miRNA Profiles Research Articles

The circulating plasma microRNA signature in human visceral leishmaniasis.

Visceral leishmaniasis (VL) is a vector-borne disease caused by the obligate intracellular protozoan Leishmania donovani in India. VL can be complicated by post-kala-azar dermal leishmaniasis (PKDL), a macular or nodular rash that develops in 10%-20% of patients after treatment of VL in India. Patients with PKDL are infectious to sand flies, promoting further transmission of the parasite. MicroRNAs (miRNAs) are 18-25 nt, non-coding RNAs that simultaneously regulate the expression of several or many target transcripts. This study was based on the hypothesis that the host response to L. donovani is modified by distinct sets of miRNAs in VL or PKDL and that these might differ from healthy controls. We investigated this hypothesis using a NanoString panel to profile the miRNAs expressed in the plasma of patients with VL or PKDL diagnosed at a hospital in Bihar, India. We compared these to plasma microRNAs of healthy control individuals from the same endemic villages. miRNAs hsa-miR-223-3p, hsa-miR-191-5p, hsa-miR-23a-3p, and hsa-1285-5p were significantly higher in the plasma samples from patients with VL compared to either PKDL or endemic controls. Prediction programs highlighted potential mRNA targeted by these miRNAs, among which we verified the down-modulation of several transcripts belonging to the NFκB and NLRP3 inflammasome pathways in circulating leukocytes of VL patients. By contrast, miRNA patterns in subjects with PKDL were similar to control subjects, possibly suggesting that the pathogenic immune response during PKDL is primarily localized in the skin.IMPORTANCEInfection of humans with the protozoan Leishmania donovani can be asymptomatic or it can cause fatal visceral leishmaniasis (VL), sometimes followed by the cutaneous complication PKDL. Parasites are spread through sand fly bites in endemic regions, and parasites in post-kala-azar dermal leishmaniasis (PKDL) skin lesions are a source of prolonged parasite transmission to sand flies, compromising disease eradication efforts. Since microRNAs can simultaneously modify the expression of multiple genes, we examined microRNAs in the blood that might be partial determinants of pathogenic responses leading to VL or PKDL. Our studies revealed several miRNAs expressed that are elevated in the plasma of patients with VL, which suppress some of the inflammatory responses that promote parasite killing. However, miRNA profiles were very similar between PKDL patients and controls, raising the possibility that major factors that lead to prolonged retention of parasites in the skin during PKDL are not systemic but are localized in the skin.

Expression profiling of circular RNAs in sepsis-induced acute gastrointestinal injury: insights into potential biomarkers and mechanisms

This study aimed to investigate the role of circular RNAs (circRNAs) in sepsis-induced acute gastrointestinal injury (AGI), focusing on their potential as biomarkers and their involvement in disease progression. Peripheral blood samples from 14 patients with sepsis-induced AGI and healthy volunteers were collected. RNA sequencing was performed to profile circRNA and miRNA expression. Differential expression analysis identified key regulatory RNAs. Functional enrichment analysis was conducted to explore biological pathways, and circRNA-miRNA interaction networks were constructed. Significant differences in circRNA and miRNA expression profiles were observed between sepsis-induced AGI patients and healthy controls. Several circRNAs, including hsa_circ_0008381 and hsa_circ_0071375, exhibited stepwise expression increases correlating with AGI severity. Functional enrichment analysis indicated that the host genes of differentially expressed circRNAs are involved in key biological processes like protein ubiquitination, organelle maintenance, and cellular signaling pathways such as mitochondrial biogenesis and lipid metabolism. CircRNA-miRNA interaction networks suggested their role as miRNA sponges, regulating key downstream processes. This study demonstrated the potential of circRNAs as diagnostic biomarkers and therapeutic targets for sepsis-induced AGI. Further research is warranted to validate their clinical utility and unravel their mechanistic roles in AGI progression.

Immune checkpoint expression and therapeutic implications in IDH1-mutant and wild-type glioblastomas.

