MicroRNAs (miRNAs) are single-stranded, endogenous non-coding small RNAs, ranging from 18 to 25 nucleotides in length. MiRNAs are essential in regulating gene expression, cell development, differentiation and function. Dysregulation in miRNAs expression may contribute to the development of autoimmunity. However, a given miRNA may have hundreds of different mRNA targets and a target might be regulated by multiple miRNAs, thus the characterisation of dysregulated miRNA expression profiles could give a better insight into the development of immunological disturbances in autoimmune diseases.
Objectives
The aim of our study was to examine the changes in miRNA expression profiles in patients with primary Sjögren9s syndrome (pSS) and systemic lupus erythematosus (SLE).
Methods
Eight pSS patients, 8 SLE patients and 7 healthy control subjects were enrolled in the investigation. MiRNAs were isolated from peripheral blood mononuclear cells, and expression patterns were determined with Illumina next-generation sequencing technology. Since the immunopathogenesis of pSS and SLE encompasses pronounced B cell hyperactivity along with specific autoantibody production, we paid a special attention on the association between miRNA expression levels and altered peripheral B cell distribution.
Results
In SLE patients 135, while in pSS patients 26 miRNAs showed altered expression. Interestingly, the 25 miRNAs including miR-146a, miR-16 and miR-21, which were over-expressed in pSS patients, were found to be elevated in SLE group, as well. On the contrary, we observed the down-regulation of miR-150–5p, which is a novel and unique finding in pSS. Levels of several miRNAs over-expressed in SLE, were not changed in pSS, such as miR-148a-3p, miR-152, miR-155, miR-223, miR-224, miR-326 and miR-342. Expression levels of miR-223–5p, miR-150–5p, miR-155–5p and miR-342–3p, which miRNAs are potentially linked to B cell functions, showed associations with the B cell proportions within peripheral blood mononuclear cells.
Conclusions
The observed differences in miRNA expression profiles and the better understanding of immune regulatory mechanisms of miRNAs may help to elucidate the pathogenesis of pSS and SLE.
Acknowledgements
This work was supported by the ÚNKP-16–4-III New National Excellence Program of the Ministry of Human Capacities.
Spiraea crenata L. is a deciduous shrub distributed across the Eurasian steppe zone. The species is of cultural and horticultural importance and occurs in scattered populations throughout its westernmost range. Currently, there is no genomic information on the tribe of Spiraeeae. Therefore, we sequenced and assembled the whole genome of S. crenata using second- and third-generation sequencing and a hybrid assembly approach to expand genomic resources for conservation and support research on this horticulturally important lineage. In addition to the organellar genomes (i.e., the plastome and the mitochondrion), we present the first draft genome of the species with an estimated size of 220 Mbp, an N50 value of 7.7 Mbp, and a BUSCO score of 96.0%. Being the first complete genome of Spiraeeae, this may not only be the first step in the genomic study of a rare plant, but also a contribution to genomic resources supporting the study of biodiversity and evolutionary history of the Rosaceae.
Abstract Activation of Toll-like receptors (TLR) 1/2 and 4 are central in inducing inflammation in sebocytes by regulating the expression of protein coding mRNAs, however the microRNA (miRNA) profile in response to TLR activation and thus the possible role of miRNAs in modulating sebocyte functions has not been elucidated. In this work we identified miR-146a to have the highest induction in the TLR1/2 and 4 activated SZ95 sebocytes and found that its increased levels led to the down-regulation of IL-8 secretion, decreased the chemoattractant potential and stimulated the proliferation of sebocytes. Assessing the gene expression profile of SZ95 sebocytes treated with a miR-146a inhibitor, the induction of GNG7 was one of the highest, while when cells were treated with a miR-146a mimic, the expression of GNG7 was down-regulated. These findings correlated with our in situ hybridization results, that compared with control, miR-146a showed an increased, while GNG7 a decreased expression in sebaceous glands of acne samples. Further studies revealed, that when inhibiting the levels of GNG7 in SZ95 sebocytes, cells increased their lipid content and decreased their proliferation. Our findings suggest, that miR-146a could be a potential player in acne pathogenesis by regulating inflammation, inducing proliferation and, through the indirect down-regulation of GNG7 , promoting the lipid production of sebocytes.
