Plasma miRNA Expression Profiles Research Articles

Exploring circulating MiRNA signature for osteosarcoma detection: Bioinformatics-based analyzing and validation

Early detection followed by efficient treatment still remain a considerable challenge for osteosarcoma (OS), indicating the importance of emerging innovative diagnostic methods. Circulating miRNAs offer a promising and non-invasive approach to assess the OS molecular landscapes. This study utilized RNAseq data from OS plasma miRNA expression profiles (PRJEB30542) and PCR Array data (GSE65071) from GEO and ENA databases. In total, 43 miRNAs demonstrated significant differential expression in OS samples of training dataset. A diagnostic model, including hsa-miR-30a-5p, hsa-miR-556–3p, hsa-miR-200a-3p, and hsa-miR-582–5p was identified through multivariate logistic regression analysis and demonstrated significant efficacy in differentiating OS patients from healthy controls in the validation group (AUC: 0.917, sensitivity: 1, specificity: 0.85). The result of target gene prediction and functional enrichment analyses revealed significant associations with terms such as epithelial morphogenesis, P53 and Wnt signaling pathways, and neoplasm metastasis. Further bioinformatics-based evaluations showed that the down-regulation of these miRNAs significantly correlates with poor prognosis and lower survival rate in OS patients and propose their tumor suppressor function in pathogenesis of OS. Furthermore, the study developed a miRNA-mRNA subnetwork that connects these miRNAs to the P53 and Wnt signaling pathways, which are critical pathways with oncogenic effects on OS progression. This comprehensive approach not only presents a promising diagnostic model but also proposes potential molecular markers for OS early diagnosis, making prognosis, and targeted therapy. The identified miRNA-mRNA functional axis holds promise as a valuable resource for further research in understanding OS pathogenesis and establishing therapeutic modalities.

Dynamic peripheral blood microRNA expression landscape during the peri-implantation stage in women with successful pregnancy achieved by single frozen-thawed blastocyst transfer.

What are the dynamic expression features of plasma microRNAs (miRNAs) during the peri-implantation period in women with successful pregnancy via single frozen-thawed blastocyst transfer? There is a significant change in the plasma miRNA expression profile before and after blastocyst transfer, during the window of implantation. The expression of miRNAs in peripheral blood has indicative functions during the peri-implantation period. Nevertheless, the dynamic expression profile of circulating miRNAs during the peri-implantation stage in women with a successful pregnancy has not been studied. Seventy-six women treated for infertility with a single frozen-thawed blastocyst transfer in a natural cycle were included in this study. Among them, 57 women had implantation success and a live birth, while 19 patients experienced implantation failure. Peripheral blood samples were collected at five different time points throughout the peri-implantation period, including D0 (ovulation day), D3, D5, D7, and D9 in this cycle of embryo transfer. The plasma miRNAs in women with blastocyst transfer were isolated, sequenced, and analyzed. Peripheral blood samples were collected in EDTA tubes and stored at -80°C until further use. miRNAs were isolated from blood, cDNA libraries were constructed, and the resulting sequences were mapped to the human genome. The plasma miRNAs were initially analyzed in a screening cohort (n = 34) with successful pregnancy. Trajectory analysis, including a global test and pairwise comparisons, was performed to detect dynamic differentially expressed (DE) miRNAs. Fuzzy c-means clustering was conducted for all dynamic DE miRNAs. The correlation between DE miRNAs and clinical characteristics of patients was investigated using a linear mixed model. Target genes of the miRNAs were predicted, and functional annotation analysis was performed. The expression of DE miRNAs was also identified in a validation set consisting of women with successful (n = 23) and unsuccessful (n = 19) pregnancies. Following small RNA sequencing, a total of 2656 miRNAs were determined as valid read values. After trajectory analysis, 26 DE miRNAs (false discovery rate < 0.05) were identified by the global test, while pairwise comparisons in addition identified 20 DE miRNAs. A total of seven distinct clusters representing different temporal patterns of miRNA expression were discovered. Nineteen DE miRNAs were further identified to be associated with at least one clinical trait. Endometrium thickness and progesterone level showed a correlation with multiple DE miRNAs (including two of the same miRNAs, hsa-miR-1-3p and hsa-miR-6741-3p). Moreover, the 19 DE miRNAs were predicted to have 403 gene targets, and there were 51 (12.7%) predicted genes likely involved in both decidualization and embryo implantation. Functional annotation for predicted targets of those clinically related DE miRNAs suggested the involvement of vascular endothelial growth factor and Wnt signaling pathways, as well as responses to hormones, immune responses, and cell adhesion-related signaling pathways during the peri-implantation stage. The raw miRNA sequence data reported in this article have been deposited in the Genome Sequence Archive (GSA-Human: HRA005227) and are publicly accessible at https://ngdc.cncb.ac.cn/gsa-human/browse/HRA005227. Although the RNA sequencing results revealed the global dynamic changes of miRNA expression, further experiments examining the clinical significance of the identified DE miRNAs in embryo implantation outcome and the relevant regulatory mechanisms involved are warranted. Understanding the dynamic landscape of the miRNA transcriptome could shed light on the physiological mechanisms involved from ovulation to the post-implantation stage, as well as identifying biomarkers that characterize stage-related biological process. The study was funded by the Major clinical research project of Tangdu Hospital (2021LCYJ004) and the Discipline Platform Improvement Plan of Tangdu Hospital (2020XKPT003). The funders had no influence on the study design, data collection, and analysis, decision to publish, or preparation of the article. There are no conflicts of interest to declare.