Programmed cell death protein 1 (PDCD1) and cluster of differentiation 274 (CD274) expression is implicated in escaping tumors from immune surveillance. Immune checkpoint inhibitors show promise in cancer therapy, yet their efficacy in glioblastomas, particularly with IDH1 mutations, remains unclear. This study analyzed two independent NGS datasets (n = 577 and n = 153) from TCGA to investigate the expression of PDCD1 and CD274 in glioblastomas and their relationship with IDH1 mutations. We used cBioPortal for mutation analysis, RNA seq for expression analysis, miRDB and miRabel for differential expression of miRNAs, and Kaplan-Meier for survival prediction. We found that 5.4% of glioblastomas harbored IDH1 mutations, correlating with improved overall survival (OS) (p = 2.196e-3). Different glioblastoma cohorts showed a diverse IDH1 mutational prevalence (4-31%). Despite this, IDH1Mu was consistently associated with better OS (p = 8.235e-5). Notably, PDCD1 and CD274 were statistically significantly highly expressed in both IDH1Wt (p < 0.0001) and IDH1Mu tumors (p < 0.0001), with higher expression linked to poorer survival outcomes (PDCD1: p = 0.009; CD274: p = 0.02). Differential co-expression analyses revealed distinct gene and miRNA profiles for IDH1Wt and IDH1Mu glioblastomas, with specific upregulation of PTEN and downregulation of MUC16 in IDH1Wt, and upregulation of PIK3R1 in IDH1Mu. Additionally, PIK3R1 and ITGB2 emerged as critical druggable targets. Our findings indicate that PDCD1 and CD274 are highly expressed irrespective of IDH1 mutation statuses, suggesting that glioblastomas could benefit from immunotherapy. Moreover, IDH1Mu glioblastomas may require a combination of PI3K/AKT/mTOR inhibitors and immunotherapy due to PIK3R1 overexpression.

Unveiling the role of miRNAs in Diminished Ovarian Reserve: an in silico network approach

MicroRNAs (miRNAs) have acquired an increased recognition to unravel the complex molecular mechanisms underlying Diminished Ovarian Reserve (DOR), one of the main responsible for infertility. To investigate the impact of miRNA profiles in granulosa cells and follicular fluid, crucial players in follicle development, this study employed a computational network theory approach to reconstruct potential pathways regulated by miRNAs in granulosa cells and follicular fluid of women suffering from DOR. Available data from published research were collected to create the FGC_MiRNome_MC, a representation of miRNA target genes and their interactions. 365 hubs were identified within the network, representing potential key regulators, and 210 nodes that act as both hubs and bottlenecks (H&BN nodes), suggesting that they may control the information flow within the network. GO enrichment analysis of the 210 H&BN nodes revealed their involvement in fundamental cellular processes relevant to ovarian function. In particular, the cluster analysis identified several shared pathways between cluster 1 and cluster 2 involved in the RAS/MAPK pathway, which plays a critical role in cell proliferation, differentiation and survival. These findings suggest that miRNAs play a significant role in DOR and highlight the potential of the RAS/MAPK pathway as a target for further investigation. Additionally, the genes identified as both hubs and bottlenecks revealed interesting connections to reproductive health in KO mice models. This in silico approach provides valuable insights into potential biomarkers and therapeutic targets for age-related reproductive disorders.

Remodeling the Proinflammatory Microenvironment in Osteoarthritis through Interleukin-1 Beta Tailored Exosome Cargo for Inflammatory Regulation and Cartilage Regeneration.

Osteoarthritis (OA) presents a significant therapeutic challenge, with few options for preserving joint cartilage and repairing associated tissue damage. Inflammation is a pivotal factor in OA-induced cartilage deterioration and synovial inflammation. Recently, exosomes derived from human umbilical cord mesenchymal stem cells (HucMSCs) have gained recognition as a promising noncellular therapeutic modality, but their use is hindered by the challenge of harvesting a sufficient number of exosomes with effective therapeutic efficacy. Given that HucMSCs are highly sensitive to microenvironmental signals, we hypothesized that priming HucMSCs within a proinflammatory environment would increase the number of exosomes secreted with enhanced anti-inflammatory properties. Subsequent miRNA profiling and pathway analysis confirmed that interleukin-1 beta (IL-1β)-induced exosomes (C-Exos) exert positive effects through miRNA regulation and signaling pathway modulation. In vitro experiments revealed that C-Exos enhance chondrocyte functionality and cartilage matrix production, as well as macrophage polarization, thereby enhancing cartilage repair. C-Exos were encapsulated in hyaluronic acid hydrogel microspheres (HMs) to ensure sustained release, leading to substantial improvements in the inflammatory microenvironment and cartilage regeneration in a rat OA model. This study outlines a strategy to tailor exosome cargo for anti-inflammatory and cartilage regenerative purposes, with the functionalized HMs demonstrating potential for OA treatment.

