare expenditures. The rapid diagnostics tool is highly desirable to identify the pathogen and its antibiotic-resistant genes directly from the samples. Our objective is to validate and evaluate the performance of Open array multiplex PCR for pathogen identification and antibiotic resistance genes. Methods/Case Report Method: Open array multiplex PCR method for 20 UTI pathogens was validated using ATCC organisms and inter-laboratory correlation using 50 urine samples. Briefly, samples were homogenized using Omni bead ruptor 96, and DNA was extracted using Hamilton Vantage. Customized open array and UTI chips with 20 most common urinary tract pathogen target and 13 resistant genes target specifically for UTI treatment were filled with Taqman open array PCR master mix and extracted DNA in a 1:1 ratio. UTI chips were prepared on Accufill and real-time PCR was performed on Quantstudio 12K flex. A total of 116 de-identified patient samples were analyzed. Results (if a Case Study enter NA) Result: The sensitivity, specificity, and accuracy of this method were more than 90% considering the reference method as the standard method. A total of 14 different types of organisms were detected. Escherichia coli (n=49) was the highest among all. Multiple pathogens were identified in 27 urine samples. Organisms such as Ureaplasma and Megasphaera 1 were detected in nine and four samples, respectively. All positive samples were resistant to at least one or two resistant genes. tetM and tetS were resistant among 72 samples, erm A, B, and C in 60 samples, ESBL in 30 and fosfo A in 21 samples. Conclusion Conclusion: The open array multiplex PCR technology may help in the early diagnosis and treatment that can improve patient care, shorten hospitalization, and reduces the economic burden.

Abstract 14006: Circulating microRNAs Predict Recovery in Pediatric Dilated Cardiomyopathy Patients

Introduction: microRNAs (miRs) are small single stranded RNAs capable of targeting expression of several genes. Circulating miRs are stable and can be important biomarkers of disease progression and diagnosis. Hypothesis: We hypothesized circulating miRs could be a reliable prognostic biomarker of recovery for pediatric dilated cardiomyopathy (DCM). Methods: TaqMan Open Array miR panel (ThermoFisher Scientific) was used to investigate expression of 381 circulating miRs. Samples originated from the Pediatric Cardiomyopathy Registry (PCMR) and were collected within 3 months of a new diagnosis of DCM. Inclusion criteria included &lt;18 years of age at diagnosis of idiopathic or familial DCM (EF&lt;50% or left ventricular end-diastolic dimension [LVEDd] z-score ≥+2). Patients with DCM secondary to musculoskeletal diseases or anthracycline toxicity were excluded. Primary outcomes, occurring within 1 year of enrollment, were defined as: [1] Death, transplant (tx) listing or initiation of mechanical circulatory support; [2] Recovered- normalization of ventricular size and function (EF≥50% and LVEDd z-score &lt;+2) or [3] Stable- persistent DCM with EF&lt;50% or LVEDd z-score ≥+2. Statistical analysis included random forest, hierarchical clustering and area under the receiver operator curve (AUC). Results: N=10 subjects were included in Group 1, of which 70% were female, 6 were white, 2 Hispanic and 3 of other/unknown races, median age 9.5y. N=5 samples were included in Group 2, of which 60% were female, 3 were white, 1 black and 1 native American, median age 1.9y. N=20 samples were included in Group 3, of which 40% were female, 10 were white, 5 black, 1 Pacific islander, 2 Hispanic and 4 of other/unknown races, median age 2.1y. The top 3 miRs differentiating Group 2 (Recovered) from Group 1 (Death/Tx) (AUC of 0.92) were hsa-miR-655, -410 and -636. The top 3 miRs differentiating Group 2 (Recovered) from Group 3 (Stable) were hsa-miR-17, -410 and -345 (AUC of 0.76). Conclusions: These results indicate circulating miRs can predict recovery in the pediatric DCM population. A unique biomarker signature of miRs specific to patients who have the potential to recover would improve risk stratification of this population.

