Idiopathic recurrent pericarditis (IRP) is a rare autoinflammatory disorder characterized by NLRP3 inflammasome overactivation, resulting in excessive IL-1β and IL-1α production. Although IL-1 blockade shows promise as a therapeutic strategy, the underlying molecular mechanisms remain incompletely understood. We investigated the effect of goflikicept, a novel heterodimeric fusion protein that inhibits both IL-1β and IL-1α, on peripheral blood mononuclear cell (PBMC) transcriptomes from patients with IRP. Single-cell RNA sequencing was used to analyze PBMC subsets and identify treatment response-related transcriptomic signatures. Goflikicept induced temporal transcriptional reprogramming, with a particularly pronounced downregulation of IL-1-related inflammatory pathways in classical monocytes by day 35 of treatment. Furthermore, goflikicept modulated the adaptive immune response, suppressing naïve B cell activity, enhancing circulating plasma cell precursor activity, and significantly altering γδ T cell and mucosal-associated invariant T cell populations. In conclusion, goflikicept effectively normalized dysregulated immune responses in IRP, suggesting a novel therapeutic approach for NLRP3-mediated diseases. This study provides the first single-cell resolution insights into the molecular mechanisms of IL-1 blockade, informing the development of targeted therapies for autoinflammatory conditions.

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair protein. It is a member of the phospholipase D family based on structural similarity. TDP1 is a key enzyme of the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, with the CRISPR/Cas9 method, we obtained HEK293A cells with a homozygous knockout of the TDP1 gene and used the TDP1 knockout cells as a cellular model for studying mechanisms of action of an anticancer therapy. In the present work, we hypothesized that the TDP1 knockout would alter the expression of DNA repair-related genes. By transcriptomic analysis, we investigated for the first time the effect of the TDP1 gene knockout on genes' expression changes in the human HEK293A cell line. We obtained original data implying a role of TDP1 in other processes besides the repair of the DNA-TOP1 complex. Differentially expressed gene analysis revealed that TDP1 may participate in cell adhesion and communication, spermatogenesis, mitochondrial function, neurodegeneration, a cytokine response, and the MAPK signaling pathway.

Introduction Modification of natural enzymes to introduce new properties and enhance existing ones is a central challenge in bioengineering. This study is focused on the development of Taq polymerase mutants that show enhanced reverse transcriptase (RTase) activity while retaining other desirable properties such as fidelity, 5 '- 3 ' exonuclease activity, effective deoxyuracyl incorporation, and tolerance to locked nucleic acid (LNA)-containing substrates. Our objective was to use AI-driven rational design combined with multiparametric wet-lab analysis to identify and validate Taq polymerase mutants with an optimal combination of these properties.Methods The experimental procedure was conducted in several stages: 1) On the basis of a foundational paper, we selected 18 candidate mutations known to affect RTase activity across six sites. These candidates, along with the wild type, were assessed in the wet lab for multiple properties to establish an initial training dataset. 2) Using embeddings of Taq polymerase variants generated by a protein language model, we trained a Ridge regression model to predict multiple enzyme properties. This model guided the selection of 14 new candidates for experimental validation, expanding the dataset for further refinement. 3) To better manage risk by assessing confidence intervals on predictions, we transitioned to Gaussian process regression and trained this model on an expanded dataset comprising 33 data points. 4) With this enhanced model, we conducted an in silico screen of over 18 million potential mutations, narrowing the field to 16 top candidates for comprehensive wet-lab evaluation.Results and Discussion This iterative, data-driven strategy ultimately led to the identification of 18 enzyme variants that exhibited markedly improved RTase activity while maintaining a favorable balance of other key properties. These enhancements were generally accompanied by lower Kd, moderately reduced fidelity, and greater tolerance to noncanonical substrates, thereby illustrating a strong interdependence among these traits. Several enzymes validated via this procedure were effective in single-enzyme real-time reverse-transcription PCR setups, implying their utility for the development of new tools for real-time reverse-transcription PCR technologies, such as pathogen RNA detection and gene expression analysis. This study illustrates how AI can be effectively integrated with experimental bioengineering to enhance enzyme functionality systematically. Our approach offers a robust framework for designing enzyme mutants tailored to specific biotechnological applications. The results of our biological activity predictions for mutated Taq polymerases can be accessed at https://huggingface.co/datasets/nerusskikh/taqpol_insilico_dms