P1299 Modulation of miR-31-5p expression in patients with Ulcerative Colitis treated with infliximab

Abstract Background Biological therapy has revolutionized the treatment of Ulcerative Colitis (UC), but biomarkers that predict response are still lacking. MicroRNAs (miRNAs) are small non-coding RNA molecules that participate in cellular processes such as proliferation, differentiation, migration, maturation and apoptosis, and therefore are related to immune regulation in physiological and pathological conditions such as Inflammatory Bowel Diseases. Therefore, the objective of the study is to investigate the expression profile of miRNAs in responding and non-responding patients treated with Infliximab and to identify a profile of miRNAs that predict therapeutic response. Methods Twelve miRNAs: miR-21-5p, miR-31-5p, miR-192-3p, miR-192-5p, miR-215-5p, miR-326, miR-378-3p, miR-378-5p, miR-422a, miR-429, miR-551a and miR-1258-3p were evaluated in naïve patients with UC before and after treatment with Infliximab (week 54). MiRNA was extracted from formalin-fixed, paraffin-embedded (FFPE) colon tissue and qRT-PCR was performed from 12 patients, of which: 5 responding and 7 non-responding, both groups evaluated pre and post treatment (n=24 samples). Results Decreased expression was found for miR-31-5p (p=0.03) when comparing responding patients pre and post treatment, meanwhile miR-192-5p (p &amp;gt; 0.99) and miR-378-3p (p &amp;gt; 0.99) were suggestive but not statistically different. The other miRNAs had not had expressive results. Conclusion Infliximab-responding patients with UC presented decreased expression of miR-31-5p. MiR-31-5p regulates IL-25 and activates Th1/Th17 mediated inflammation in UC. Therefore, our results reinforce the importance of miR-31-5p expression in UC and indicate a relationship between this miRNA and the effectiveness of the treatment.

Altered expression of miRNA profile in peripheral blood mononuclear cells following the third dose of inactivated COVID-19 vaccine.

COVID-19 vaccination is the most effective strategy for preventing severe disease and death. Inactivated vaccines are the most accessible type of COVID-19 vaccines in developing countries. Several studies, including work from our group, have demonstrated that the third dose (booster vaccination) of inactivated COVID-19 vaccine induces robust humoral and cellular immune responses. The present study aimed to examine miRNA expression profile in participants who received a homologous third dose of the CoronaVac vaccine. Samples of peripheral blood mononuclear cells (PBMCs) were collected from healthcare volunteers both before and 1-2 weeks after the booster dose. miRNA microarray analysis in a discovery cohort of six volunteers identified 67 miRNAs with differential expression. Subsequently, the expression of six miRNAs related to immune responses was examined in a validation cohort of 31 participants via qRT-PCR. Our results validated the differential expression of miR-25-5p, miR-34c-3p, and miR-206 post-booster, with a significant correlation to the receptor binding domain (RBD)-specific antibody. Bioinformatic analysis suggested that miR-25-5p, miR-34c-3p, and miR-206 may target multiple pathways involved in immune regulation and inflammation. Therefore, our study highlights miR-25-5p, miR-34c-3p, and miR-206 in PBMCs as promising biomarkers for assessing the immune response induced by the booster dose of the CoronaVac vaccine.