Blood orange juice intake modulates plasma and PBMC microRNA expression in overweight and insulin-resistant women: impact on MAPK and NFκB signaling pathways

Blood orange consumption presents potential health benefits and may modulate epigenetic mechanisms such as microRNAs (miRNAs) expression. MiRNAs are non-coding RNAs responsible for post-transcriptional gene regulation, and these molecules can also be used as biomarkers in body fluids. This study was designed to investigate the effect of chronic blood orange juice (BOJ) intake on the inflammatory response and miRNA expression profile in plasma and blood cells in overweight women. The study cohort was comprised of twenty women aged 18–40 years old, diagnosed as overweight, who consumed 500 mL/d of BOJ for four weeks. Clinical data were collected at baseline and after 4 weeks of juice consumption, e.g., anthropometric and hemodynamic parameters, food intake, blood cell count, and metabolic and inflammatory biomarkers. BOJ samples were analyzed and characterized. Additionally, plasma and blood cells were also collected for miRNA expression profiling and evaluation of the expression of genes and proteins in the MAPK and NFκB signaling pathways. BOJ intake increased the expression of miR-144-3p in plasma and the expression of miR-424-5p, miR-144-3p, and miR-130b-3p in peripheral blood mononuclear cells (PBMC). Conversely, the beverage intake decreased the expression of let-7f-5p and miR-126-3p in PBMC. Computational analyses identified different targets of the dysregulated miRNA on inflammatory pathways. Furthermore, BOJ intake increased vitamin C consumption and the pJNK/JNK ratio and decreased the expression of IL6 mRNA and NFκB protein. These results demonstrate that BOJ regulates the expression of genes involved in the inflammatory process and decreases NFкB-protein expression in PBMC.

Whole Blood Holding Time Prior to Plasma Processing Alters microRNA Expression Profile.

MicroRNAs (miRNAs) can exhibit aberrant expression under different physiological and pathological conditions. Therefore, differentially expressed circulating miRNAs have been a focus of biomarker discovery research. However, the use of circulating miRNAs comes with challenges which may hinder the reliability for their clinical application. These include varied sample collection protocols, storage times/conditions, sample processing and analysis methods. This study focused on examining the effect of whole blood holding time on the stability of plasma miRNA expression profiles. Whole blood samples were collected from healthy pregnant women and were held at 4°C for 30 min, 2 h, 6 h or 24 h prior to processing for plasma isolation. Plasma RNA was extracted and the expression of 179 miRNAs were analyzed. Unsupervised principal component analysis demonstrated that whole blood holding time was a major source of variation in miRNA expression profiles with 53 of 179 miRNAs showing significant changes in expression. Levels of specific miRNAs previously reported to be associated with pregnancy-associated complications such as hsa-miR-150-5p, hsa-miR-191-5p, and hsa-miR-29a-3p, as well as commonly used endogenous miRNA controls, hsa-miR-16-5p, hsa-miR-25-3p, and hsa-miR-223-3p were significantly altered with increase in blood holding time. Current protocols for plasma-based miRNA profiling for diagnostics describe major differences in whole blood holding periods ranging from immediately after collection to 26 h after. Our results demonstrate holding time can have dramatic effects on analytical reliability and reproducibility. This highlights the importance of standardization of blood holding time prior to processing for plasma in order to minimize introduction of non-biological variance in miRNA profiles.

Oxidative Stress-Related miRNAs in Patients with Severe Acne Vulgaris.

