Search

Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the 2 serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants. Pan-transcriptomic analysis of rice under cold stress reveals alternative splicing control of cold tolerance. [ABSTRACT FROM AUTHOR]

Neuropeptides are crucial in regulation of a rich variety of developmental, physiological, and behavioral functions throughout the life cycle of insects. Using an integrated approach of multiomics, we identified neuropeptide precursors in the greater wax moth Galleria mellonella, which is a harmful pest of honeybee hives with a worldwide distribution. Here, a total of 63 and 67 neuropeptide precursors were predicted and annotated in the G. mellonella genome and transcriptome, in which 40 neuropeptide precursors were confirmed in the G. mellonella peptidome. Interestingly, we identified 12 neuropeptide precursor genes present in G. mellonella but absent in honeybees, which may be potential novel pesticide target sites. Honeybee hives were contaminated with heavy metals such as lead, enabling its bioaccumulation in G. mellonella bodies through the food chain, we performed transcriptome sequencing to analyze the effects of Pb stress on the mRNA expression level of G. mellonella neuropeptide precursors. After treatment by Pb, the expression of neuropeptide F1 was found to be significantly downregulated, implying that this neuropeptide might be associated with responding to the heavy metal stress in G. mellonella. This study comprehensively identified neuropeptide precursors in G. mellonella, and discussed the effects of heavy metals on insect neuropeptides, with the example of G. mellonella. The results are valuable for future elucidation of how neuropeptides regulate physiological functions in G. mellonella and contribute to our understanding of the insect's environmental plasticity and identify potential new biomarkers to assess heavy metal toxicity in insects. [ABSTRACT FROM AUTHOR]

Objectives: Astragaloside IV (AS-IV) is a natural triterpenoid saponin compound with a variety of pharmacological effects, and several studies have clarified its anti-inflammatory effects, which may make it an effective alternative treatment against inflammation. In the study, we aimed to investigate whether AS-IV could attenuate the inflammatory response to acute lung injury and its mechanisms. Methods: Different doses of AS-IV (20mg·kg-1, 40mg·kg-1, and 80mg·kg-1) were administered to the ALI rat model, followed by collection of serum and broncho alveolar lavage fluid (BALF) for examination of the inflammatory response, and HE staining of the lung and colon tissues, and interpretation of the potential molecular mechanisms by quantitative real-time PCR (qRT-PCR), Western blotting (WB). In addition, fecal samples from ALI rats were collected and analyzed by 16S rRNA sequencing. Results: AS-IV decreased the levels of TNF-α, IL-6, and IL-1β in serum and BALF of mice with Acute lung injury (ALI). Lung and colon histopathology confirmed that AS-IV alleviated inflammatory infiltration, tissue edema, and structural changes. qRT-PCR and WB showed that AS-IV mainly improved inflammation by inhibiting the expression of PI3K, AKT and mTOR mRNA, and improved the disorder of intestinal microflora by increasing the number of beneficial bacteria and reducing the number of harmful bacteria. Conclusion: AS-IV reduces the expression of inflammatory factors by inhibiting the PI3K/AKT/mTOR pathway and optimizes the composition of the gut microflora in AIL rats. [ABSTRACT FROM AUTHOR]

Objective: We aimed to study the involvement of ferroptosis in the pathogenesis of bronchopulmonary dysplasia (BPD) by conducting bioinformatics analyses and identifying and validating the associated ferroptosis-related genes to explore new directions for treating BPD. Methods: The dataset GSE32472 on BPD was downloaded from the public genome database. Using R language, differentially expressed genes (DEGs) between the BPD and normal group were screened. In the present study, we adopted weighted gene correlation network analysis (WGCNA) for identifying BPD-related gene modules and ferroptosis-related genes were extracted from FerrDb. Their results were intersected to obtain the hub genes. After that, to explore the hub gene-related signaling pathways, the hub genes were exposed to gene ontology enrichment analysis. With the purpose of verifying the mRNA expression of the hub genes, a single-gene gene set enrichment analysis and quantitative reverse transcription polymerase chain reaction were conducted. Immune cell infiltration in BPD was analyzed using the CIBERSORT inverse fold product algorithm. Results: A total of 606 DEGs were screened. WGCNA provided the BPD-related gene module darkgreen4. The intersection of DEGs, intramodular genes, and ferroptosis-related genes revealed six ferroptosis-associated hub genes (ACSL1, GALNT14, WIPI1, MAPK14, PROK2, and CREB5). Receiver operating characteristic curve analysis demonstrated that the hub genes screened for BPD were of good diagnostic significance. According to the results of immune infiltration analysis, the proportions of CD8, CD4 naive, and memory resting T cells and M2 macrophage were elevated in the normal group, and the proportions of M0 macrophage, resting mast cell, and neutrophils were increased in the BPD group. Conclusions: A total of six ferroptosis-associated hub genes in BPD were identified in this study, and they may be potential new therapeutic targets for BPD. [ABSTRACT FROM AUTHOR]