Abstract 14074: Unique Circulating microRNA Profile in Pediatric Heart Transplant Recipients

Introduction: MicroRNAs (miRs) are small noncoding RNAs capable of modulating the expression of many genes. Hypothesis: Our hypothesis was that circulating miRs would be a biomarker of acute cellular rejection (ACR) in pediatric heart transplant recipients (PHTR). Methods: An array for 381 miRs was performed using serum from 52 PHTR and 21 healthy pediatric controls (HC). ACR was defined as ISHLT biopsy score ≥2R. Patients with antibody mediated rejection were excluded. RNA was extracted using the miRNeasy Mini Kit (Qiagen), and arrays were performed using the TaqMan Open Array miR panel (Thermo Fisher Scientific). Statistical analysis included Random Forest (RF) with area under the receiver operator curve (AUC) based on the top 3 differentiating miRs by RF, and Wilcoxon rank-sum t-test (significant q-value &lt; 0.05). Results: Of the 52 PHTR, median age 8.5 years, 44% female, race/ethnicity white in 83%, 12% African American, 13% Asian/other, and 13% Hispanic; 22 PHTR had ACR at time of serum collection. There were 21 HC, median age 5.6 years, 38% female, race/ethnicity white in 76%, 24% Asian/other, and 19% Hispanic. There were 66 miRs significantly different between HC and all PHTR (AUC of 0.91). For HC vs PHTR without ACR there were 50 differential miRs (AUC of 0.94), and for HC vs PHTR with ACR there were 51 differential miRs (AUC 0.96). Table 1 demonstrates miRs that are differentially expressed compared to HC based on the presence or absence of ACR. Circulating miRs were not different between PHTR with (n=22) and without ACR (n=30). Conclusions: The circulating miR profile of PHTR is unique compared to HC, suggesting a strong influence of the transplant mileu on miR expression. There were 17 miRs with differential expression compared to HC based on the presence or absence of ACR. These results support future investigations in larger populations to determine if circulating miRs could serve as biomarkers of ACR in PHTR, and whether these miRs contribute to the pathophysiology of ACR.

Association between SNPs in microRNAs and microRNAs-Machinery Genes with Susceptibility of Leprosy in the Amazon Population.

Leprosy is a chronic neurodermatological disease caused by the bacillus Mycobacterium leprae. Recent studies show that SNPs in genes related to miRNAs have been associated with several diseases in different populations. This study aimed to evaluate the association of twenty-five SNPs in genes encoding miRNAs related to biological processes and immune response with susceptibility to leprosy and its polar forms paucibacillary and multibacillary in the Brazilian Amazon. A total of 114 leprosy patients and 71 household contacts were included in this study. Genotyping was performed using TaqMan Open Array Genotyping. Ancestry-informative markers were used to estimate individual proportions of case and control groups. The SNP rs2505901 (pre-miR938) was associated with protection against the development of paucibacillary leprosy, while the SNPs rs639174 (DROSHA), rs636832 (AGO1), and rs4143815 (miR570) were associated with protection against the development of multibacillary leprosy. In contrast, the SNPs rs10739971 (pri-let-7a1), rs12904 (miR200C), and rs2168518 (miR4513) are associated with the development of the paucibacillary leprosy. The rs10739971 (pri-let-7a1) polymorphism was associated with the development of leprosy, while rs2910164 (miR146A) and rs10035440 (DROSHA) was significantly associated with an increased risk of developing multibacillary leprosy.

Increased Serum Mir-150-3p Expression Is Associated with Radiological Lung Injury Improvement in Patients with COVID-19.

Coronavirus disease 2019 (COVID-19) is caused by the SARS-CoV-2 virus, responsible for an atypical pneumonia that can progress to acute lung injury. MicroRNAs are small non-coding RNAs that control specific genes and pathways. This study evaluated the association between circulating miRNAs and lung injury associated with COVID-19. Methods: We evaluated lung injury by computed tomography at hospital admission and discharge and the serum expression of 754 miRNAs using the TaqMan OpenArray after hospital discharge in 27 patients with COVID-19. In addition, miR-150-3p was validated by qRT-PCR on serum samples collected at admission and after hospital discharge. Results: OpenArray analysis revealed that seven miRNAs were differentially expressed between groups of patients without radiological lung improvement compared to those with lung improvement at hospital discharge, with three miRNAs being upregulated (miR-548c-3p, miR-212-3p, and miR-548a-3p) and four downregulated (miR-191-5p, miR-151a-3p, miR-92a-3p, and miR-150-3p). Bioinformatics analysis revealed that five of these miRNAs had binding sites in the SARS-CoV-2 genome. Validation of miR-150-3p by qRT-PCR confirmed the OpenArray results. Conclusions: The present study shows the potential association between the serum expression of seven miRNAs and lung injury in patients with COVID-19. Furthermore, increased expression of miR-150 was associated with pulmonary improvement at hospital discharge.