Acne vulgaris is a common chronic inflammatory skin disease in adolescents and oxidative stress plays an important role in acne pathology. However, the pathology of acne has not yet been fully elucidated. miRNAs are small noncoding RNAs, and there is increasing evidence for their role in the pathogenesis of skin diseases such as psoriasis, atopic dermatitis, and other inflammatory diseases. The aim of the study was to investigate serum malondialdehyde (MDA) and glutathione (GSH) levels with plasma miRNA expression profile related with oxidative stress in patients with severe acne vulgaris. Fifty seven female patients with severe acne and 40 healthy women were included in the study. Plasma miRNA-31, miRNA-200a, and miRNA-21 levels were evaluated by using real-time quantitative polymerase chain rection analysis. MDA and GSH levels were measured as per the manufacturer's procedures using commercial ELISA kits. Plasma miRNA-21 levels were statistically significantly higher in patients with severe acne compared to the control group (P =0.003). Plasma miRNA-200a (P =0.303) and miRNA-31 (P =.652) levels were slightly higher in patients with severe acne compared to the control group, but this difference was not statistically significant. Serum MDA levels (P =.047) were higher in patients with severe acne compared to control group, while serum GSH levels (P =.001) were lower. These results show that oxidative damage is involved in acne etiopathogenesis and especially miRNA-21 may have an important role in the pathogenesis of acne vulgaris.

The Severity of Muscle Performance Deterioration in Sarcopenia Correlates With Circulating Muscle Tissue-Specific miRNAs

Sarcopenia is defined as an age-associated loss of skeletal muscle function and muscle mass and is common in older adults. Sarcopenia as a disease is currently of interest not only to orthopedists and surgeons but also to internists, endocrinologists, rheumatologists, cardiologists, diabetologists, gynaecologists, geriatricians and paediatricians. In cooperation with the 5th Internal Medicine Clinic, we, as a unit of clinical research, aimed to describe a sarcopenic specific miRNA expression profile for disease diagnostics and classification of the severity of muscle performance deterioration. This study included a total of 80 patients (age 55-86 years) hospitalized at the V. Internal medicine clinic of LFUK and UNB with different severity of muscle performance deterioration. The study participants were evaluated and classified according to short physical performance battery score (SPPB). In this study, we investigated the role of circulating miRNAs in sarcopenia in the elderly. We hypothesized that sarcopenia effects the expression of muscle tissue-specific miRNAs (MyomiRNAs), which could be potentially reflected in the blood plasma miRNA expression profile. The expression of specific circulating miRNAs in patients with different muscle performances was analyzed. Patients' blood plasma was evaluated for the expression of myomiRNAs: miRNA-29a, miRNA-29b, miRNA-1, miRNA-133a, miRNA-133b, miRNA-206, miRNA-208b and miRNA-499, and the data were correlated with diagnostic indicators of the disease. We showed a specific sarcopenia miRNA profile that could be considered a possible biomarker for the disease. Patients with low muscle performance showed increased miRNA-1, miRNA-29a and miRNA-29b expression and decreased for the miRNA-206, miRNA-133a, miRNA-133b, miRNA-208b and miRNA-499 expression. We show that the severity of muscle performance deterioration in sarcopenia correlates with specific miRNA expression. We also propose the profile of miRNAs expression in blood plasma as a specific biomarker for sarcopenia diagnostics. Future clinical studies will be necessary to eventually naturally have to elucidate the underlined molecular mechanism responsible for specific miRNAs expression in sarcopenia pathology and progression of the disease.

Circulating miRNAs miR-574-5p and miR-3135b are potential metabolic regulators for serum lipids and blood glucose in gestational diabetes mellitus

Objectives MicroRNAs (miRNAs) are potentially involved in the regulation of glucose and lipid metabolism. The aim of this study was to investigate potential miRNA regulators for serum lipids and blood glucose in gestational diabetes mellitus. Methods Plasma samples were obtained from 53 women with GDM and 46 normal pregnant women. Fasting blood glucose and a blood lipid profile were measured. Plasma miRNA expression profiles were analyzed using microarray. To verify the microarray data, the expression of miRNAs was evaluated by real-time PCR. Gene ontology (GO) and genes and genomics (KEGG) pathway enrichment of the predicted target genes of miRNAs were analyzed. Results The miRNA expression profiles of plasma samples from healthy and GDM women are distinct. We identified 93 differently expressed miRNAs. Compared with healthy pregnant women, 48 miRNAs including miR-574-5p and miR-3135b exhibited significantly lower expression in plasma samples from GDM patients. The expression of miR-574-5p was significantly correlated with levels of blood glucose and LDL-C; miR-3135b was significantly correlated with HDL-C. Some predicted common target genes of these two miRNAs are associated with the metabolism of glucose and lipids as well as the insulin signaling pathway. Conclusions miR-574-5p and miR-3135b may serve as metabolic regulators of glucose and lipids for GDM.