Exercise offers numerous benefits to cancer patients and plays an essential role in postsurgical cancer rehabilitation. However, there is a lack of research examining the effects of exercise after the surgical stress of nephrectomy. To address this gap, we created an animal model that simulated patients who had undergone nephrectomy with or without an exercise intervention. Next, we performed a bioinformatic analysis based on the data generated by the RNA sequencing of the lung tissue sample. An overrepresentation analysis was conducted using two genome databases (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes [KEGG]). A KEGG analysis of the exercise-treated nephrectomy mice revealed enrichment in immune-related pathways, particularly in the NF-κB and B cell-related pathways. The expression of CD79A and IGHD, which are responsible for B cell differentiation and proliferation, was upregulated in the nephrectomy mice. Differential gene expression was categorized as significantly upregulated or downregulated according to nephrectomy and exercise groups. Notably, we identified several gene expression reversals in the nephrectomy groups with exercise that were not found in the nephrectomy without exercise or control groups. Our preliminary results potentially reveal a genetic landscape for the underlying mechanisms of the effects of exercise on our nephrectomy model. [ABSTRACT FROM AUTHOR]

Cooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice. [ABSTRACT FROM AUTHOR]

Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease marked by inflammatory cell infiltration and joint damage. The Chinese government has approved the prescription medication sinomenine (SIN), an effective anti-inflammation drug, for treating RA. This study evaluated the possible anti-inflammatory actions of SIN in RA based on bioinformatics analysis and experiments. Six microarray datasets were acquired from the gene expression omnibus (GEO) database. We used R software to identify differentially expressed genes (DEGs) and perform function evaluations. The CIBERSORT was used to calculate the abundance of 22 infiltrating immune cells. The weighted gene co-expression network analysis (WGCNA) was used to discover genes associated with M1 macrophages. Four public datasets were used to predict the genes of SIN. Following that, function enrichment analysis for hub genes was performed. The cytoHubba and least absolute shrinkage and selection operator (LASSO) were employed to select hub genes, and their diagnostic effectiveness was predicted using the receiver operator characteristic (ROC) curve. Molecular docking was undertaken to confirm the affinity between the SIN and hub gene. Furthermore, the therapeutic efficacy of SIN was validated in LPS-induced RAW264.7 cells line using Western blot and Enzyme-linked immunosorbent assay (ELISA). The matrix metalloproteinase 9 (MMP9) was identified as the hub M1 macrophages-related biomarker in RA using bioinformatic analysis and molecular docking. Our study indicated that MMP9 took part in IL-17 and TNF signaling pathways. Furthermore, we found that SIN suppresses the MMP9 protein overexpression and pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) in the LPS-induced RAW264.7 cell line. In conclusion, our work sheds new light on the pathophysiology of RA and identifies MMP9 as a possible RA key gene. In conclusion, the above findings demonstrate that SIN, from an emerging research perspective, might be a potential cost-effective anti-inflammatory medication for treating RA. [ABSTRACT FROM AUTHOR]

The environmental factor aryl hydrocarbon receptor (AhR), a key protein connecting the external environmental signals (e.g., environmental endocrine disruptor TCDD) to internal cellular processes, is involved in the activation of peripheral macrophages and inflammatory response in human body. Thus, there is widespread interest in finding compounds to anti‐inflammatory response in macrophages by targeting human AhR. Here, ensemble docking based‐virtual screening was first used to screen a library (~200,000 compounds) against human AhR ligand binding domain (LBD) and 25 compounds were identified as potential inhibitors. Then, 9 out of the 25 ligands were found to down‐regulate the mRNA expression of CYP1A1 (a downstream gene of AhR signaling) in AhR overexpressing macrophages. The most potent compound AE‐411/41415610 was selected for further study and found to reduce both mRNA and protein expressions level of CYP1A1 in mouse peritoneal macrophage. Moreover, protein chip signal pathway analysis indicated that AE‐411/41415610 play a role in regulating JAK–STAT and AKT–mTOR pathways. In sum, the discovered hits with novel scaffolds provided a starting point for future design of more effective AhR‐targeted lead compounds to regulate CYP1A1 expression of inflammatory peritoneal macrophages. [ABSTRACT FROM AUTHOR]

