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Background: Immunoglobulin A nephropathy (IgAN) is a major cause of chronic kidney disease (CKD) and kidney failure. Necroptosis is a novel type of programmed cell death that has been proved to be associated with the pathogenesis of infectious disease, cardiovascular disease, neurological disorders and so on. However, the role of necroptosis in IgAN remains unclear. Methods: In this study, we explored the role of necroptosis-related genes in the pathogenesis of IgAN using a comprehensive bioinformatics method. Microarray datasets GSE93798 and GSE115857 were downloaded from Gene Expression Omnibus (GEO). "limma" package of R software was employed to identify necroptosis-related differentially expressed genes (NRDEGs) between IgAN and healthy controls. GO and KEGG functional enrichment analysis was performed by Clusterprofiler. Least absolute shrinkage and selection operator (LASSO) regression analysis identified hub NRDEGs. We further established a diagnostic model consisting of 7 diagnostic hub NRDEGs and validated the efficacy by an external dataset. The expression of hub genes was confirmed in sc-RNA dataset GSE171314. Immune infiltration, gene set enrichment analysis and transcription factor binding motifs enrichment analysis were conducted to further uncover their roles. Results: 1076 differentially expressed genes were identified between healthy individuals and IgAN patients from RNA-seq dataset GSE9379. Then we cross-linked them with necroptosis-related genes to obtain 9 NRDEGs. LASSO regression analysis screened out 7 hub genes (JUN, CD274, SERTAD1, NFKBIA, H19, UCHL1 and EZH2) of IgAN. We further conducted functional enrichment analysis and constructed the diagnostic model based on dataset GSE93798. GSE115857 was used as the independent validation cohort and indicated a great predictive efficacy. Immune infiltration, gene set enrichment analysis and transcription factor binding motifs enrichment analysis revealed their potential function. Finally, we screened out four drugs that were predicted to have therapeutic value of IgAN. Conclusions: In summary, we identified 7 hub necroptosis-associated genes, which can be used as potential genetic biomarkers for IgAN prediction and treatment. Four drugs were predicted as the potential therapeutic solutions. Collectively, we provided insights into the necroptosis-related mechanisms and treatment of IgAN at the transcriptome level. [ABSTRACT FROM AUTHOR]

Flowering in plants is pivotal for initiating and advancing reproductive processes, impacting regional adaptation and crop yield. Despite numerous cloned and identified flowering time genes, research in cotton remains sparse. This study identified GhSWEET42 as a key determinant of the flowering time in cotton, demonstrating that its heterologous expression in Arabidopsis accelerated flowering under LD conditions compared to WT. Transgenic plants exhibited upregulated expression of the flowering inducers AtFT, AtSOC1, AtGI, and AtFKF1, alongside downregulated expression of the repressors AtTSF, AtFLC, and AtRGL2, correlating with the earlier flowering phenotype. GhSWEET42 showed a constitutive expression pattern, with elevated levels in the leaves, petals, and flower buds, and was notably higher in early-maturing cotton varieties. Subcellular localization assays confirmed GhSWEET42's presence on the cell membrane. Transcriptome analysis between WT and GhSWEET42-overexpressing Arabidopsis plants revealed 2393 differentially expressed genes (DEGs), spanning 221 biological processes, 93 molecular functions, and 37 cellular components according to Gene Ontology (GO) enrichment analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis categorized the DEGs into metabolism and environmental information processing. These findings enhance the understanding of GhSWEET42's function and provide a foundation for elucidating the molecular mechanisms governing flowering time regulation in cotton. [ABSTRACT FROM AUTHOR]

Psoriasis is characterized by keratinocyte (KC) hyperproliferation and inflammatory cell infiltration, but the mechanisms remain unclear. In an imiquimod-induced mouse psoriasiform model, p38 activity is significantly elevated in KCs and p38α specific deletion in KCs ameliorates skin inflammation. p38α signaling promotes KC proliferation and psoriasis-related proinflammatory gene expression during psoriasis development. Mechanistically, p38α enhances KC proliferation and production of inflammatory cytokines and chemokines by activating STAT3. While p38α signaling in KCs does not affect the expression of IL-23 and IL-17, it substantially amplifies the IL-23/IL-17 pathogenic axis in psoriasis. The therapeutic effect of IL-17 neutralization is associated with decreased p38 and STAT3 activities in KCs and targeting the p38α-STAT3 axis in KCs ameliorates the severity of psoriasis. As IL-17 also highly activates p38 and STAT3 in KCs, our findings reveal a sustained signaling circuit important for psoriasis development, highlighting p38α-STAT3 axis as an important target for psoriasis treatment. p38α signaling promotes keratinocyte proliferation and psoriasis-related proinflammatory gene expression in psoriasis by activating STAT3, and further amplifies the IL-23/IL-17 pathogenic axis. [ABSTRACT FROM AUTHOR]