MicroRNA expression profiles in the seminal plasma of nonobstructive azoospermia patients with different histopathologic patterns

To investigate microRNA (miRNA) expression profiles in the seminal plasma of nonobstructive azoospermia (NOA) patients with different histopathologic patterns and evaluate potential noninvasive diagnostic biomarkers of NOA. Sequencing and validation using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Reproductive center and research institute. Thirteen patients with NOA (7 Sertoli cell-only syndrome [SCOS] and 6 hypospermatogenesis to spermatogenesis arrest [SA]) and 7 normal fertile controls for sequencing, six samples per group for validation; 54 patients with NOA (27 SCOS and 27 SA) and 19 normal fertile controls for large-sample qRT-PCR analysis. None. MicroRNA expression profiles in the seminal plasma of patients with NOA with different histopathologic patterns were assessed using high-throughput sequencing and validated using qRT-PCR. There were 78 overexpressed and 132 underexpressed miRNAs in patients with SCOS and 32 up-regulated and 90 down-regulated miRNAs in patients with SA compared with fertile men with normozoospermia. Two down-regulated and one up-regulated miRNA were validated using qRT-PCR, which indicated that the qRT-PCR and sequencing results were basically consistent. Hsa-miR-34c-5p expression was significantly lower in the seminal plasma of patients with NOA than normal fertile controls. The area under the receiver operating characteristic curve(AUC) for hsa-miR-34c-5p was 0.979 and 0.987 in the seminal plasma of patients with SA and patients with SCOS, respectively, compared with normal fertile controls. The AUC was 0.799 for hsa-miR-34c-5p in the seminal plasma between patients with SA and patients with SCOS. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed miRNA target genes revealed that the Notch signaling pathway was one of the most abundant signaling pathways. The expression of Hes5, an effector of the Notch signaling pathway, was significantly higher in the seminal plasma of patients with NOA than normal fertile controls. MicroRNA expression profiles in seminal plasma were altered in patients with NOA compared with normal fertile controls. The profiles differed in patients with NOA with different pathologic patterns. We speculate that miR-34c-5p in seminal plasma could be a potential noninvasive biomarker to diagnose patients with NOA and distinguish different pathologic types of NOA. The Notch signaling pathway may be involved in the pathogenesis of NOA.

197-LB: microRNA Expression Profiles and Progression from Normoglycemia to Prediabetes in a Biracial Cohort

Background: MicroRNA (miRNA) profiles are associated with diabetes risk, but data on prediabetes are scant. Methods: We studied participants (age 49.7 ±5.42 y; BMI 28.6 ±5.77 kg/m2) in the Pathobiology of Prediabetes in a Biracial Cohort (POP-ABC) study, whose primary outcome was progression from normoglycemia to prediabetes (IFG/IGT) during 5-y follow up. We analyzed miRNA expression in participants with incident prediabetes (Progressors, n=10) and a matched group of Nonprogressors (n=10). Total RNA was extracted from plasma. NGS sequencing libraries were prepared using QIAseq miRNA Library Prep Kit and RNA sequencing was performed by QIAGEN Genomic Services. Over 12 million reads per samples were performed. To minimize false discovery, Benjamini-Hochberg corrected p-values were used to assess the significance of differential miRNA expression. Results: Based on entries in mirbase_20, we identified 226 known miRNAs that were expressed at &amp;gt;1tags per million (TPM) and 151 known microRNAs that were expressed at &amp;gt;10 TPM in all samples analyzed. 25 miRNAs were differentially expressed in baseline plasma from Progressors to prediabetes vs. Nonprogressors (P=0.04- &amp;lt;0.0001). The top 5 most upregulated miRNAs in Progressors (vs. Nonprogressors) were miR 216a-5p, miR 217, miR 211-5p, miR 149-5p and miR 204-5p (log fold-change 3.61 to 6.49, P&amp;lt;0.0001). The top 5 most downregulated miRNAs in Progressors (vs. Nonprogressors) were miR 34c-5p, miR 550a-3p, miR 3200-3p, miR 144-5p and miR 144-3p (log fold-change -2.26 to -3.79, P= 0.0009-&amp;lt;0.0001). The most differentially expressed miRNA (miR 216a-5p; 6.49-log-fold higher in Progressors) is linked to the regulation of 78 genes, of which. 30 are involved in glucose, lipid, endocrine and metabolic pathways. Conclusions: Plasma miRNA expression profile at baseline distinguished progressors to prediabetes from nonprogressors during longitudinal follow-up in the POP-ABC study. miR 216a-5p may be a novel biomarkers of early dysglycemia. Disclosure I. Owei: None. A.O. Dokun: None. F.B. Stentz: None. S. Dagogo-Jack: Consultant; Self; AstraZeneca, Janssen Pharmaceuticals, Inc., Merck &amp; Co., Inc., Sanofi US. Stock/Shareholder; Self; Dance Biopharm Holdings, Inc., Jana Care Inc. Funding National Institutes of Health (R01DK067269)

Differential microRNAs expression in seminal plasma of normospermic patients with different sperm DNA fragmentation indexes