Background: Cardiovascular disease had a global prevalence of 523 million cases and 18.6 million deaths in 2019. The current standard for diagnosing coronary artery disease (CAD) is coronary angiography either by invasive catheterization (ICA) or computed tomography (CTA). Prior studies employed single-molecule, amplification-independent RNA sequencing of whole blood to identify an RNA signature in patients with angiographically confirmed CAD. The present studies employed Illumina RNAseq and network co-expression analysis to identify systematic changes underlying CAD. Methods: Whole blood RNA was depleted of ribosomal RNA (rRNA) and analyzed by Illumina total RNA sequencing (RNAseq) to identify transcripts associated with CAD in 177 patients presenting for elective invasive coronary catheterization. The resulting transcript counts were compared between groups to identify differentially expressed genes (DEGs) and to identify patterns of changes through whole genome co-expression network analysis (WGCNA). Results: The correlation between Illumina amplified RNAseq and the prior SeqLL unamplified RNAseq was quite strong (r = 0.87), but there was only 9% overlap in the DEGs identified. Consistent with the prior RNAseq, the majority (93 %) of DEGs were down-regulated similar to 1.7-fold in patients with moderate to severe CAD (>20% stenosis). DEGs were predominantly related to T cells, consistent with known reductions in Tregs in CAD. Network analysis did not identify preexisting modules with a strong association with CAD, but patterns of T cell dysregulation were evident. DEGs were enriched for transcripts associated with ciliary and synaptic transcripts, consistent with changes in the immune synapse of developing T cells. Conclusions: These studies confirm and extend a novel mRNA signature of a Treg-like defect in CAD. The pattern of changes is consistent with stress-related changes in the maturation of T and Treg cells, possibly due to changes in the immune synapse.

Abstract Background Cardiovascular disease had a global prevalence of 523 million cases and 18.6 million deaths in 2019. The current standard for diagnosing coronary artery disease (CAD) is coronary angiography. Surprisingly, despite well-established clinical indications, up to 40% of the one million invasive cardiac catheterizations return a result of ‘no blockage’. The present studies employed RNA sequencing of whole blood to identify an RNA signature in patients with angiographically confirmed CAD. Methods Whole blood RNA was depleted of ribosomal RNA (rRNA) and analyzed by single-molecule sequencing of RNA (RNAseq) to identify transcripts associated with CAD (TRACs) in a discovery group of 96 patients presenting for elective coronary catheterization. The resulting transcript counts were compared between groups to identify differentially expressed genes (DEGs). Results Surprisingly, 98% of DEGs/TRACs were down-regulated ~ 1.7-fold in patients with mild to severe CAD (> 20% stenosis). The TRACs were independent of comorbid risk factors for CAD, such as sex, hypertension, and smoking. Bioinformatic analysis identified an enrichment in transcripts such as FoxP1, ICOSLG, IKZF4/Eos, SMYD3, TRIM28, and TCF3/E2A that are likely markers of regulatory T cells (Treg), consistent with known reductions in Tregs in CAD. A validation cohort of 80 patients confirmed the overall pattern (92% down-regulation) and supported many of the Treg-related changes. TRACs were enriched for transcripts associated with stress granules, which sequester RNAs, and ciliary and synaptic transcripts, possibly consistent with changes in the immune synapse of developing T cells. Conclusions These studies identify a novel mRNA signature of a Treg-like defect in CAD patients and provides a blueprint for a diagnostic test for CAD. The pattern of changes is consistent with stress-related changes in the maturation of T and Treg cells, possibly due to changes in the immune synapse.

Introduction: The restless legs syndrome (RLS) is a common heritable neurologic disorder which is characterized by an irresistible desire to move and unpleasant sensations in the legs. Methods: We aim to identify new variants associated with RLS by performing genome-wide linkage and subsequent association analysis of forty member's family with history of RLS. Results: We found evidence of linkage for three loci 7q21.11 (HLOD = 3.02), 7q21.13-7q21.3 (HLOD = 3.02) and 7q22.3 (HLOD = 3.09). Fine-mapping of those regions in association study using exome sequencing identified SEMA3A (p-value = 8.5.10(-)(4)), PPP1R9A (p-value = 7.2.10(-4)), PUS7 (p-value = 8.7.10(-4)), CDHR3 (p-value = 7.2.10(-4)), HBP1 (p-value = 1.5.10(-4)) and COGS (p-value = 1.5.10(-4)) genes with p-values below significance threshold. Conclusion: Linkage analysis with subsequent association study of exome variants identified six new genes associated with RLS mapped on 7q21 and q22.