Altered expression profile of plasma exosomal microRNAs in exclusive electronic cigarette adult users

Little is known about how exclusive e-cigarette use affects exosomal microRNA (miRNA) expression, which is crucial in inflammation and disease processes like cancer. We compared exosomal miRNA profiles between exclusive e-cigarette users and non-users. We used plasma samples from 15 exclusive e-cigarette users and 15 non-users from the Population Assessment of Tobacco and Health (PATH) Wave 1 study (2013–2014) and sequenced miRNAs with Illumina NextSeq 500/550. We performed differential analyses using DESeq2 in R/Bioconductor, adjusting for race, and conducted gene enrichment analyses on target genes regulated by significant miRNAs. Further, molecular-based techniques using the miRNA mimics and inhibitors were applied for the validation of the expressions of the miRNAs in vitro. We identified four miRNAs that were upregulated in exclusive e-cigarette users compared to non-users: hsa-miR-100-5p, hsa-miR-125a-5p, hsa-miR-125b-5p, and hsa-miR-99a-5p, after adjusting for the confounding effects of race. However, none of the miRNAs remained statistically significant after controlling for the false discovery rate (FDR) at 5%. Subgroup analysis of White participants only identified four miRNAs (hsa-miR-100-5p, hsa-miR-125b-5p, hsa-miR-200b-3p, and hsa-miR-99a-5p) that were also upregulated in e-cigarette users with one miRNA hsa-miR-200b-3p remaining statistical significance after controlling for the FDR at 5%. GO enrichment analysis showed that these miRNAs are involved in processes like transcription regulation and cellular protein modification. KEGG pathway analysis indicated their involvement in cancer pathways, including small cell lung cancer, renal cell carcinoma, and signaling pathways (neurotrophin, ErbB, PI3K-Akt, FoxO, Hippo, MAPK, TGF-beta). Overexpression of hsa-miR-125b-5p promoted DNA damage in bronchial epithelial cells. These findings suggest an elevation of carcinogenic cellular signaling pathways in exclusive e-cigarette users.

Identification of puberty related miRNAs in the hypothalamus of female mice.

Puberty is a crucial developmental stage marked by the transition from childhood to adulthood, organized by complex hormonal signaling within the neuroendocrine system. The hypothalamus, a central region in this system, regulates pubertal functions through the hypothalamic-pituitary-gonadal (HPG) axis. Gonadotropin-releasing hormone (GnRH) neurons, essential in puberty control, release GnRH in a pulsatile manner, initiating the production of sex hormones. Major influence in pubertal timing has been attributed to genetic predisposition, environmental factors, and nutritional status. MicroRNAs (miRNAs), small non-coding RNA molecules, have emerged as key regulators in various cellular processes by either repressing genes or activating them by inhibiting their repressors. The present study aims to investigate the involvement of miRNAs in the control of puberty. Small RNA sequencing was used to identify and compare the total population of miRNAs in the hypothalamus of female mice before, during and after puberty. Bioinformatic analysis was applied to analyse the expression profile of miRNAs with altered levels followed by pathway enrichment analysis. Expression levels of several miRNAs were found up- or down-regulated from pre-pubertal to pubertal stage. Furthermore, monitoring the levels of these miRNAs at the post-pubertal stage revealed four expression patterns, in which pathway analysis displayed the associations of these miRNAs with developmental processes, cell cycle regulation, metabolic biosynthesis and epigenetic regulation. The findings of the present study improve our understanding of the molecular pathways underlying puberty and stress the significance of miRNAs in fine-tuning gene expression within the hypothalamus during this critical developmental stage.

Expression Profile of MicroRNAs in Breast Milk of Women With Inflammatory Bowel Disease: Correlation With Disease Activity and Medical Treatments.

Although most inflammatory bowel disease (IBD) medications are considered safe during pregnancy, their impact on microRNAs (miRNAs) in breast milk is largely unknown. MiRNAs in milk, carried by milk-derived extracellular vesicles (MDEs), are transmitted to the newborn's gut to regulate genes. Aberrant miRNA expression profiles have been found in IBD within tissue, blood, and feces, but data on mother's milk are scarce. We collected breast milk samples from 32 mothers with Crohn's disease (CD), 14 mothers with ulcerative colitis (UC), and 44 healthy controls. We analyzed miRNA expression through qualitative real-time polymerase chain reaction and Affymetrix miRNA chips. Target genes of differentially expressed miRNAs were predicted using miRATBase. Statistical analyses were conducted using GraphPad Prism software with Mann-Whitney tests. Milk-derived extracellular vesicles from mothers with IBD showed altered miRNA profiles compared to controls. Specifically, miR-21 and miR-320 were downregulated, while Let-7a was upregulated in IBD mothers. The expression patterns varied between CD and UC, with significantly lower MiR-21 in UC and higher Let-7a in CD. Additionally, anti-tumor necrosis factor treatment during pregnancy was associated with reduced miR-21 and miR-148a levels in MDEs. Pathway analysis revealed that these miRNAs are involved in immune regulation, particularly interleukin signaling pathways. This study highlights that miRNAs in breast milk are differentially expressed in mothers with IBD, influenced by the disease and its treatments. These findings emphasize the impact of maternal health on milk composition and potential implications for infant immune development. Understanding these findings may guide personalized treatment strategies for mothers and promote breastfeeding among mothers with IBD.