Sperm DNA fragmentation index (SDF), as an important supplement to routine semen parameters, has been proposed to discriminate between fertile and infertile men, and predicts the outcomes of natural conception and in vitro fertilization. Unfortunately there are uncertainty and contradictory evidences regarding the importance of SDF. An important reason is the fact that significant and fundamental research about SDF is rare. This study was designed to characterize the microRNA (miRNA) expression profile in seminal plasma of normospermic patients with different SDF and their implications in human fertility. Using next-generation sequencing (NGS), a total of 897 human miRNAs were detected from 10 seminal plasma samples, out of which 431 differentially expressed miRNAs in 5 pairs of seminal plasma samples (each pair of seminal plasma samples obtained from the same male), with 14 miRNAs were identified in all the pairs. According to the fold change and expression level, 7 miRNAs including miR-374b-5p, miR-429, hsa-miR-26b-5p, miR-21−5p, miR-4257, miR-135b-5p and miR-134−5p were selected for further excavation. MiR-374b-5p and miR-26b-5p were significantly different in 3 sets of individual seminal plasma samples with different SDF from total 90 infertile patients (30 patients each set). Our results demonstrate that the profile of miR-374b and miR-26b with significantly decreased expression could be used as a first indication of increased SDF. And miR-374b and miR-26b could serve as adjunct biomarkers for the diagnosis of idiopathic infertile males.

Clinical Significance of Circulating miR-1273g-3p and miR-122-5p in Pancreatic Cancer

The burden of pancreatic cancer (PanC) requires innovation in the current diagnostic approach. This study aimed to uncover new circulating microRNAs (miRNAs) that would distinguish patients with PanC from healthy subjects (HS) compared with the cancer antigen 19-9 (CA 19-9), and predict patients' clinical phenotypes and outcomes. MiRNA expression profiles in plasma were investigated by using a two-stage process. In a discovery phase, miRNAs levels were analyzed using the GeneChip™ miRNA 4.0 Affymetrix assay in 10 pools of plasma samples from PanC patients and HS; in a validation phase, significantly altered miRNAs were re-tested in independent cohorts of cancer patients and controls by droplet digital PCR (ddPCR). The diagnostic performance of the resulting miRNAs was compared to CA 19-9 determinations, and the associations of miRNAs plasma levels with patients' clinical phenotypes and outcomes were also taken into account. Bioinformatics selection of miRNAs differentially expressed in plasma uncovered miR-18a-5p, miR-122-5p, miR-1273g-3p, and miR-6126 as candidate oncogenic miRNAs in PanC. The ddPCR technology confirmed the significant over-expression of miR-122-5p, miR-1273g-3p, and miR-6126 in PanC compared to HS, in line with the trend of the CA 19-9 levels. Plasma levels of miR-1273g-3p, in combination with CA 19-9, showed higher power in distinguishing PanC patients from HS compared to the CA 19-9 tested alone, with a gain in both sensitivity and negative predictive value indicating a low false-negative rate (SE = 90.2% and NPV = 92.3% vs. SE = 82.1% and NPV = 87.9%). None of the oncogenic miRNAs were able to distinguish between a neoplastic and a proliferative/inflammatory disease of the pancreas, and were not able to stratify subjects according to the clinical risk for the disease. The only valuable association in PanC patients was found between miR-1273g-3p and tumor stage, and increased miR-122-5p levels emerged as independent negative prognostic factor for PanC patients (HR = 1.58, 95% CI = 1.03–2.43, p = 0.037). Our data highlighted a role for circulating miR-1273g-3p and miR-122-5p as new diagnostic and prognostic biomarkers for PanC.

Deep Sequencing Identified Dysregulated Circulating MicroRNAs in Late Onset Preeclampsia.

To characterize global microRNA (miRNA) expression profile in the first trimester maternal plasma of women who subsequently develop late-onset preeclampsia (LOPE) compared to uncomplicated pregnancies. Five first trimester plasma samples from women who developed LOPE and 5 controls were analyzed using next generation sequencing technology (NGS) followed by target prediction, Gene Ontology analysis and pathway identification. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed for confirmation in an independent cohort of 12 LOPE cases and 12 controls. miR-23b-5p and miR-99b-5p were down-regulated by >1.5 fold in LOPE complicated pregnancies (p value <0.05) compared to controls. Target prediction showed that the major targets of these miRNAs are associated with glycometabolism and immune response. miR-23b-5p and miR-99b-5p are possibly implicated in the pathogenic mechanisms leading to the induction of LOPE and may serve as candidate non-invasive biomarkers for early prediction and prevention.

Circulating MicroRNAs as Novel Potential Biomarkers for Left Ventricular Remodeling in Postinfarction Heart Failure.