Background: SERPINB2, a biomarker of Type‐2 (T2) inflammatory processes, has been described in the context of asthma. Chronic rhinosinusitis with nasal polyps (CRSwNP) is also correlated with T2 inflammation and elevated 15LO1 induced by IL‐4/13 in nasal epithelial cells. The aim of this study was to evaluate the expression and location of SERPINB2 in nasal epithelial cells (NECs) and determine whether SERPINB2 regulates 15LO1 and downstream T2 markers in NECs via STAT6 signalling. Methods: SERPINB2 gene expression in bulk and single‐cell RNAseq database was analysed by bioinformatics analysis. SERPINB2, 15LO1 and other T2 markers were evaluated from CRSwNP and HCs NECs. The colocalization of SERPINB2 and 15LO1 was evaluated by immunofluorescence. Fresh NECs were cultured at an air‐liquid interface with or without IL‐13, SERPINB2 Dicer‐substrate short interfering RNAs (DsiRNAs) transfection, exogenous SERPINB2, 15‐HETE recombinant protein and pSTAT6 inhibitors. 15LO1, 15‐HETE and downstream T2 markers were analysed by qRT‐PCR, western blot and ELISA. Results: SERPINB2 expression was increased in eosinophilic nasal polyps compared with that in noneosinophilic nasal polyps and control tissues and positively correlated with 15LO1 and other downstream T2 markers. SERPINB2 was predominantly expressed by epithelial cells in NP tissue and was colocalized with 15LO1. In primary NECs in vitro, SERPINB2 expression was induced by IL‐13. Knockdown or overexpression SERPINB2 decreased or enhanced expression of 15LO1 and 15‐HETE in NECs, respectively, in a STAT6‐dependent manner. SERPINB2 siRNA also inhibited the expression of the 15LO1 downstream genes, such as CCL26, POSTN and NOS2. STAT6 inhibition similarly decreased SERPINB2‐induced 15LO1. Conclusions: SERPINB2 is increased in NP epithelial cells of eosinophilic CRSwNP (eCRSwNP) and contributes to T2 inflammation via STAT6 signalling. SERPINB2 could be considered a novel therapeutic target for eCRSwNP. [ABSTRACT FROM AUTHOR]

Background: Osteoporosis (OP) and type 2 diabetes (T2D) are commonly encountered metabolic disorders in clinical practice, but the comorbidity mechanism has not been clarified. This study explored the underlying mechanisms for utilizing bioinformatics methods. Furthermore, it predicted traditional Chinese medicines (TCMs) with preventive and therapeutic effects. Materials and Methods: GSE35958 and GSE43950 were retrieved and downloaded from the GEO database, and differential expression analysis was performed to identify differentially expressed genes (DEGs) with similar expression patterns in OP and T2D. Then, the common DEGs were uploaded to the STRING database to construct a protein interaction network. Enrichment analysis of the screened genes was conducted using R language packages. Relevant TCMs were searched and screened based on gene targets using the Encyclopedia of traditional Chinese medicine (ETCM) database. Molecular docking of active ingredients of the TCMs and related gene targets was performed using AutoDock Vina software. Results: By analyzing the gene expression microarrays, GSE35958 and GSE43950, 34 genes with the same expression pattern shared by OP and T2D were identified. Among these genes, 32 were upregulated and two were downregulated. Protein interaction network analysis revealed that tumor necrosis factor, vascular endothelial growth factor A, and CD44 might play key roles in the co-pathogenesis of T2D and OP. TCMs, including Wolfberry (枸杞), Ginseng (人参), and Yam (山药), were screened based on key genes. Molecular docking results demonstrated binding activity between all active ingredients and the related gene targets. Conclusion: This study explored the potential molecular co-pathogenesis of OP and T2D through bioinformatic analysis and preliminarily predicted traditional herbal medicines that may have preventive and therapeutic effects. [ABSTRACT FROM AUTHOR]

The lncRNA TRG-AS1 and its co-expressed gene P2RY10 are important for colorectal cancer (CRC) occurrence and development. The purpose of our research was to explore the roles of TRG-AS1 and P2RY10 in CRC progression. The abundance of TRG-AS1 and P2RY10 in CRC cell lines (HT-29 and LoVo) and normal colon cells FHC was determined and difference between CRC cells and normal cells was compared. LoVo cells were transfected with si-TRG-AS1 and si-P2RY10 constructs. Subsequently, the viability, colony formation, and migration of the transfected cells were analyzed using cell counting kit-8, clonogenicity, and scratch-wound/Transwell® assays, respectively. Cells overexpressing GNA13 were used to further explore the relationship between TRG-AS1 and P2RY10 along with their downstream functions. Finally, nude mice were injected with different transfected cell types to observe tumor formation in vivo. TRG-AS1 and P2RY10 were significantly upregulated in HT-29 and LoVo compared to FHC cells. TRG-AS1 knockdown and P2RY10 silencing suppressed the viability, colony formation, and migration of LoVo cells. TRG-AS1 knockdown downregulated the expression of P2RY10, GNA12, and GNA13, while P2RY10 silencing downregulated the expression of TRG-AS1, GNA12, and GNA13. Additionally, GNA13 overexpression reversed the cell growth and gene expression changes in LoVo cells induced by TRG-AS1 knockdown or P2RY10 silencing. In vivo experiments revealed that CRC tumor growth was suppressed by TRG-AS1 knockdown and P2RY10 silencing. TRG-AS1 knockdown repressed the growth of HT-29 and LoVo by regulating P2RY10 and GNA13 expression. [ABSTRACT FROM AUTHOR]

