Integrative transcriptomic profiling of mRNA, miRNA, circRNA, and lncRNA in alveolar macrophages isolated from PRRSV-infected porcine

IntroductionThe porcine reproductive and respiratory syndrome virus (PRRSV) continues to pose a significant threat to the global swine industry, attributed largely to its immunosuppressive properties and the chronic nature of its infection. The absence of effective vaccines and therapeutics amplifies the urgency to deepen our comprehension of PRRSV’s intricate pathogenic mechanisms. Previous transcriptomic studies, although informative, are partially constrained by their predominant reliance on in vitro models or lack of long-term infections. Moreover, the role of circular RNAs (circRNAs) during PRRSV invasion is yet to be elucidated.MethodsIn this study, we employed an in vivo approach, exposing piglets to a PRRSV challenge over varied durations of 3, 7, or 21 days. Subsequently, porcine alveolar macrophages were isolated for a comprehensive transcriptomic investigation, examining the expression patterns of mRNAs, miRNAs, circRNAs, and long non-coding RNAs (lncRNAs).ResultsDifferentially expressed RNAs from all four categories were identified, underscoring the dynamic interplay among these RNA species during PRRSV infection. Functional enrichment analyses indicate that these differentially expressed RNAs, as well as their target genes, play a pivotal role in immune related pathways. For the first time, we integrated circRNAs into the lncRNA-miRNA-mRNA relationship, constructing a competitive endogenous RNA (ceRNA) network. Our findings highlight the immune-related genes, CTLA4 and SAMHD1, as well as their associated miRNAs, lncRNAs, and circRNAs, suggesting potential therapeutic targets for PRRS. Importantly, we corroborated the expression patterns of selected RNAs through RT-qPCR, ensuring consistency with our transcriptomic sequencing data.DiscussionThis study sheds lights on the intricate RNA interplay during PRRSV infection and provides a solid foundation for future therapeutic strategizing

SNP in human ARHGEF3 promoter is associated with DNase hypersensitivity, transcript level and platelet function, and Arhgef3 KO mice have increased mean platelet volume

Genome-wide association studies have identified a genetic variant at 3p14.3 (SNP rs1354034) that strongly associates with platelet number and mean platelet volume in humans. While originally proposed to be intronic, analysis of mRNA expression in primary human hematopoietic subpopulations reveals that this SNP is located directly upstream of the predominantly expressed ARHGEF3 isoform in megakaryocytes (MK). We found that ARHGEF3, which encodes a Rho guanine exchange factor, is dramatically upregulated during both human and murine MK maturation. We show that the SNP (rs1354034) is located in a DNase I hypersensitive region in human MKs and is an expression quantitative locus (eQTL) associated with ARHGEF3 expression level in human platelets, suggesting that it may be the causal SNP that accounts for the variations observed in human platelet traits and ARHGEF3 expression. In vitro human platelet activation assays revealed that rs1354034 is highly correlated with human platelet activation by ADP. In order to test whether ARHGEF3 plays a role in MK development and/or platelet function, we developed an Arhgef3 KO/LacZ reporter mouse model. Reflecting changes in gene expression, LacZ expression increases during MK maturation in these mice. Although Arhgef3 KO mice have significantly larger platelets, loss of Arhgef3 does not affect baseline MK or platelets nor does it affect platelet function or platelet recovery in response to antibody-mediated platelet depletion compared to littermate controls. In summary, our data suggest that modulation of ARHGEF3 gene expression in humans with a promoter-localized SNP plays a role in human MKs and human platelet function-a finding resulting from the biological follow-up of human genetic studies. Arhgef3 KO mice partially recapitulate the human phenotype

Modification and Expression of mRNA m6A in the Lateral Habenular of Rats after Long-Term Exposure to Blue Light during the Sleep Period

Artificial lighting, especially blue light, is becoming a public-health risk. Excessive exposure to blue light at night has been reported to be associated with brain diseases. However, the mechanisms underlying neuropathy induced by blue light remain unclear. An early anatomical tracing study described the projection of the retina to the lateral habenula (LHb), whereas more mechanistic reports are available on multiple brain functions and neuropsychiatric disorders in the LHb, which are rarely seen in epigenetic studies, particularly N6-methyladenosine (m6A). The purpose of our study was to first expose Sprague-Dawley rats to blue light (6.11 ± 0.05 mW/cm2, the same irradiance as 200 lx of white light in the control group) for 4 h, and simultaneously provide white light to the control group for the same time to enter a sleep period. The experiment was conducted over 12 weeks. RNA m6A modifications and different mRNA transcriptome profiles were observed in the LHb. We refer to this experimental group as BLS. High-throughput MeRIP-seq and mRNA-seq were performed, and we used bioinformatics to analyze the data. There were 188 genes in the LHb that overlapped between differentially m6A-modified mRNA and differentially expressed mRNA. The Kyoto Encyclopedia of Genes and Genomes and gene ontology analysis were used to enrich neuroactive ligand–receptor interaction, long-term depression, the cyclic guanosine monophosphate-dependent protein kinase G (cGMP-PKG) signaling pathway, and circadian entrainment. The m6A methylation level of the target genes in the BLS group was disordered. In conclusion, this study suggests that the mRNA expression and their m6A of the LHb were abnormal after blue light exposure during the sleep period, and the methylation levels of target genes related to synaptic plasticity were disturbed. This study offers a theoretical basis for the scientific use of light

The pseudogene DUXAP10 contributes to gefitinib resistance in NSCLC by repressing OAS2 expression

Gefitinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI),is the currently recommended first-line therapy for advanced EGFR-mutant lung cancer, and understanding the mechanism of resistance is the key to formulating therapeutic strategies for EGFR-TKIs. In this study, we evaluate the expression patterns and potential biological functions of the pseudogene DUXAP10 in gefitinib resistance. We find that pseudogene DUXAP10 expression is significantly upregulated in NSCLC gefitinib-resistant cells and tissues. Gain and loss of function assays reveal that knockdown of DUXAP10 by siRNA reverses gefitinib resistance both in vitro and in vivo. Furthermore, DUXAP10 interacts with the histone methyltransferase enhancer of zeste homolog 2 (EZH2) to repress the expression of 2′,5′-oligoadenylate synthetase (OAS2). Overall, our study highlights the pivotal role of DUXAP10 in gefitinib resistance, and the DUXAP10/EZH2/OAS2 axis might be a promising therapeutic target to overcome acquired gefitinib resistance in NSCLC

Sulforaphane suppresses paraquat-induced oxidative damage in bovine in vitro-matured oocytes through Nrf2 transduction pathway

Sulforaphane (SFN), a bioactive phytocompound extracted from cruciferous plants, has received increasing attention due to its vital cytoprotective role in eliminating oxidative free radical through activation of nuclear factor erythroid 2-related factor (Nrf2)-mediated signal transduction pathway. This study aims at a better insight into the protective benefit of SFN in attenuating paraquat (PQ)-caused impairment in bovine in vitro-matured oocytes and the possible mechanisms involved therein. Results showed that addition of 1 μM SFN during oocyte maturation obtained higher proportions of matured oocytes and in vitro-fertilized embryos. SFN application attenuated the toxicological effects of PQ on bovine oocytes, as manifested by enhanced extending capability of cumulus cell and increased extrusion proportion of first polar body. Following incubation with SFN, oocytes exposed to PQ exhibited reduced intracellular ROS and lipid accumulation levels, and elevated T-SOD and GSH contents. SFN also effectively inhibited PQ-mediated increase in BAX and CASPASE-3 protein expressions. Besides, SFN promoted the transcription of NRF2 and its downstream antioxidative-related genes GCLC, GCLM, HO-1, NQO-1, and TXN1 in a PQ-exposed environment, indicating that SFN prevents PQ-caused cytotoxicity through activation of Nrf2 signal transduction pathway. The mechanisms underlying the role of SFN against PQ-induced injury included the inhibition of TXNIP protein and restoration of the global O-GlcNAc level. Collectively, these findings provide novel evidence for the protective role of SFN in alleviating PQ-caused injury, and suggest that SFN application may be an efficacious intervention strategy against PQ cytotoxicity

Role of RhoA-Specific Guanine Exchange Factors in Regulation of Endomitosis in Megakaryocytes

SummaryPolyploidization can precede the development of aneuploidy in cancer. Polyploidization in megakaryocytes (Mks), in contrast, is a highly controlled developmental process critical for efficient platelet production via unknown mechanisms. Using primary cells, we demonstrate that the guanine exchange factors GEF-H1 and ECT2, which are often overexpressed in cancer and are essential for RhoA activation during cytokinesis, must be downregulated for Mk polyploidization. The first (2N–4N) endomitotic cycle requires GEF-H1 downregulation, whereas subsequent cycles (>4N) require ECT2 downregulation. Exogenous expression of both GEF-H1 and ECT2 prevents endomitosis, resulting in proliferation of 2N Mks. Furthermore, we have shown that the mechanism by which polyploidization is prevented in Mks lacking Mkl1, which is mutated in megakaryocytic leukemia, is via elevated GEF-H1 expression; shRNA-mediated GEF-H1 knockdown alone rescues this ploidy defect. These mechanistic insights enhance our understanding of normal versus malignant megakaryocytopoiesis, as well as aberrant mitosis in aneuploid cancers.Video Abstrac

rs1354034 is the leading SNP and an eQTL for ARHGEF3 expression.

<p>(A) Visual summary of the statistical evidence for variant-phenotype association at the locus of rs1354034 from data generated by the TEMPLE targeted sequencing study. It shows the variant specific P-values from Fisher’s exact tests against null hypotheses that genotype frequencies are the same in the high and low platelet count samples. The color of each point represents the <i>r</i>² between the corresponding variant and rs1354034, estimated from the TEMPLE genotypes. The continuous line indicates the local recombination rate estimated from HapMap data. (The tool used to generate the plot is available at doi:10.1093/bioinformatics/btq41.) (B) Shown is rs 1354034 (blue X) and its LD structure in +/- 250 kb window. There is no SNP in linkage disequilibrium (threshold <i>r</i>² >0.8) found 250k bp up- or downstream of the rs1354034 locus (data from 1000 Genome Project), suggesting rs1354034 is the leading SNP of ARHGEF3. (C) A strong association of the rs1354034 genotype with ARHGEF3 mRNA levels (p = 1.37x10^-15, ordinary linear regression). This association stayed significant even after accounting for subject age, gender and race (p = 2.39 x 10⁻¹¹, multiple linear regression). Primary data for 5C in online <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178095#pone.0178095.s003" target="_blank">S1 Table</a>.</p

rs1354034 is located in a DNase I hypersensitive region in primary human MKs.

<p>Shown is the chromatin locus containing the ARHGEF3 gene. rs1354034 (orange arrow) is located in an open-chromatin (DNase I peak) non-coding region upstream of the transcription start site of ENST00000296315 (the most commonly transcribed mRNA in MK, indicated by an asterisk). Green: DNase 1 peaks, Purple: H3K27Ac ChIP peaks, Blue: intron/exon boundaries, Bottom: major ENST’s identified for ARHGEF3.</p