Breast milk-derived extracellular vesicle miRNAs are associated with maternal asthma and atopy.

Background: Breast milk-derived extracellular vesicle (EV) miRNAs may program child health outcomes associated with maternal asthma and atopy. The authors investigated associations between maternal asthma/atopy and EV miRNAs in the Programming of Intergenerational Stress Mechanisms cohort. Methods: Breast milk-derived EV miRNAscollected 6.1 ± 5.9 weeks postnatally (n=80 mothers) were profiled using the TaqMan OpenArray Human MicroRNA Panel. The authors assessed associations using adjusted robust regression. Results: Nine EV miRNAs were associated with asthma during pregnancy (a priori criteria: nominal p<0.05; |Bregression| >0.2). miR-1290 was associated with asthma and atopy during pregnancy (p<0.05; |Bregression| >0.2). Enriched Kyoto Encyclopedia of Genes and Genomes pathways included TGF-β signaling and extracellular matrix-receptor interaction (false discovery rate <0.05). Conclusion: In this study, maternal asthma and atopy were associated with breast milk-derived EV miRNAs. Additional studies are needed to understand whether EV miRNAs have direct effects on infant and child health.

Relationship Between Circulating MicroRNAs and Left Ventricular Hypertrophy in Hypertensive Patients.

ObjectiveLeft ventricular hypertrophy (LVH) is a common complication of hypertension and microRNAs (miRNAs) are considered to play an important role in cardiac hypertrophy development. This study evaluated the relationship between circulating miRNAs and LVH in hypertensive patients.MethodsTwo cohorts [exploratory (n = 42) and validation (n = 297)] of hypertensive patients were evaluated by clinical, laboratory and echocardiography analysis. The serum expression of 754 miRNAs in the exploratory cohort and 6 miRNAs in the validation cohort was evaluated by the TaqMan OpenArray® system and quantitative polymerase chain reaction, respectively.ResultsAmong the 754 analyzed miRNAs, ten miRNAs (miR-30a-5p, miR-let7c, miR-92a, miR-451, miR-145-5p, miR-185, miR-338, miR-296, miR-375, and miR-10) had differential expression between individuals with and without LVH in the exploratory cohort. Results of multivariable regression analysis adjusted for confounding variables showed that three miRNAs (miR-145-5p, miR-451, and miR-let7c) were independently associated with LVH and left ventricular mass index in the validation cohort. Functional enrichment analysis demonstrated that these three miRNAs can regulate various genes and pathways related to cardiac remodeling. Furthermore, in vitro experiments using cardiac myocytes demonstrated that miR-145-5p mimic transfection up-regulated the expression of brain and atrial natriuretic peptide genes, which are markers of cardiac hypertrophy, while anti-miR-145-5p transfection abrogated the expression of these genes in response to norepinephrine stimulus.ConclusionsOur data demonstrated that circulating levels of several miRNAs, in particular miR-145-5p, miR-451, and let7c, were associated with LVH in hypertensive patients, indicating that these miRNAS may be potential circulating biomarkers or involved in hypertension-induced LV remodeling.

Genetic Variants of MicroRNA and DROSHA Genes in Association With the Risk of Tuberculosis in the Amazon Population.

Tuberculosis (TB) is a chronic infection caused by Mycobacterium tuberculosis (Mtb) with high incidence and mortality. Studies reported that host genetic variants might be associated with the risk of tuberculosis. The aim of this study was to perform an association study between 26 single nucleotide polymorphisms (SNPs) and tuberculosis and evaluate whether these SNPs may confer risk factors to tuberculosis in the Amazon population. There were 52 males and 126 females, with total of 178 healthy controls. Genotyping was performed using TaqMan Open Array Genotyping. Ancestry-informative markers were used to estimate the ancestral proportions of the individuals in the case and control groups. The results indicated that the SNPs rs10035440 (DROSHA), rs7372209 (miR26-a1), rs1834306 (miR100), rs4919510 (miR608), and rs10739971 (pri-let-7a-1) were significantly associated with high risk and rs3746444 (miR499) and rs6505162 (miR423), with low risk of developing tuberculosis in the Amazon population. Our study concluded that seven miRNA polymorphisms were associated with tuberculosis. Our study contributes to a better understanding of TB pathogenesis and may promote the development of new diagnostic tools against M. tuberculosis infection.