This dataset contains the following tables:ST1 - original_expression.csv -- original raw gene expression counts from scRNA-Seq experiments from DOI: 10.1016/j.cell.2018.02.001 (https://figshare.com/articles/MCA_DGE_Data/5435866) -- only mammary gland samples were used hereST2 - transfer_annotation.csv -- the table with samples annotation (both original and those obtained with style transfer)ST3 - reconstructed_expression.csv -- gene expression values of original samples obtained with our VAE modelST4 - transferred_expression.csv -- semisynthetic samples obtained with style transferSF1 - model training pseudocode

MOTIVATION:The transcriptomic data are being frequently used in the research of biomarker genes of different diseases and biological states. The most common tasks there are the data harmonization and treatment outcome prediction. Both of them can be addressed via the style transfer approach. Either technical factors or any biological details about the samples which we would like to control (gender, biological state, treatment, etc.) can be used as style components.RESULTS:The proposed style transfer solution is based on Conditional Variational Autoencoders, Y-Autoencoders and adversarial feature decomposition. To quantitatively measure the quality of the style transfer, neural network classifiers which predict the style and semantics after training on real expression were used. Comparison with several existing style-transfer based approaches shows that proposed model has the highest style prediction accuracy on all considered datasets while having comparable or the best semantics prediction accuracy.AVAILABILITY AND IMPLEMENTATION:https://github.com/NRshka/stvae-source.SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

In vitro cellular models are promising tools for studying normal and pathological conditions. One of their important applications is the development of genetically engineered biosensor systems to investigate, in real time, the processes occurring in living cells. At present, there are fluorescence, protein-based, sensory systems for detecting various substances in living cells (for example, hydrogen peroxide, ATP, Ca2+ etc.,) or for detecting processes such as endoplasmic reticulum stress. Such systems help to study the mechanisms underlying the pathogenic processes and diseases and to screen for potential therapeutic compounds. It is also necessary to develop new tools for the processing and analysis of obtained microimages. Here, we present our web-application CellCountCV for automation of microscopic cell images analysis, which is based on fully convolutional deep neural networks. This approach can efficiently deal with non-convex overlapping objects, that are virtually inseparable with conventional image processing methods. The cell counts predicted with CellCountCV were very close to expert estimates (the average error rate was < 4%). CellCountCV was used to analyze large series of microscopic images obtained in experimental studies and it was able to demonstrate endoplasmic reticulum stress development and to catch the dose-dependent effect of tunicamycin.

Проанализированы данные полногеномного секвенирования более 1200 образцов пациентов с диффузной В-крупноклеточной лимфомой (ДВККЛ) базы CBioPortal for Cancer Genomics. Также выполнено собственное полноэкзомное секвенирование 7 образцов ДВККЛ с рецидивами в ЦНС. Выделены характеристики, ассоциированные с высоким риском вторичного вовлечения ЦНС при лимфоме. Значимые различия в частоте мутаций между подвыборками с поражением ЦНС в рецидиве и без вовлечения ЦНС были получены по генам BCR/NF-kВ пути (MYD88, CD79B) и системы ремоделирования хроматина (ARID1A, SMARCA4). The genome-wide sequencing data of more than 1200 Diffuse Large B-cell Lymphomas (DLBCL) samples of the CBioPortal database for Genomic cancer were analyzed. We also performed our own full-exome sequencing of 7 samples of DLBCL with relapses in the central nervous system (CNS). Characteristics associated with a high level of secondary CNS involvement in lymphoma were selected. Differences were obtained in the BCR/NF-kB genotypes (MYD88, CD79B) and chromatin remodeling system (ARID1A, SMARCA4).

Generation of patient-specific induced pluripotent stem cells (iPSCs) and their subsequent differentiation into cardiomyocytes opened new opportunities for studying pathogenesis of inherited cardiovascular diseases. One of these diseases is hypertrophic cardiomyopathy (HCM) for which no efficient therapy methods have been developed so far. In this study, the approach based on patient-specific iPSCs was applied to create a model of the disease. Genetic analysis of a hypertrophic cardiomyopathy patient revealed R326Q mutation in the MYBPC3 gene. iPSCs of the patient were generated and characterized. The cells were differentiated into cardiomyocytes together with the control iPSCs from a healthy donor. The patient's iPSC-derived cardiomyocytes exhibited early HCM features, such as abnormal calcium handling and increased intracellular calcium concentration. Therefore, cardiomyocytes obtained by directed differentiation of iPSCs from the HCM patient can be used as a model system to study HCM pathogenesis.