Simple Summary: Our study investigates the genetic basis of translucent eggshell formation by analyzing gene expression in the oviduct's isthmus region of hens laying translucent eggs. Our findings highlight that alterations in collagen-related pathways are central to changes in the eggshell's physical structure, leading to translucence. This research offers insights for strategies to reduce translucent egg formation. The presence of translucent eggshells is a type of egg quality issue that impacts egg sales. While many researchers have studied them, the exact mechanisms behind their formation remain unclear. In this study, we conducted a transcriptomic differential expression analysis of the isthmus region of the oviduct in both normal egg- and translucent egg-laying hens. The analysis revealed that differentially expressed gene pathways were predominantly concentrated in the synthesis, modification, and transport of eggshell membrane proteins, particularly collagen proteins, which provide structural support. These findings suggest that variations in the physical structure of the eggshell membrane, resulting from changes in its chemical composition, are the fundamental cause of translucent eggshell formation. This research provides a theoretical reference for reducing the occurrence of translucent eggs. [ABSTRACT FROM AUTHOR]

Background: High-affinity potassium transporters (HKTs) are crucial in facilitating potassium uptake by plants. Many types of HKTs confer salt tolerance to plants through regulating K+ and Na+ homeostasis under salinity stress. However, their specific functions in cassava (Manihot esculenta) remain unclear. Results: Herein, an HKT gene (MeHKT1) was cloned from cassava, and its expression is triggered by exposure to salt stress. The expression of a plasma membrane-bound protein functions as transporter to rescue a low potassium (K+) sensitivity of yeast mutant strain, but the complementation of MeHKT1 is inhibited by NaCl treatment. Under low K+ stress, transgenic Arabidopsis with MeHKT1 exhibits improved growth due to increasing shoot K+ content. In contrast, transgenic Arabidopsis accumulates more Na+ under salt stress than wild-type (WT) plants. Nevertheless, the differences in K+ content between transgenic and WT plants are not significant. Additionally, Arabidopsis expressing MeHKT1 displayed a stronger salt-sensitive phenotype. Conclusion: These results suggest that under low K+ condition, MeHKT1 functions as a potassium transporter. In contrast, MeHKT1 mainly transports Na+ into cells under salt stress condition and negatively regulates the response of transgenic Arabidopsis to salt stress. Our results provide a reference for further research on the function of MeHKT1, and provide a basis for further application of MeHKT1 in cassava by molecular biological means. [ABSTRACT FROM AUTHOR]

Transcriptional regulation plays a key role in the control of seed dormancy, and many transcription factors (TFs) have been documented. However, the mechanisms underlying the interactions between different TFs within a transcriptional complex regulating seed dormancy remain largely unknown. Here, we showed that TF PHYTOCHROME‐INTERACTING FACTOR4 (PIF4) physically interacted with the abscisic acid (ABA) signaling responsive TF ABSCISIC ACID INSENSITIVE4 (ABI4) to act as a transcriptional complex to promote ABA biosynthesis and signaling, finally deepening primary seed dormancy. Both pif4 and abi4 single mutants exhibited a decreased primary seed dormancy phenotype, with a synergistic effect in the pif4/abi4 double mutant. PIF4 binds to ABI4 to form a heterodimer, and ABI4 stabilizes PIF4 at the protein level, whereas PIF4 does not affect the protein stabilization of ABI4. Subsequently, both TFs independently and synergistically promoted the expression of ABI4 and NCED6, a key gene for ABA anabolism. The genetic evidence is also consistent with the phenotypic, physiological and biochemical analysis results. Altogether, this study revealed a transcriptional regulatory cascade in which the PIF4–ABI4 transcriptional activator complex synergistically enhanced seed dormancy by facilitating ABA biosynthesis and signaling. [ABSTRACT FROM AUTHOR]

Background: It has been reported that ferroptosis participates in the pathophysiological mechanism of spinal cord injury (SCI). Our preliminary experiments verified that dendrobium nobile polysaccharide (DNP) improved the behavioral function of SCI rats. Therefore, the purpose of this study was to examine the role of DNP on ferroptosis and its neuroprotective mechanism in SCI rats. Methods: Adult female sprague dawley (SD) rats were exposed to SCI by Allen's method, followed by an intragastric injection of 100 mg/kg DNP per day for 2 weeks. Behavioral features were verified by the Basso-Beattie-Bresnahan (BBB) scale and footprint evaluation. Iron content and glutathione (GSH) were assessed spectrophotometrically. Mitochondrial morphology was examined by transmission electron microscopy. The expression of ferroptosis-related genes, including System Xc-light chain (xCT), G-rich RNA sequence binding Factor 1 (GRSF1) and glutathione peroxidase 4 (Gpx4), was examined by real-time polymerase chain reaction (PCR) and western blot. The spinal cavity was defined using hematoxylin-eosin (HE) staining, and neuronal modifications were detected by immunofluorescence. Results: Compared with the SCI group, the BBB score of rats in the DNP group increased at 7 d, 14 d, 21 d, and 28 d. The differences between the two groups were statistically significant. At 12 h post-injury the iron content began to decrease. At 24 h post-injury the iron content decreased significantly in the DNP group. The morphological changes of the mitochondrial crest and membrane in the DNP group were ameliorated within 24 h. Compared with the sham group, the expression of xCT, GSH, Gpx4, and GRSF1 were significantly reduced after SCI. After DNP treatment, the expression of xCT, Gpx4, and GSH were higher. The tissue cavity area was significantly reduced and the amount of NeuN+ cells was increased in the DNP group at 14 d and 28 d after SCI. Conclusions: DNP facilitated the post-injury recovery in SCI rats via the inhibition of ferroptosis. [ABSTRACT FROM AUTHOR]