Circulating microRNAs (miRNAs) have been proposed as potential biomarkers for left ventricular remodeling in postinfarction heart failure (HF). However, the diagnostic reproducibility of the use of circulating miRNAs may be affected by the temporal expression of miRNAs following myocardial infarction (MI). In the current study, using a MI-induced HF rat cohort (4-, 8-, and 12-week post-MI groups), we investigated the temporal expression of plasma miRNAs during the development of left ventricular remodeling. The plasma miRNA expression profile was obtained using miRNA sequencing. The expression of candidate miRNAs in plasma and tissues was examined with real-time PCR. Target genes of candidate miRNAs were predicted using a parallel miRNA-messenger RNA expression profiling approach. The value of plasma miRNAs as biomarkers for left ventricular remodeling was evaluated in patients with postinfarction HF (n = 32) and control patients with stable angina and without significant coronary lesions and HF (n = 16) with real-time PCR. Although the expression levels of miR-20a-5p, miR-340-5p, and let-7i-5p were temporally regulated in plasma, myocardium, and peripheral blood mononuclear cells, the expression levels of plasma miRNAs, especially miR-20a-5p, were associated with the development of left ventricular remodeling in the postinfarction HF rat cohort. The target genes of these 3 miRNAs were associated with the mechanistic target of rapamycin, nuclear factor-κB, tumour necrosis factor, apoptosis, and p53 signaling pathways. Additionally, the plasma levels of miR-20a-5p, miR-340-5p, and let-7i-5p were significantly increased in patients with postinfarction HF. However, only the expression levels of miR-20a-5p presented significant positive correlations with left ventricular internal end diastolic dimension and left ventricular end diastolic volume. In conclusion, the expression levels of plasma miR-20a-5p were significantly associated with the degree of left ventricular dilatation, and plasma miR-20a-5p may be a potential biomarker for postinfarction left ventricular remodeling.

Circulating miRNA expression profile and bioinformatics analysis in patients with occult hepatitis B virus infection.

Emerging suggest that microRNAs (miRNAs) play vital roles in the occurrence and development of hepatitis B virus (HBV) infectious disease. However, miRNAs in occult hepatitis B virus infection (OBI), a special stage of HBV infection, remain largely unknown. Herein, we conducted this study to identify differentially expressed miRNAs and then to investigate the potential roles of these miRNAs in OBI. Plasma miRNA expression profiles of three OBI patients and three healthy controls were analyzed with high through-put miRNA sequencing technology. Altered expression of miRNAs was further confirmed with reverse transcription quantitative polymerase chain reaction (qRT-PCR). Finally, bioinformatics analysis was conducted to investigate the involved pathways and target genes for these differentially expressed miRNAs. Totally, 32 differentially expressed miRNAs were identified between OBI and healthy controls by miRNA sequencing (fold change ≥ 1.5, P < .1, and counts per million reads ≥ 1), including 16 downregulated and 16 upregulated miRNAs. Differential expression of hsa-miR-486-5p, -25-3p, and -92a-3p and -1-3p was further validated by qRT-PCR analysis, which was consistent with miRNA sequencing analysis. Moreover, these four miRNAs might distinguish OBI from HCs efficiently. Bioinformatics analyses indicated that the differentially expressed miRNAs were primarily involved in various biological processes related to gene expression and transcription, cell development and metabolism, protein modification and kinase activity regulation, as well as multiple signaling pathways such as PI3K/Akt signaling pathway. This study provided a global view of miRNA expression in plasma from OBI patients. These differentially expressed miRNAs might play important roles in the development of OBI, which provided intriguing insights into the screening and molecular mechanism of OBI.

MicroRNA-140-5p: A novel circulating biomarker for early warning of late-onset post-stroke depression

We aimed to explore the circulating microRNAs biomarkers in the acute stage following cerebral ischemia to earlier warn late-onset post-stroke depression (PSD). A total of 251 consecutive patients with acute ischemic stroke were recruited. They were divided into three groups depending on whether PSD had occurred at 2 weeks or 3 months since stroke: early-onset PSD, late-onset PSD, and non-depressed group. Microarray assay was conducted to identify the different expression profiles of plasma miRNAs. Comprehensive bioinformatics analysis for their integrating putative target genes was performed. The key miRNA was validated in a larger cohort and its function was further studied in ischemic mice brain. We screened three differentially expressed miRNAs in the late-onset PSD individuals, miR-140-5p and miR-221-3p were significantly upregulated while miR-1246 was downregulated. The bioinformatics analysis demonstrated that their predicted target genes were mainly enriched in axon development and Ras signaling pathway. Logistic regression analysis revealed that miR-140-5p was an independent risk factor for late-onset PSD (P = 0.017, OR = 2.313, 95%CI 1.158 to 4.617). The miR-140-5p expression on admission was significantly positively correlated with HDRS scores assessed at 3 months after stroke (P = 0.0007). The predictive value of miR-140-5p for late-onset PSD is 83.3% sensitivity and 72.6% specificity (AUC = 0.8127, P < 0.0001). AAV-mediated overexpression of miR-140-5p decreased the protein level of IL1rap, IL1rapl1, VEGF, and MEGF10 in the ischemic mouse hippocampus and inhibited neurogenesis and capillary density. MiR-140-5p might be involved in the pathogenesis of late-onset PSD and used as a novel early warning biomarker.