Identification of key miRNAs and target genes in extracellular vesicles derived from low-intensity pulsed ultrasound-treated stem cells

ObjectivesThis study aimed to investigate the impact of low-intensity pulsed ultrasound (LIPUS) treatment on the miRNA and mRNA profiles of stem cell-derived extracellular vesicles (EVs). Specifically, it sought to identify key miRNAs and their target mRNAs associated with enhanced therapeutic efficacy in LIPUS-treated stem cell-derived EVs.MethodsUtilizing miRNA deep-sequencing data from the Gene Expression Omnibus database, differential gene analysis was performed. MiRNA-mRNA target analysis, functional and pathway enrichment analysis, protein-protein interaction network construction, and hub gene identification were conducted. Validation of differentially expressed miRNAs was performed via RT-qPCR in human umbilical cord mesenchymal stem cells (hUC-MSCs) treated with LIPUS.ResultsTen differentially expressed miRNAs were identified, with six upregulated and four downregulated miRNAs in LIPUS-treated stem cell-derived EVs. Functional enrichment analysis revealed involvement in biological processes such as regulation of metabolic processes, cellular component organization, and response to stress, as well as signaling pathways like cell cycle, MAPK signaling, and Hippo signaling. Protein-protein interaction network analysis identified key hub genes including MYC, GAPDH, HSP90AA1, EP300, JUN, PTEN, DAC1, STAT3, HSPA8, and HIF1A associated with LIPUS treatment. RT-qPCR validation confirmed differential expression of selected miRNAs (hsa-miR-933, hsa-miR-3943, hsa-miR-4633-5p, hsa-miR-592, hsa-miR-659-5p, hsa-miR-4766-3p) in LIPUS-treated hUC-MSCs.ConclusionThis study sheds light on the potential therapeutic mechanisms underlying LIPUS-treated stem cell-derived EVs. The identified differentially expressed miRNAs and their potential target mRNAs offer valuable insights into the biological processes influenced by LIPUS treatment. While further investigation is necessary to validate their roles as therapeutic targets, this study lays the groundwork for future research on optimizing SC-EV therapy with LIPUS preconditioning.

MicroRNAs signatures as potential molecular markers in mild cognitive impairment: a meta-analysis

Mild cognitive impairment (MCI) is characterized by a decline in cognitive functioning without significant interference in daily activities. Its high heterogeneity and elevated conversion rate to dementia pose challenges for accurate diagnosis and monitoring, highlighting the urgent need to identify methodologies focused on the early detection and intervention of MCI. Due to their biological characteristics, microRNAs (miRNAs) are potential candidates as non-invasive molecular markers for the identification and assessment of MCI progression. Therefore, in this study, we conducted a meta-analysis to identify the miRNAs commonly deregulated in MCI, focusing on expression profiles in plasma, serum, and extracellular vesicle samples. Our analysis identified eight upregulated miRNAs, including hsa-miR-149-3p, and four downregulated miRNAs, such as Let-7f-5p. Notably, hsa-miR-149-3p emerged as a central node in interaction networks, suggesting its crucial role in regulating cellular processes relevant to MCI. Additionally, pathway analysis revealed significant enrichment in biological processes associated with transcriptional regulation and neurodegeneration. Our results underscore the potential of circulating miRNAs as non-invasive molecular markers for MCI and open the possibility for new methodologies that enable more accurate diagnosis and monitoring of disease progression. Validating the expression of miRNAs such as hsa-miR-149-3p and Let-7f-5p, along with identifying their functional role in the specific context of MCI, is essential to establish their biological relevance. This work contributes to the understanding of the miRNA profile in mild cognitive impairment using easily accessible samples, which could be useful for the development of various strategies aimed at preventing or delaying MCI in individuals at risk of developing dementia, including Alzheimer’s disease.