Introduction: This study aimed to determine whether bone morphogenetic protein-4 (BMP-4), which increases in response to intimal hyperplasia, promotes phenotype transition in vascular smooth muscle cells (VSMCs). Methods: Balloon injury was used to induce intimal hyperplasia in rats. Hematoxylin-eosin staining was used to detect the alteration of vascular structure. Serum levels of BMP-4 and lactate were detected by ELISA. Human aortic smooth muscle cells (HA-SMCs) were cultured. Protein and mRNA expression levels were detected through Western blot and real-time PCR. Cell migration was measured by transwell assay. Results: Our data showed that serum concentration of BMP-4 was upregulated after balloon injury. Treatment with BMP-4 inhibitor DMH1 (4-(6-(4-isopropoxyphenyl)pyrazolo(1,5-a)pyrimidin-3-yl)quinoline) suppressed the abnormal expression of BMP-4 and inhibited the intimal hyperplasia induced by balloon injury. Compared to BMP-4-negative medium, BMP-4-positive medium was associated with higher synthetic VSMC marker expression levels and lower in contractile gene markers in cultured HA-SMCs. Transfection of monocarboxylic acid transporters-4 (MCT-4) siRNA inhibited the excretion of lactate induced by BMP-4. Conclusion: Our analyses provided evidence that BMP-4 and its regulator Smad-4 are key regulators in MCT-4-mediated lactate excretion. This indicates that BMP-4 stimulates the phenotypic transition of VSMCs via SMAD-4/MCT-4 signaling pathway. [ABSTRACT FROM AUTHOR]

Key message: Overexpression of the Aux/IAA protein TaIAA15-1A from wheat improves drought tolerance by regulating the ABA signalling pathway in transgenic Brachypodium. Drought is a major abiotic stress that causes severe crop yield loss. Aux/IAA genes have been shown to be involved in drought stress responses. However, to the best of our knowledge, there has been little research on the molecular mechanism of the wheat Aux/IAA gene in the context of drought tolerance. In this study, we found that expression of the wheat Aux/IAA gene TaIAA15-1A was upregulated by PEG6000, NaCl, SA, JA, IAA and ABA. Transgenic plants overexpressing TaIAA15-1A showed higher drought tolerance than wild-type (WT) plants. The physiological analyses showed that the transgenic lines exhibited a higher survival rate, shoot length, and relative water content than the WT plants. The activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were enhanced in transgenic lines, causing a reduction in the hydrogen peroxide (H2O2) and superoxide anion radical (O2−) contents. Transcriptome analysis showed that TaIAA15-1A overexpression alters the expression of these genes involved in the auxin signalling pathway, ABA signalling pathway, phenolamides and antioxidant pathways. The results of exogenous ABA treatment suggested that TaIAA15-1A overexpression increased sensitivity to ABA at the germination and postgermination stages compared to WT plants. These results indicate that TaIAA15-1A plays a positive role in plant drought tolerance by regulating ABA-related genes and improving antioxidative stress ability and has potential application in genetically modified crops. [ABSTRACT FROM AUTHOR]

In plants, the B-box (BBX) transcription factors (TFs) are a subfamily of zinc-finger TFs that act to regulate diverse plant growth and development processes. The BBX TFs have been the subject of considerable attention, and are well characterized in diverse plant species, including in rice (Oryza sativa) and Arabidopsis thaliana, but less so in the economically important soybean (Glycine max). In this work, we systematically identified and characterized 57 soybean BBX genes (GmBBX1 to GmBBX57). These genes were mapped to all 20 soybean chromosomes and were divided into five clades with high intra-clade intron–exon similarity. The majority of GmBBX gene promoter cis-acting elements were responsive to light, abscisic acid, salicylic acid and methyl jasmonate, as well as a diverse array of other stimuli. Quantitative RT-PCR indicated that several GmBBX genes exhibited tissue-specific and phytohormone- and abiotic stress-responsiveness. The results of this study will be useful in the continued characterization of soybean BBX gene functions and provide new ideas for soybean breeding. [ABSTRACT FROM AUTHOR]