Differential MicroRNA Expression Profiles as Potential Biomarkers for Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains a clinical challenge due to its poor prognosis. Therefore, the early diagnosis of PDAC is extremely important for achieving a cure. MicroRNAs (miRNAs) could serve as a potential biomarker for the early detection and prognosis of PDAC. In this work we analyzed plasma samples from healthy persons and PDAC patients to assess differential miRNA expression profiles by next generation sequencing technology and bioinformatics analysis. In this way, 165 mature miRNAs were found to be significantly deregulated in the patient group, of which 75 and 90 mature miRNAs were up- and down-regulated compared with healthy individuals, respectively. Furthermore, 1029 novel miRNAs were identified. In conclusion, plasma miRNA expression profiles are different between healthy individuals and patients with PDAC. These data provide a possibility for use of miRNA as diagnostic and prognostic biomarkers of PDAC.

Evaluation of Plasma Extracellular Vesicle MicroRNA Signatures for Lung Adenocarcinoma and Granuloma With Monte-Carlo Feature Selection Method.

Extracellular Vesicle (EV) is a compilation of secreted vesicles, including micro vesicles, large oncosomes, and exosomes. It can be used in non-invasive diagnosis. MicroRNAs (miRNAs) processed by exosomes can be detected by liquid biopsy. To objectively evaluate the discriminative ability of miRNAs from whole plasma, EV and EV-free plasma, we analyzed the miRNA expression profiles in whole plasma, EV and EV-free plasma of 10 lung adenocarcinoma and 9 granuloma patients. With Monte-Carlo feature selection method, the top discriminative miRNAs in whole plasma, EV and EV-free plasma were identified, and they were quite different. Using the Repeated Incremental Pruning to Produce Error Reduction (RIPPER) method, we learned the classification rules: in whole plasma, granuloma patients did not express hsa-miR-223-3p while the lung adenocarcinoma patients expressed hsa-miR-223-3p; in EV, the hsa-miR-23b-3p was highly expressed in granuloma patients but not lung adenocarcinoma patients; in EV-free plasma, hsa-miR-376a-3p was expressed in granuloma patients but barely expressed in lung adenocarcinoma patients. For prediction performance, whole plasma had the highest weighted accuracy and EV outperformed EV-free plasma. Our results suggested that EV can be used as lung cancer biomarker. However, since it is less stable and not easy to detect, there are still technological difficulties to overcome.

A panel of three plasma microRNAs for colorectal cancer diagnosis

BackgroundDifferential microRNA (miRNA) expression profiles in plasma or serum were identified, providing foundation for studying their potentially diagnostic role in colorectal cancer (CRC). MethodsWe performed S-poly(T) Plus PCR assay to select and validate differentially expressed plasma miRNAs from a sample set including 101 CRC patients, 20 patients with colorectal noncancerous polyps (NCP), and 134 healthy controls. And bioinformatics methods was used to integrated predicted or validated targets of the differentially dysregulated miRNAs and analyzed their overrepresented pathways. ResultsAfter the two-phase selection and validation process, we identified a miRNA panel (miR-144-3p, miR-425-5p, and miR-1260b) with high diagnostic efficiency for CRC; the panel distinguished CRC patients from controls with 93.8% sensitivity and 91.3% specificity. Results indicated that the dysregulated miRNAs in CRC were functionally involved in several key cancer-related pathways, such as axonal guidance, PI3K, and calcium signaling pathways. ConclusionsOur study demonstrated that a plasma 3-miRNA panel may serve as a novel noninvasive biomarker to diagnose CRC. This plasma 3-miRNA panel may be related to CRC development. However, further studies are needed to highlight its theoretical strengths.

Integrating miRNA and mRNA expression profiles in plasma of laying hens associated with heat stress.