Characterizing Circulating microRNA Signatures of Type 2 Diabetes Subtypes.

Type 2 diabetes (T2D) is a heterogeneous disease influenced by both genetic and environmental factors. Recent studies suggest that T2D subtypes may exhibit distinct gene expression profiles. In this study, we aimed to identify T2D cluster-specific miRNA expression signatures for the previously reported five clinical subtypes that characterize the underlying pathophysiology of long-standing T2D: severe insulin-resistant diabetes (SIRD), severe insulin-deficient diabetes (SIDD), mild age-related diabetes (MARD), mild obesity-related diabetes (MOD), and mild early-onset diabetes (MEOD). We analyzed the circulating microRNAs (miRNAs) in 45 subjects representing the five T2D clusters and 7 non-T2D healthy controls by single-end small RNA sequencing. Bioinformatic analyses identified a total of 430 known circulating miRNAs and 13 previously unreported novel miRNAs. Of these, 71 were upregulated and 37 were downregulated in either controls or individual clusters. Each T2D subtype was associated with a specific dysregulated miRNA profile, distinct from that of healthy controls. Specifically, 3 upregulated miRNAs were unique to SIRD, 1 to MARD, 9 to MOD, and 18 to MEOD. Among the downregulated miRNAs, 11 were specific to SIRD, 9 to SIDD, 2 to MARD, and 1 to MEOD. Our study confirms the heterogeneity of T2D, represented by distinguishable subtypes both clinically and epigenetically and highlights the potential of miRNAs as markers for distinguishing the pathophysiology of T2D subtypes.

Clinical-grade extracellular vesicles derived from umbilical cord mesenchymal stromal cells: preclinical development and first-in-human intra-articular validation as therapeutics for knee osteoarthritis

Osteoarthritis (OA) is a joint disease characterized by articular cartilage degradation. Persistent low-grade inflammation defines OA pathogenesis, with crucial involvement of pro-inflammatory M1-like macrophages. While mesenchymal stromal cells (MSC) and their small extracellular vesicles (sEV) hold promise for OA treatment, achieving consistent clinical-grade sEV products remains a significant challenge. This study aims to develop fully characterized, reproducible, clinical-grade batches of sEV derived from umbilical cord (UC)-MSC for the treatment of OA while assessing its efficacy and safety. Initially, a standardized, research-grade manufacturing protocol was established to ensure consistent sEV production. UC-MSC-sEV characterization under non-cGMP conditions showed consistent miRNA and protein profiles, suggesting their potential for standardized manufacturing. In vitro studies evaluated the efficacy, safety, and potency of sEV; animal studies confirmed their effectiveness and safety. In vitro, UC-MSC-sEV polarized macrophages to an anti-inflammatory M2b-like phenotype, through STAT1 modulation, indicating their potential to create an anti-inflammatory environment in the affected joints. In silico studies confirmed sEV's immunosuppressive signature through miRNA and proteome analysis. In an OA mouse model, sEV injected intra-articularly (IA) induced hyaline cartilage regeneration, validated by histological and μCT analyses. The unique detection of sEV signals within the knee joint over time highlights its safety profile by confirming the retention of sEV in the joint. The product development of UC-MSC-sEV involved refining, standardizing, and validating processes in compliance with GMP standards. The initial assessment of the safety of the clinical-grade product via IA administration in a first-in-human study showed no adverse effects after a 12 month follow-up period. These results support the progress of this sEV-based therapy in an early-phase clinical trial, the details of which are presented and discussed in this work. This study provides data on using UC-MSC-sEV as local therapy for OA, highlighting their regenerative and anti-inflammatory properties and safety in preclinical and a proof-of-principle clinical application.Graphical

MicroRNA Profiling in Chronic Limb-Threatening Ischemia Their Role in Arteriogenesis