Ferroptosis, a lipid peroxidation-mediated programmed cell death, is closely linked to tumor development, including prostate cancer (PCa). Despite established connections between ferroptosis and PCa, a comprehensive investigation is essential for understanding its impact on patient prognosis. Methods: A risk model incorporating four ferroptosis-related genes was developed and validated. Elevated risk scores correlated with an increased likelihood of biochemical recurrence (BCR), diminished immune infiltration, and adverse clinicopathological characteristics. To corroborate these results, we performed validation analyses utilizing datasets from both the Cancer Genome Atlas Cohort (TCGA) and the Gene Expression Synthesis Cohort (GEO). Moreover, we conducted further investigations into the pivotal gene identified in our model to explore its impact on tumor characteristics through cell proliferation and invasion assays, as well as animal studies conducted in vivo. Additionally, we conducted further experiments involving ferroptosis-related analysis to validate its association with ferroptosis. Results: The risk model demonstrated exceptional predictive capabilities for prognosis and therapeutic outcomes in PCa patients. Mitogen-activated protein kinase 9 (MAPK9) emerged as a crucial gene within the model. In vivo and in vitro experiments explored MAPK9's role in ferroptosis and its influence on tumor migration and proliferation. Conclusion: The findings provide a novel perspective for advancing ferroptosis exploration in PCa, bridging basic research and clinical applications. [ABSTRACT FROM AUTHOR]

Background: This study aimed to investigate the relationship between signal regulatory protein gamma (SIRPG) and tumor immune microenvironment phenotypes or T cell mediated-adaptive antitumor immunity, and its predictive value for response to PD-1 blockade in cancers. Methods: Pan-cancer analysis of SIRPG expression and immune deconvolution was performed using transcriptomic data across 33 tumor types. Transcriptomic and clinical data from 157 patients with non-small-cell lung cancer (NSCLC) and melanoma received PD-1 blockade were analyzed. Expression characteristics of SIRPG were investigated using single-cell RNA sequencing (scRNA-seq) data of 103,599 cells. The effect of SIRPG expression was evaluated via SIRPG knockdown or overexpression in Jurkat T cells. Results: The results showed that most cancers with high SIRPG expression had significantly higher abundance of T cells, B cells, NK cells, M1 macrophages and cytotoxic lymphocytes and increased expression level of immunomodulatory factors regulating immune cell recruitment, antigen presentation, T cell activation and cytotoxicity, but markedly lower abundance of neutrophils, M2 macrophages, and myeloid-derived suppressor cells. High SIRPG expression was associated with favorable response to PD-1 blockade in both NSCLC and melanoma. scRNA-seq data suggested SIRPG was mainly expressed in CD8+ exhausted T and CD4+ regulatory T cells, and positively associated with immune checkpoint expression including PDCD1 and CTLA4. In vitro test showed SIRPG expression in T cells could facilitate expression of PDCD1 and CTLA4. Conclusion: High SIRPG expression is associated with an inflamed immune phenotype in cancers and favorable response to PD-1 blockade, suggesting it would be a promising predictive biomarker for PD-1 blockade and novel immunotherapeutic target. [ABSTRACT FROM AUTHOR]

The calmodulin-binding protein 60 (CBP60) family is a gene family unique to plants, and its members play a crucial role in plant defense responses to pathogens and growth and development. Considering that cotton is the primary source of natural cotton textile fiber, the functional study of its CBP60 gene family members is critical. In this research, we successfully identified 162 CBP60 members from the genomes of 21 species. Of these, 72 members were found in four cotton species, divided into four clades. To understand the function of GhCBP60B in cotton in depth, we conducted a detailed analysis of its sequence, structure, cis-acting elements, and expression patterns. Research results show that GhCBP60B is located in the nucleus and plays a crucial role in cotton growth and development and response to salt and drought stress. After using VIGS (virus-induced gene silencing) technology to conduct gene silencing experiments, we found that the plants silenced by GhCBP60B showed dwarf plants and shortened stem nodes, and the expression of related immune genes also changed. In further abiotic stress treatment experiments, we found that GhCBP60B-silenced plants were more sensitive to drought and salt stress, and their POD (peroxidase) activity was also significantly reduced. These results imply the vital role of GhCBP60B in cotton, especially in regulating plant responses to drought and salt stress. This study systematically analyzed CBP60 gene family members through bioinformatics methods and explored in depth the biological function of GhCBP60B in cotton. These research results lay a solid foundation for the future use of the GhCBP60B gene to improve cotton plant type and its drought and salt resistance. [ABSTRACT FROM AUTHOR]