Although vitrification has been widely applied in assisted reproductive technology, it is unknown whether storage time has any impact on the mRNA and lncRNA expression profiles in human embryos. Eleven women (aged 23–35 years) who had undergone in vitro fertilization treatment were recruited for this study. The transcriptomes of 3 fresh eight-cell embryos and 8 surviving vitrified-warmed eight-cell embryos (4 embryos were cryostored for 3 years, and the others were cryostored for 8 years) were analyzed through single-cell RNA-Seq. No differentially expressed mRNAs or lncRNAs were identified between the 3-years group and 8-years group. A total of 128 mRNAs and 365 lncRNAs were differentially expressed in the 8 vitrified-warmed embryos compared with the fresh embryos. The vitrification-warming impact was moderate, and it was mainly related to the pathways of metabolism, stress response, apoptosis, cell cycle, cell adhesion, and signaling for TFG-β and Hippo. The analysis of target mRNAs suggested that lncRNAs might contribute to the regulation of mRNAs after vitrification-warming. Our findings indicated that long-term storage after vitrification does not affect the mRNA and lncRNA expression profiles in human embryos, however, the procedure of vitrification-warming would lead to minor alteration of transcriptome. [ABSTRACT FROM AUTHOR]

Factor-based induced reprogramming approaches have tremendous potential for human regenerative medicine, but the efficiencies of these approaches are still low. In this study, we analyzed the global transcriptional profiles of mouse induced pluripotent stem cells (miPSCs) and mouse embryonic stem cells (mESCs) from seven different labs and present here the first successful clustering according to cell type, not by lab of origin. We identified 2131 different expression genes (DEs) as candidate pluripotency-associated genes by comparing mESCs/miPSCs with somatic cells and 720 DEs between miPSCs and mESCs. Interestingly, there was a significant overlap between the two DE sets. Therefore, we defined the overlap DEs as 'consensus DEs' including 313 miPSC-specific genes expressed at a higher level in miPSCs versus mESCs and 184 mESC-specific genes in total and reasoned that these may contribute to the differences in pluripotency between mESCs and miPSCs. A classification of 'consensus DEs' according to their different expression levels between somatic cells and mESCs/miPSCs shows that 86% of the miPSC-specific genes are more highly expressed in somatic cells, while 73% of mESC-specific genes are highly expressed in mESCs/miPSCs, indicating that the miPSCs have not efficiently silenced the expression pattern of the somatic cells from which they are derived and failed to completely induce the genes with high expression levels in mESCs. We further revealed a strong correlation between oocyte-enriched factors and insufficiently induced mESC-specific genes and identified 11 hub genes via network analysis. In light of these findings, we postulated that these key hub genes might not only drive somatic cell nuclear transfer (SCNT) reprogramming but also augment the efficiency and quality of miPSC reprogramming. [ABSTRACT FROM AUTHOR]

Radiotherapy-induced muscle injury (RIMI) is a major complication of radiotherapy for nasopharyngeal carcinoma. Transcription factor (TF) expression and alternative splicing are crucial events in transcriptional and posttranscriptional regulation, respectively, and are known to be involved in key signaling pathways contributing to a variety of human disorders, including radiation injury. To investigate the TFs and alternative splicing events involved in RIMI, we constructed a tree shrew model as described previously in which the RIMI group received 20 Gy of irradiation on the tensor veli palatini (TVP) muscles. The irradiated muscles were evaluated by RNA sequencing (RNA-seq) 6 months later, and the results compared with those for normal TVP muscles. The alt5p and alt3p events were the two main types of differentially regulated alternative splicing events (RASEs) identified via the Splice sites Usage Variation Analysis (SUVA) software, and these RASEs were highly conserved in RIMI. According to functional enrichment analysis, the differentially RASEs were primarily enriched in pathways related to transcriptional regulation. Furthermore, we identified 16 alternative splicing TFs (ASTFs) in ASTF–differentially expressed gene (DEG) networks based on co-expression analysis, and the regulatory networks were chiefly enriched in pathways linked to cell proliferation and differentiation. This study revealed that RASEs and ASTF–DEG networks may both play important regulatory roles in gene expression network alteration in RIMI. Future studies on the targeting mechanisms and early interventions directed at RASEs and ASTF–DEG networks may aid in the treatment of RIMI. • Radiotherapy-induced muscle injury(RIMI) is a major complication of radiotherapy for nasopharyngeal carcinoma. • Tree shrew model simulating radiotherapy for NPC is useful for research into RIMI. • RASEs and ASTF–DEG networks may both play important regulatory roles in gene expression network alteration in RIMI. [ABSTRACT FROM AUTHOR]