AbstractChronic limb-threatening ischemia (CLTI) represents poses a substantial threat with escalating mortality and amputation rates. Despite the existence of various clinical techniques for diagnosing CLTI, the role of microRNAs (miRNAs) in arteriogenesis remains ambiguous. Comprehensive knowledge on miRNAs may facilitate the advancement of targeted therapy pertaining to the enhancement of collateral blood flow in obstructed vessels. Therefore, this study aimed at analyzing arteriogenesis-associated plasma miRNA profiles in patients with CLTI using gene expression. Samples were acquired from the collateral arteries (CA group, n = 3) and the contralateral healthy limb (healthy artery; HA group, n = 3) of a single set of patients with CLTI. The RNA extracted from the samples was assessed for concentration and purity. A normalization factor was used to address variations in analyte abundance and/or quality across the samples. Subsequently, individual RNA molecules were directly quantified and subjected to comparative analysis between the CA and HA groups to identify the miRNAs involved in arteriogenesis. The five arteriogenesis-related miRNAs exhibiting maximum upregulation were miR-301b–3p, miR-221–5p, miR–639, miR-34a–5p, and let-7a–5p, while the five most downregulated miRNAs included miR-151a–5p, miR-371a–5p, miR-651–5p, miR-510–5p, and miR-660–5p. Summarily, this study documented marked upregulation and downregulation of miRNAs associated with arteriogenesis in the collateral arteries of patients with CLTI as compared with their contralateral healthy limbs. Possible mechanisms involved, including the regulation of YAP/TAZ pathway, TGFBR3 mRNA, SIRT1 expression, and other processes have shown to be modulated by miRNAs fluctuations.

Circulating MicroRNAs in Patients with Psoriasis Treated with Anti-IL-23: A Cohort Study.

Psoriasis is characterized by aberrant keratinocyte activity and immune cell infiltration, driven by immune-mediated pathways. MicroRNAs (miRNAs) play crucial roles in regulating these processes, offering insights into disease mechanisms and therapeutic targets. This study aimed to investigate changes in circulating miRNAs in psoriasis patients undergoing risankizumab therapy, an anti-IL-23 monoclonal antibody, to understand its impact on disease pathogenesis and treatment response. Plasma samples from 12 psoriasis patients were collected before (T0) and after 1year (T1) of risankizumab treatment and analyzed using small RNA sequencing. Findings were validated in a separate cohort of 23 patients using quantitative real-time PCR (qRT-PCR). T-regulatory cell (Treg) numbers and pro-inflammatory cytokine levels were also assessed. Significant clinical improvement was observed in all patients after 1year of treatment, accompanied by increased Treg counts and reduced levels of pro-inflammatory cytokines. Twenty-four miRNAs exhibited differential expression post-treatment; 9 were downregulated and 15 upregulated. Notably, miR-200a-3p showed a significant correlation with baseline Psoriasis Area Severity Index (PASI), indicating its potential as a severity marker. Risankizumab therapy also decreased peripheral blood levels of IL-23, IL-1β, and IL-8. This study identifies specific circulating miRNAs, including miR-200a-3p, as potential biomarkers for monitoring treatment responses in psoriasis patients. The findings underscore the therapeutic efficacy of risankizumab in modulating miRNA profiles and immune pathways associated with psoriasis pathogenesis. Overall, these results provide new insights into the mechanisms of risankizumab action and highlight miRNAs as promising candidates for personalized medicine approaches in psoriasis management.

Integrated analysis of miRNAs and mRNAs in thousands of single cells

The simultaneous sequencing of multiple types of biomolecules can facilitate understanding various forms of regulation occurring in cells. Cosequencing of miRNA and mRNA at single-cell resolution is challenging, and to date, only a few such studies (examining a quite limited number of cells) have been reported. Here, we developed a parallel single-cell small RNA and mRNA coprofiling method (PSCSR-seq V2) that enables miRNA and mRNA coexpression analysis in many cells. The PSCSR-seq V2 method is highly sensitive for miRNA analysis, and it also provides rich mRNA information about the examined cells at the same time. We employed PSCSR-seq V2 to profile miRNA and mRNA in 2310 cultured cells, and detected an average of 181 miRNA species and 7354 mRNA species per cell. An integrated analysis of miRNA and mRNA profiles linked miRNA functions with the negative regulation of tumor suppressor and reprogramming of cellular metabolism. We coprofiled miRNA and mRNA in 9403 lung cells and generated a coexpression atlas for known cell populations in mouse lungs, and detected conserved expression patterns of miRNAs among lineage-related cells. Based on this information, we identified informative age-associated miRNAs in mouse and human lung cells including miR-29, which can be understood as a conserved marker for immunosenescence. PSCSR-seq V2 offers unique functionality to users conducting functional studies of miRNAs in clinical and basic biological research.