High temperature is one of the most common environmental stressors plaguing animal husbandry worldwide. Little is known about the regulatory roles of miRNAs in response to heat stress in laying hens. To systematically identify heat stress-responsive miRNAs and their targets in laying hens, the differential expression of miRNAs and mRNAs was compared under heat stress and normal temperature. We identified 16 miRNAs and 502 genes that were significantly changed in heat-stressed laying hens. By comparing the differentially expressed genes (DEGs) and the putative targets of the altered miRNAs based on bioinformatics prediction, 82 coordinated genes were identified. Gene ontology classification analyses of the 82 putative target genes showed that the biological category 'cellular response to stress' was prominently annotated. Notably, the response-related gene autophagy-related protein 9A was most likely controlled by the upregulated miRNAs gga-miR-92-5p, gga-miR-1618-5p, gga-miR-1737, and gga-miR-6557 in response to heat stress. Analysis of DEGs also revealed an increase in lipid metabolism in heat-stressed laying hens. Some of these genes were negatively correlated with the altered miRNAs, suggesting that they are potential targets of the miRNAs. Taken together, our results advance our understanding of the regulatory mechanism of heat-stress-induced injury in laying hens, specifically with regard to miRNAs.

The Role of microRNAs in the Pathogenesis of Erdheim-Chester Disease and Their Potential Use As Biomarkers for Diagnosis and Prognosis of the Disease

Background: Erdheim-Chester disease (ECD) is a rare hematological malignancy, belonging to the L-group histiocytoses. ECD is characterized by multi-systemic proliferations of mature histiocytes in a background of inflammatory stroma. The inflammatory and neoplastic characteristics of the disease comprise a complex medical challenge for its diagnosis and treatment.MicroRNAs (miRNAs/miRs) are short non-coding RNAs (~22 nucleotides) that regulate gene expression in a sequence specific manner and play an important role in cancer development and progression. Since miRNAs are released into the blood by tumor cells, they may be used as biomarkers to distinguish between cancer patients and healthy individuals and to assist in determining treatment response. Moreover, miRNA-mRNA interactions can determine the molecular mechanism by which miRNAs and their target genes are involved in ECD and may suggest novel therapeutic options for these patients. To date, this is the first study elucidating the role of miRNA in ECD.Aims: The main focus of this study is to identify miRNAs that are differentially expressed in ECD patients compared to healthy controls and any clinical utility they have as potential biomarkers in ECD diagnosis, as well as to investigate their role in ECD pathogenesis, which may lead to new therapeutic options.Preliminary results: Using the nCounter Human miRNA Expression Assay (NanoString Technologies), we analyzed the plasma miRNA expression profiles of 6 ECD patients (BRAF V600E) compared to 6 healthy individuals. Of the 800 mature miRNAs analyzed, 234 miRNAs showed different expression levels in these samples. Principal component analysis (PCA) was applied to experimental quality control. The miRNAs from healthy donors were clustered separately from the ECD samples indicating a distinct miRNA expression pattern between these groups (Fig. 1A, 1B). Among the 131 miRNAs remaining in the final analysis (FDR<0.05),110 miRNAs were downregulated in ECD patients compared to those of healthy controls, and 21 miRNAs were upregulated in ECD samples compared to those of the controls.We validated the analysis method by quantitative real-time polymerase chain reaction (qRT-PCR) and found a positive correlation between miRs-15a, 16, 125a, 223, 21, 34a, 155 and miR-630 expression obtained by the NanoString array. This may indicate the potential use of miRNAs as biomarkers in ECD.To determine potential target genes and signaling pathways implicated in ECD, we analyzed the predicted pathways of the top 30 downregulated miRNAs that were differentially expressed between the two groups using the Ingenuity® Pathway Analysis (IPA) and DIANA-miRPath v3.0 database. Reassuringly, the analysis identified cancer, inflammatory disease, and inflammatory response (p<0.01) as the main disease and disorder related with the miRNA expression pattern, as well as oncogenic pathways such as MAPK, PI3K-AKT, RAS, ErbB, Hippo, and mTOR as the main molecular pathways related to the differentially-expressed miRNAs (p<0.009). This finding suggests that low expression of miRNAs results in up regulation of target genes that participate in cell survival signaling. These augmented pathways may be inhibited by novel therapeutic treatments such as PI3K inhibitors, mTOR pathway inhibitors, and MEK inhibitors in ECD patients.Next, we examined if there is any correlation between the predicted target genes of the miRNAs (obtained by IPA) and the experimentally validated gene expression pattern in ECD patients. To that end, we downloaded RNA-seq results of ECD patients from the GEO database (GSE74442 deposited by Diamond et al) and compared this list to our predicted miRNA targets in ECD patients, using Gene Set Enrichment Analysis (GSEA). We found a positive correlation between the gene expression reported in the literature and the predicted target of our deregulated miRNAs (Fig. 2), indicating that the predicted target genes are enriched in this data set, suggesting that the differentially expressed miRNAs might have a crucial role in the pathogenesis of ECD.Conclusions: Our preliminary data highlight the unique inflammatory and neoplastic features characteristic of ECD. These deregulated miRNAs may highlight new candidate gene targets allowing for a better understanding of the molecular mechanisms underlying the development of ECD and propose novel therapeutic treatments for these patients. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.