The hydrocephalus can be either an independent disease or a concomitant symptom of a number of pathologies, therefore representing an urgent issue in the present-day clinical practice. Deep Learning is an evolving technology and the part of a broader field of Machine Learning. Deep learning is currently actively researched in the field of radiology. The aim of this study was to evaluate deep learning applicability to the diagnostics of hydrocephalus with the use of MRI images. We retrospectively collected, annotated, and preprocessed the brain MRI data of 200 patients with and without radiological signs of hydrocephalus. We applied a state-of-the-art deep convolutional neural network in conjunction with transfer learning method to train a hydrocephalus classifier model. Using deep convolutional neural networks, we achieved a high quality of machine learning model. Accuracy, sensitivity, and specificity of hydrocephalus signs identification was 97%, 98%, and 96% respectively. In this study, we demonstrated the capacity of deep neural networks to identify hydrocephalus syndrome using brain MRI images. Applying transfer learning technique, the high quality of classification was achieved although trained on rather limited data.

Reprogramming of somatic cells to a pluripotent state is a complex, multistage process that is regulated by many factors. Among these factors, non-coding RNAs and microRNAs (miRNAs) have been intensively studied in recent years. MiRNAs play an important role in many processes, particularly in cell reprogramming. In this study, we investigated the reprogramming of rat fibroblasts with a deleted locus encoding a cluster comprising 14 miRNAs (from miR-743a to miR-465). The deletion of this locus was demonstrated to decrease significantly the efficiency of the cell reprogramming. In addition, the cells produced by the reprogramming differed from rat embryonic and induced pluripotent stem cells, which was an indication that reprogramming in these cells had not been completed. We suggest that this miRNA cluster or some of its members are involved in regulating the reprogramming of rat cells to a pluripotent state.

Self-renewal of cultured pluripotent stem cells is a complex process, which includes multiple functional and regulatory levels. Transcription factors, their target genes, chromatin modifiers, signaling pathways, and regulatory noncoding RNAs are involved in the maintaining of self-renewal. Studies of molecular and genetic bases of maintaining self-renewal and pluripotency in cultured mammalian cells are important to understand processes in preimplantation embryogenesis and to develop efficient techniques to obtain pluripotent stem cell lines for experimental biology and medicine. MicroRNAs (miRNAs) play an important role in pluripotency maintaining and reprogramming. However, involvement of this class of noncoding RNAs and functions of individual molecules are poorly studied. The goal of this study was the search for the miRNAs potentially involved in the pluripotency maintaining and reprogramming of Rattus norvegicus cells. We analyzed the expression of miRNAs in rat embryonic stem cells, induced pluripotent stem cells and embryonic fibroblasts using bioinformatic methods and data obtained with next generation sequencing. The analysis of differential expression between groups of rat pluripotent cells and fibroblasts, and the analysis of experimentally confirmed target genes of differentially expressed known rat miRNAs revealed novel potential players of pluripotency maintaining and reprogramming processes. In addition, novel members of these processes were revealed among novel rat miRNAs. The use of bioinformatic and systems biology approaches is the first step, which is necessary for choosing candidates for the subsequent experimental studies. The results obtained substantially improve our understanding of the self-renewal regulation system of the laboratory rat, a popular biomedical object, and our knowledge about the system in mammals.