Background: Gamma-glutamyltransferase 5 (GGT5), one of the two members in the GGT family (GGT1 and GGT5), plays a crucial role in oxidative regulation, inflammation promotion, and drug metabolism. Particularly in the tumorigenesis of various cancers, its significance has been recognized. Nevertheless, GGT5's role in gastric cancer (GC) remains ambiguous. This study delves into the function and prognostic significance of GGT5 in GC through a series of in vitro experiments. Methods: Employing online bioinformatics analysis tools such as The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Kaplan–Meier plotter, and cBioPortal, we explored GGT5 characteristics and functions in GC. This encompassed aberrant expression, prognostic value, genomic alterations and mutations, immune cell infiltration, and associated signaling pathways. Immunohistochemistry was conducted to assess GGT5 expression in GC and adjacent normal tissues. Subsequently, univariate and multivariate logistic regression analyses were applied to investigate the associations between GGT5 and clinical characteristics. CCK8, wound healing, and migration assays were utilized to evaluate the impact of GGT5 on cell viability and migration. Additionally, Gene Set Enrichment Analysis (GSEA) and Western blot analysis were performed to scrutinize the activity of the epithelial–mesenchymal transformation (EMT) signaling pathway under GGT5 regulation. Results: GGT5 exhibits upregulation in gastric cancer, with its overexpression significantly linked to histological differentiation in GC patients (P < 0.05). Multivariate analysis indicates that elevated GGT5 expression is an independent risk factor associated with poorer overall survival in gastric cancer patients (P < 0.05). In vitro experiments reveal that downregulation of GGT5 hampers the proliferation and migration of GC cell lines. Finally, GSEA using TCGA data highlights a significant correlation between GGT5 expression and genes associated with EMT, a finding further confirmed by Western blot analysis. Conclusions: GGT5 emerges as a promising prognostic biomarker and potential therapeutic target for GC. [ABSTRACT FROM AUTHOR]

Background Evidence suggests that mitochondrial abnormalities increase the risk of two neurodevelopmental disorders: undiagnosed developmental disorder (UDD) and autism spectrum disorder (ASD). However, which nuclear-encoded mitochondrial-related genes (NEMGs) were associated with UDD–ASD is unclear. Aim To explore the association between de novo variants (DNVs) of NEMGs and UDD–ASD. Design Comprehensive analysis based on DNVs of NEMGs identified in patients (31 058 UDD probands and 10 318 ASD probands) and 4262 controls. Methods By curating NEMGs and cataloging publicly published DNVs in NEMGs, we compared the frequency of DNVs in cases and controls. We also applied a TADA- denovo model to highlight disease-associated NEMGs and characterized them based on gene intolerance, functional networks and expression patterns. Results Compared with levels in 4262 controls, an excess of protein-truncating variants and deleterious missense variants in 1421 cataloged NEMGs from 41 376 patients (31 058 UDD and 10 318 ASD probands) was observed. Overall, 3.23% of de novo deleterious missense variants and 3.20% of de novo protein-truncating variants contributed to 1.1% and 0.39% of UDD–ASD cases, respectively. We prioritized 130 disease-associated NEMGs and showed distinct expression patterns in the developing human brain. Disease-associated NEMGs expression was enriched in both excitatory and inhibitory neuronal lineages from the developing human cortex. Conclusions Rare genetic alterations of disease-associated NEMGs may play a role in UDD–ASD development and lay the groundwork for a better understanding of the biology of UDD–ASD. [ABSTRACT FROM AUTHOR]

MAPKKs, as one of the main members of the mitogen-activated protein kinase (MAPK) cascade pathway, are located in the middle of the cascade and are involved in many physiological processes of plant growth and development, as well as stress tolerance. Previous studies have found that StMAPKK5 is responsive to drought and salt stress. To further investigate the function and regulatory mechanism of StMAPKK5 in potato stress response, potato variety 'Atlantic' was subjected to drought and NaCl treatments, and the expression of the StMAPKK5 gene was detected by qRT-PCR. StMAPKK5 overexpression and RNA interference-mediated StMAPKK5 knockdown potato plants were constructed. The relative water content, superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities, as well as proline (Pro) and malondialdehyde (MDA) contents of plant leaves, were also assayed under drought and NaCl stress. The StMAPKK5 interacting proteins were identified and validated by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). The results showed that the expression of StMAPKK5 was significantly up-regulated under drought and NaCl stress conditions. The StMAPKK5 protein was localized in the nucleus, cytoplasm, and cell membrane. The expression of StMAPKK5 affected the relative water content, the enzymatic activities of SOD, CAT, and POD, and the proline and MDA contents of potatoes under drought and salt stress conditions. These results suggest that StMAPKK5 plays a significant role in regulating drought and salt tolerance in potato crop. Yeast two-hybrid (Y2H) screening identified four interacting proteins: StMYB19, StZFP8, StPUB-like, and StSKIP19. BiFC confirmed the authenticity of the interactions. These findings suggest that StMAPKK5 is crucial for potato growth, development, and response to adversity. [ABSTRACT FROM AUTHOR]