Kisspeptin neurons residing in the rostral periventricular area of the third ventricle (KP RP3V ) and the arcuate nucleus (KP ARC ) mediate positive and negative estrogen feedback, respectively. Here, we aim to compare transcriptional responses of KP RP3V and KP ARC neurons to estrogen. Transgenic mice were ovariectomized and supplemented with either 17β-estradiol (E2) or vehicle. Fluorescently tagged KP RP3V neurons collected by laser-capture microdissection were subjected to RNA-seq. Bioinformatics identified 222 E2-dependent genes. Four genes encoding neuropeptide precursors ( Nmb, Kiss1, Nts, Penk ) were robustly, and Cartpt was subsignificantly upregulated, suggesting putative contribution of multiple neuropeptides to estrogen feedback mechanisms. Using overrepresentation analysis, the most affected KEGG pathways were neuroactive ligand-receptor interaction and dopaminergic synapse. Next, we re-analyzed our previously obtained KP ARC neuron RNA-seq data from the same animals using identical bioinformatic criteria. The identified 1583 E2-induced changes included suppression of many neuropeptide precursors, granins, protein processing enzymes, and other genes related to the secretory pathway. In addition to distinct regulatory responses, KP RP3V and KP ARC neurons exhibited sixty-two common changes in genes encoding three hormone receptors ( Ghsr, Pgr, Npr2 ), GAD-65 ( Gad2 ), calmodulin and its regulator ( Calm1, Pcp4 ), among others. Thirty-four oppositely regulated genes ( Kiss1, Vgf, Chrna7, Tmem35a ) were also identified. The strikingly different transcriptional responses in the two neuron populations prompted us to explore the transcriptional mechanism further. We identified ten E2-dependent transcription factors in KP RP3V and seventy in KP ARC neurons. While none of the ten transcription factors interacted with estrogen receptor-α, eight of the seventy did. We propose that an intricate, multi-layered transcriptional mechanism exists in KP ARC neurons and a less complex one in KP RP3V neurons. These results shed new light on the complexity of estrogen-dependent regulatory mechanisms acting in the two functionally distinct kisspeptin neuron populations and implicate additional neuropeptides and mechanisms in estrogen feedback.
Spiraea crenata L. is a deciduous shrub distributed across the Eurasian steppe zone. The species is of cultural and horticultural importance and occurs in scattered populations throughout its westernmost range. Currently, there is no genomic information on the tribe of Spiraeeae. Therefore, we sequenced and assembled the whole genome of S. crenata using second- and third-generation sequencing and a hybrid assembly approach to expand genomic resources for conservation and support research on this horticulturally important lineage. In addition to the organellar genomes (i.e., the plastome and the mitochondrion), we present the first draft genome of the species with an estimated size of 220 Mbp, an N50 value of 7.7 Mbp, and a BUSCO score of 96.0%. Being the first complete genome of Spiraeeae, this may not only be the first step in the genomic study of a rare plant, but also a contribution to genomic resources supporting the study of biodiversity and evolutionary history of the Rosaceae.
Abstract Chondrogenic progenitor cells (CPCs) may be used as an alternative source of cells with potentially superior chondrogenic potential compared to mesenchymal stem cells (MSCs), and could be exploited for future regenerative therapies targeting articular cartilage in degenerative diseases such as osteoarthritis (OA). In this study, we hypothesised that CPCs derived from OA cartilage may be characterised by a distinct channelome. First, a global transcriptomic analysis using Affymetrix microarrays was performed. We studied the profiles of those ion channel and transporter families that may be relevant to chondroprogenitor cell physiology. Following validation of the microarray data, we examined the role of calcium-dependent potassium channels in CPCs and observed functional large conductance calcium-activated potassium channels (BK) involved in the maintenance of chondroprogenitor phenotype. In line with our very recent results, we found that the KCNMA1 gene was upregulated in CPCs and observed currents that could be attributed to the BK channel in both cell types. Through characterisation of their channelome we demonstrate that CPCs are a distinct cell population but are highly similar to MSCs in many respects. This work adds key mechanistic data to the in-depth characterisation of CPCs and their phenotype in the context of cartilage regeneration.
Osteoclasts play a central role in cancer-cell-induced osteolysis, but the molecular mechanisms of osteoclast activation during bone metastasis formation are incompletely understood. By performing RNA sequencing on a mouse breast carcinoma cell line with higher bone-metastatic potential, here we identify the enzyme CYP11A1 strongly upregulated in osteotropic tumor cells. Genetic deletion of Cyp11a1 in tumor cells leads to a decreased number of bone metastases but does not alter primary tumor growth and lung metastasis formation in mice. The product of CYP11A1 activity, pregnenolone, increases the number and function of mouse and human osteoclasts in vitro but does not alter osteoclast-specific gene expression. Instead, tumor-derived pregnenolone strongly enhances the fusion of pre-osteoclasts via prolyl 4-hydroxylase subunit beta (P4HB), identified as a potential interaction partner of pregnenolone. Taken together, our results demonstrate that Cyp11a1-expressing tumor cells produce pregnenolone, which is capable of promoting bone metastasis formation and osteoclast development via P4HB.
The concept of tissue-specific gene expression posits that lineage-determining transcription factors (LDTFs) determine the open chromatin profile of a cell via collaborative binding, providing molecular beacons to signal-dependent transcription factors (SDTFs). However, the guiding principles of LDTF binding, chromatin accessibility and enhancer activity have not yet been systematically evaluated. We sought to study these features of the macrophage genome by the combination of experimental (ChIP-seq, ATAC-seq and GRO-seq) and computational approaches. We show that Random Forest and Support Vector Regression machine learning methods can accurately predict chromatin accessibility using the binding patterns of the LDTF PU.1 and four other key TFs of macrophages (IRF8, JUNB, CEBPA and RUNX1). Any of these TFs alone were not sufficient to predict open chromatin, indicating that TF binding is widespread at closed or weakly opened chromatin regions. Analysis of the PU.1 cistrome revealed that two-thirds of PU.1 binding occurs at low accessible chromatin. We termed these sites labelled regulatory elements (LREs), which may represent a dormant state of a future enhancer and contribute to macrophage cellular plasticity. Collectively, our work demonstrates the existence of LREs occupied by various key TFs, regulating specific gene expression programs triggered by divergent macrophage polarizing stimuli.