Prenatal maternal stress in rats alters the epigenetic and transcriptomic landscape of the maternal-fetal interface across four generations

Prenatal maternal stress (PNMS) determines lifetime mental and physical health. Here, we show in rats that PNMS has consequences for placental function and fetal brain development across four generations (F0-F3). Using a systems biology approach, comprehensive DNA methylation (DNAm), miRNA, and mRNA profiling revealed a moderate impact of PNMS in the F1 generation, but drastic changes in F2 and F3 generations, suggesting compounding effects of PNMS with each successive generation. Both maternal and placental miRNA gene targets included de novo DNA methyltransferases, indicating robust PNMS-induced disruption in the complex epigenetic regulatory network between miRNAs and DNAm. Transgenerational programming mainly involved genes and biological pathways associated with neurological and psychiatric diseases which were linked to maternal-fetal crosstalk facilitated by the placenta. The highly correlated placenta-brain profiles support the use of placenta as a noninvasive biomarker resource to predict pathological changes in the neonatal brain. The transgenerational persistence of critical DNAm, miRNA and mRNA signatures may explain familial non-genetic disease risks.

Micro-RNA 451-a as a Circulating Biomarker for Neuroblastoma.

Micro ribonucleic acids (miRNAs) are small non-coding RNAs that modulate the expression of various genes. They have an important role in cancer pathogenesis. Differential expression of multiple miRNAs have been used as potential diagnostic and prognostic markers. Various cancers have lately been employed as therapeutic targets. This prospective study included untreated pediatric neuroblastoma (NB) patients. In the discovery phase, global miRNA profiling was done using next-generation sequencing (NGS) on biopsy tissue samples of NB patients. In this phase, the top expressing miRNA was identified and chosen for further validation as circulating miRNA in blood samples of a different set of NB patients by real-time polymerase chain reaction (PCR). Based on the read counts on the global miRNA profiling in the discovery phase, we found that the miRNA that consistently had high reads across the majority of the NB samples were miRNA 451-a, 19b-3p, 106b-5p, and 21-5p. Of these, we selected miRNA 451-a and 19-b for the validation phase of the study as they had consistent overexpression. In the validation phase, the expression of the circulating miRNA 451-a in the blood was found to be higher. The average value for the relative fold (RF) expression for miRNA 451-a was 1.52. miRNA 451-a is overexpressed both in the cancer tissue and the blood of NB patients. It can serve as a potential diagnostic marker. Further studies can elucidate its role in the pathogenesis of NB and it can have utility as a therapeutic target.

Genome-Wide microRNA Expression Profiling in Human Spermatozoa and Its Relation to Sperm Quality.

Sperm samples are separated into bad and good quality samples in function of their phenotype, but this does not indicate their genetic quality. Here, we used GeneChip miRNA arrays to analyze microRNA expression in ten semen samples selected based on high-magnification morphology (score 6 vs. score 0) to identify miRNAs linked to sperm phenotype. We found 86 upregulated and 21 downregulated miRNAs in good-quality sperm (score 6) compared with bad-quality sperm samples (score 0) (fold change > 2 and p-value < 0.05). MiR-34 (FC × 30, p = 8.43 × 10-8), miR-30 (FC × 12, p = 3.75 × 10-6), miR-122 (FC × 8, p = 0.0031), miR-20 (FC × 5.6, p = 0.0223), miR-182 (FC × 4.83, p = 0.0008) and miR-191 (FC × 4, p = 1.61 × 10-6) were among these upregulated miRNAs. In silico prediction algorithms predicted that miRNAs upregulated in good-quality sperm targeted 910 genes involved in key biological functions of spermatozoa, such as cell death and survival, cellular movement, molecular transport, response to stimuli, metabolism, and the regulation of oxidative stress. Genes deregulated in bad-quality sperm were involved in cell growth and proliferation. This study reveals that miRNA profiling may provide potential biomarkers of sperm quality.