Breast cancer is a females' prevalent malignancy, resulting in higher mortality rates than other cancers. Therefore, exploring effective therapeutic targets and diagnostic biomarkers is critical for improving drugs' curative effect in treating breast cancer patients. The MDA-MB-231 and Michigan Cancer Foundation-7 (MCF-7) cells were transfected by pc-CDCA2, Small interfering RNA Negative Control (siNC), siCDCA2, and pc-KISS1 to investigate the effects of cell division cycle associated 2 (CDCA2) and kisspeptin 1 (KISS1) protein on breast cancer cell's viability, migration and invasion. Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) was used to examine the CDCA2 mRNA expression. Impact of CDCA2 and KISS1 on invasion ability, motility and viability of breast cancer cells were detected via colony-forming unit, Cell Counting Kit-8 (CCK-8) and transwell assay. The Annexin V-Fluorescein Isothiocyanate (annexin V-FITC) staining was employed to determine the cellular apoptosis ratio based on flow cytometry. Findings indicated that CDCA2 expression got increased in breast cancer tissues, which greatly enhanced the cell proliferation, migration and invasion ability. Moreover, the regulation of CDCA2 may suppress the activation of KISS1 in breast cancer cells. In summary, the findings depicted that in breast cancer cells, the CDCA2 expression was enhanced to promote cells motility, invasiveness and viability through inhibition of KISS1 expression. Therefore, targeted gene therapy to suppress the expression levels of CDCA2 and upregulation of the KISS1 have the potential to be promising therapeutic strategies for treating breast cancer metastasis. [ABSTRACT FROM AUTHOR]

Background: Multiple myeloma (MM) is the second most common refractory hematologic cancer. Searching for new targets and prognostic markers for MM is significant. Methods: GSE39754, GSE6477 and GSE24080 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in MM versus healthy people from GSE39754 and GSE6477 were screened using limma package, and MM-related module genes were chosen with the use of Weighted gene co-expression network analysis (WGCNA), and the two were intersected using ggVennDiagram for obtaining MM-related DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out. Then, protein–protein interactions (PPI) analysis in String database was used to obtain hub genes, while prognosis was analyzed by survival package in GSE24080. Receiver operating characteristic (ROC) curve was adopted for evaluating diagnostic value of hub genes. Besides, univariable/multivariable Cox regression were employed to screen independent prognostic biomarkers. Gene set enrichment analysis (GSEA) was used to find possible mechanism. Finally, western-blotting and reverse transcription-polymerase chain reaction (RT-PCR) verify TYROBP expression within MM and healthy people. We performed cell adhesion and transwell assays for investigating TYROBP function in MM cell adhesion and migration. Results: Through differential analyses, 92 MM-related DEGs were obtained. 10 hub genes were identified by PPI and CytoHubba. Their diagnostic and prognostic significance was analyzed. Down-regulation of genes like TYROBP, ELANE, MNDA, and MPO related to dismal MM prognosis. Upon univariable/multivariable Cox regression, TYROBP independently predicted MM prognosis. GSEA pathway was enriched, indicating that TYROBP expression affected MM development via cell adhesion molecular pathway. Upon Western-blotting and RT-PCR assays, TYROBP expression among MM patients decreased relative to healthy donors. Cell adhesion and transwell migration assays revealed increased MM cell adhesion and decreased migration upon TYROBP up-regulation. Conclusion: In summary, TYROBP is a potential prognostic marker for MM. [ABSTRACT FROM AUTHOR]

Background. Circadian rhythm disruption involves tumorigenesis and tumor progression. However, the influences of circadian rhythm on the tumor microenvironment (TME) and the prognosis of hepatocellular carcinoma (HCC) are unknown. Methods. Bulk RNA-seq and single-cell RNA-seq from TCGA, ICGC, and GEO were used to comprehensively identify prognostic circadian control cells and circadian rhythm associated genes (CRRGs) using R and Python packages. Besides, the circadian rhythm-related prognostic signature was identified and validated. The biological function, immune infiltration, and therapeutic response associated with circadian rhythm-related (CR) risk were detected. Results. A total of 252 differentially expressed CRRGs in HCC were identified, and HCC with a high CR score revealed poor survival. We annotated 11 major cell types in TME; immune cells (B cells, myeloid, CD4+ cells, CD8+ cells, NK cells, Tregs) with high CR score, and hepatocyte, bio-potent cells, fibroblasts, and endothelial cells with low CR score were identified. Moreover, five CRRGs (RPL29, PFKFB3, RPS7, SLC6A6, and RPLP2) were selected and validated as the prognostic signature in HCC. The risk score was calculated based on the prognostic signature, and patients then were divided into high-risk and low-risk groups according to the median value of the risk score. High risk is linked to several metabolism-related pathways and canonical cancer-related pathways and is negatively associated with immunotherapeutic responses and positively associated with some chemotherapeutic drugs. Conclusion. Our finding provides the novel circadian rhythm-related prognostic signature and represents a novel viable "time-dependent" therapeutic option for HCC treatment. [ABSTRACT FROM AUTHOR]