Background Anti-inflammatory agents are used widely in treating numerous pain and inflammatory conditions. With a focus on the COX/LOX pathways in cutaneous wound repair in mice, the therapeutic activities of Tr14 (Traumeel), a multicomponent/multitarget natural product, and diclofenac (NSAID), a non-selective cyclooxygenase (COX) inhibitor were compared. The COX enzymes convert arachidonic acid into prostaglandins and thromboxanes, while the lipoxygenase (LOX) pathway generates more pro-inflammatory leukotrienes. Differential effects were identified via transcriptome analysis (RNAseq). Objectives To compare the transcriptomic changes after administration of Tr14 or diclofenac in a mouse cutaneous wound healing model, with particular emphasis on the COX/LOX pathway. Methods After abrasive wounding, the wounds were treated with topical Tr14 (34 mg/ml) in combination with subcutaneous Tr14 injections (9.5 mg/ml), or with subcutaneous Tr14 injections only, or topical diclofenac at clinically relevant doses (2 mg/ml). Skin samples were analysed for RNA transcript profiling by RNAseq at specific times (12 hour, 24 hour, 36 hour, 72 hour, 96 hour, 120 hour, 192 hour) after injury. Differentially expressed genes (DEGs) were computed at each time point between diclofenac vs control or Tr14 vs control, using EdgeR. Results At early time points (12–36 hour), both control and Tr14-treated wounds showed marked increase in the inducible COX2 enzyme mRNA, while diclofenac-treated wounds did not, likely due to blocking the PGE2 necessary for the feedback induction. Tr14, in contrast, had a striking inhibitory effect on mRNA levels for leukotriene A4 hydrolase, which converts LTA4 to LTB4; microsomal glutathione S-transferase, which converts LTA4 to LTC4; and gamma-glutamyltransferase (LTC4 u003eLTD4). In contrast, Tr14, but not diclofenac strongly induced Nrf2 mRNA at 12–36 hours. Conclusions Tr14 and diclofenac had very different effects on the COX/LOX synthetic pathway after cutaneous wounding. Tr14 allowed normal autoinduction of COX2 mRNA by PGE2, but suppressed mRNA levels for the key enzymes in the leukotriene synthetic pathway. A likely explanation for these effects is that Tr14 strongly induced Nrf2 mRNA, which is known to co-repress the leukotriene enzymes via transcription factor Bach1. Disclosure of Interest None declared

Aim of the study. Aim of the study was to estimate the occurrence of pathogenic mutations in the BRCA1 gene in Russian breast cancer patients.Material and methods. Complete coding sequence of the BRCA1 gene of 445 early onset breast cancer patients (under 40 years) from Novosibirsk region (Russia) were analyzed by targeted Next Generation Sequencing (NGS) using Ion Torrent platform. Results. Forty (9%) carriers of various pathogenic mutations were revealed. Thirty five (7,9%) patients carried 5382insC mutation, described earlier as a founder mutation for Slavic population. Five (1.1%) patients carried various pathogenic mutations, namely C61G, 462delCC, E143X, 4153delA, and IVS18+1G>T. Besides, 29 genetic variants with no clinical significance or with unknown clinical significance were detected in BRCA1 gene among 445 early onset breast cancer patients. Conclusions. Data on the frequency of genetic variations in the BRCA1 gene among early onset breast cancer patients in the Novosibirsk Region (Russia) were obtained. Proportion of the 5382insC mutation is 87.5% of all pathogenic mutations in the BRCA1 gene found in patients.

Background Anti-inflammatory agents are used widely in treating numerous pain and inflammatory conditions. With a focus on the specialised pro-resolving mediators (SPM) pathways in cutaneous wound repair in mice, the therapeutic activities of Tr14 (Traumeel), a multicomponent/multitarget natural product, and diclofenac (NSAID), a non-selective cyclooxygenase (COX) inhibitor were compared. COX inhibitors can block the synthesis of prostaglandins and thromboxanes from arachidonic acid, and can have important effects on the synthesis of resolvins and protectins produced by similar enzymes from eicosopentanoic and docosohexanoic acid substrates. Differential effects were identified via transcriptome analysis (RNAseq). Objectives To compare the transcriptomic changes after administration of Tr14 or diclofenac in a mouse cutaneous wound healing model, with particular emphasis on the SPM pathways, which include resolvins and protectins. Methods After abrasive wounding, the wounds were treated with topical Tr14 (34 mg/ml) in combination with subcutaneous Tr14 injections (9.5 mg/ml), or with subcutaneous Tr14 injections only, or topical diclofenac at clinically relevant doses (2 mg/ml). Skin samples were analysed for RNA transcript profiling by RNAseq at specific times (12 hour, 24 hour, 36 hour, 72 hour, 96 hour, 120 hour, 192 hour) after injury. Differentially expressed genes (DEGs) were computed at each time point between diclofenac vs control or Tr14 vs control, using EdgeR. Results At early time points (12–36 hour), Tr14-treated wounds, and to a lesser extent diclofenac-treated wounds, showed marked induction of 3 lipoxygenase enzyme mRNAs involved in SPM synthesis. Even more striking was a pronounced effect of Tr14 at 12–36 hours on Fpr1 and Fpr2 mRNAs, which are the transmembrane receptors for the SPM lipid mediators. Consistent with elevated levels of enzymes regulating SPM synthesis, and SPR receptors, there was a noticeable decrease in the mRNA levels of the p65/RelA subunit of NFkB at 72–96 hours. NFkB is a critical transcription factor in inflammation, regulating numerous cytokines and chemokines. Conclusions Tr14 and diclofenac had very different effects on the SPM synthetic pathway after cutaneous wounding. Tr14 stimulated mRNA levels of several key regulators of SPM synthesis, and had a marked effect on the mRNA levels of the SPM receptors. Tr14, not diclofenac, suppressed mRNA levels for NFkB subunit p65/RelA, which may explain some of the anti-inflammatory and proresolving properties of Tr14. Disclosure of Interest None declared

Background Anti-inflammatory agents are used widely in treating numerous inflammatory conditions. The effect of Tr14, a multitargeted natural product, was compared to diclofenac, a non-selective cyclooxygenase inhibitor, on cutaneous wound repair in mice. Objectives To compare the effect of diclofenac with Tr14 on the transcriptome after cutaneous wounding in the mouse. Methods After abrasive wounding, the wounds were treated with topical Tr14 or diclofenac at clinically relevant doses. An additional group received subcutaneous Tr14 injections. The healing wounds were analyzed for RNA transcript profiling by RNAseq at specific times (12h, 24h, 36h, 72h, 96h, 120h, 196h) after injury. Differentially expressed genes (DEGs) were computed at each time point between diclofenac vs control or Tr14 vs control using EdgeR. Results Across time points, Tr14 treatment modulated a number of transcripts related to key wound repair pathways such as cellular differentiation, wound contraction, and cell mobility. Diclofenac, in contrast, changed gene expression mainly in two areas: Prominent effects were observed with regard to DNA chromatin regulation and ribosomal function, further effects were observed on the prostaglandin pathway and wound repair factors. In many of the key pathways modulated by Tr14, such as the defense response and cell motility, diclofenac tended to have an opposite effect on gene expression. At 12 hours post-injury, there were 521 transcripts significantly elevated and 1027 transcripts that were decreased by diclofenac treatment. By comparison, using a similar number of transcripts altered by Tr14 treatment, only 4 transcripts were increased in common, and 5 transcripts were decreased in common, suggesting that the therapies have different effects on the transcriptome. Conclusions The overall patterns of the Tr14 and diclofenac responses in the transcriptome during wound repair are very different. The Tr14 effect is most pronounced on the defense response, cell motility, and anti-apoptotic pathways. In contrast, diclofenac mainly affected histones and chromatin remodeling systems, as well as ribosomal systems that would be expected to alter the translational pattern of diclofenac-treated cells. Disclosure of Interest G. St. Laurent, III: None declared, B. Seilheimer: None declared, M. Tackett: None declared, J. Zhou: None declared, D. Shtokalo: None declared, Y. Vyatkin: None declared, P. Kapranov: None declared, I. Toma: None declared, T. Mccaffrey Speakers bureau: TM has received speaker9s honorarium from HEEL, GmbH

MicroRNAs (miRNAs) constitute a class of small noncoding RNAs that plays an important role in the post-transcriptional regulation of gene expression. Much evidence has demonstrated that miRNAs are involved in regulating the human and mouse pluripotency. Nevertheless, to our knowledge, miRNAs in the pluripotent stem cells of one of the most commonly used model organisms – the Rattus norvegicus have not been studied. In the present study, we performed deep sequencing of small RNA molecules in the embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells of laboratory rats. Bioinformatics analysis revealed 674 known miRNAs and 394 novel miRNA candidates in all of the samples. Expression of known pluripotency-associated miRNAs, such as the miR-290–295 and miR-183-96-182 clusters as well as members of the miR-200 family, was detected in rat pluripotent stem cells. Analysis of the targets of differentially expressed known and novel miRNAs showed their involvement in the regulation of pluripotency and the reprogramming process in rats. Bioinformatics and systems biology approaches identified potential pathways that are regulated by these miRNAs. This study contributes to our understanding of miRNAs in the regulation of pluripotency and cell reprogramming in the laboratory rat.