Background: The selenomethionine cycle (SeMTC) is a crucial pathway for the metabolism of selenium. The basic bioinformatics and functions of four enzymes involved in the cycle including S-adenosyl-methionine synthase (MAT), SAM-dependent methyltransferase (MTase), S-adenosyl-homocysteine hydrolase (SAHH) and methionine synthase (MTR), have been extensively reported in many eukaryotes. The identification and functional analyses of SeMTC genes/proteins in Cardamine hupingshanensis and their response to selenium stress have not yet been reported. Results: In this study, 45 genes involved in SeMTC were identified in the C. hupingshanensis genome. Phylogenetic analysis showed that seven genes from ChMAT were clustered into four branches, twenty-seven genes from ChCOMT were clustered into two branches, four genes from ChSAHH were clustered into two branches, and seven genes from ChMTR were clustered into three branches. These genes were resided on 16 chromosomes. Gene structure and homologous protein modeling analysis illustrated that proteins in the same family are relatively conserved and have similar functions. Molecular docking showed that the affinity of SeMTC enzymes for selenium metabolites was higher than that for sulfur metabolites. The key active site residues identified for ChMAT were Ala269 and Lys273, while Leu221/231 and Gly207/249 were determined as the crucial residues for ChCOMT. For ChSAHH, the essential active site residues were found to be Asn87, Asp139 and Thr206/207/208/325. Ile204, Ser111/329/377, Asp70/206/254, and His329/332/380 were identified as the critical active site residues for ChMTR. In addition, the results of the expression levels of four enzymes under selenium stress revealed that ChMAT3-1 genes were upregulated approximately 18-fold, ChCOMT9-1 was upregulated approximately 38.7-fold, ChSAHH1-2 was upregulated approximately 11.6-fold, and ChMTR3-2 genes were upregulated approximately 28-fold. These verified that SeMTC enzymes were involved in response to selenium stress to varying degrees. Conclusions: The results of this research are instrumental for further functional investigation of SeMTC in C. hupingshanensis. This also lays a solid foundation for deeper investigations into the physiological and biochemical mechanisms underlying selenium metabolism in plants. [ABSTRACT FROM AUTHOR]

Background: Diabetic peripheral neuropathy (DPN) is a prevalent and serious complication of diabetes mellitus, impacting the nerves in the limbs and leading to symptoms like pain, numbness, and diminished function. While the exact molecular and immune mechanisms underlying DPN remain incompletely understood, recent findings indicate that mitochondrial dysfunction may play a role in the advancement of this diabetic condition. Methods: Two RNA transcriptome datasets (codes: GSE185011 and GSE95849), comprising samples from diabetic peripheral neuropathy (DPN) patients and healthy controls (HC), were retrieved from the Gene Expression Omnibus (GEO) database hosted by the National Center for Biotechnology Information (NCBI). Subsequently, differential expression analysis and gene set enrichment analysis were performed. Protein–protein interaction (PPI) networks were constructed to pinpoint key hub genes associated with DPN, with a specific emphasis on genes related to mitochondria and peripheral neuropathy disease (PND) that displayed differential expression. Additionally, the study estimated the levels of immune cell infiltration in both the HC and DPN samples. To validate the findings, quantitative polymerase chain reaction (qPCR) was employed to confirm the differential expression of selected genes in the DPN samples. Results: This research identifies four hub genes associated mitochondria or PN. Furthermore, the analysis revealed increased immune cell infiltration in DPN tissues, particularly notable for macrophages and T cells. Additionally, our investigation identified potential drug candidates capable of regulating the expression of the four hub genes. These findings were corroborated by qPCR results, reinforcing the credibility of our bioinformatics analysis. Conclusions: This study provides a comprehensive overview of the molecular and immunological characteristics of DPN, based on both bioinformatics and experimental methods. [ABSTRACT FROM AUTHOR]

Post-traumatic stress disorder (PTSD) is one of the most serious sequelae of trauma with serious impact worldwide. Studies have suggested an association between PTSD and major depressive disorder (MDD), but the underlying common mechanisms remain unclear. This study aimed to further explore the molecular mechanism between PTSD and MDD via comprehensive bioinformatics analysis. The microarray data of PTSD and MDD were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify the co-expressed genes associated with PTSD and MDD. Gene Set Enrichment Analysis (GSEA), enrichment analyses based on Disease Ontology (DO), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed using R software. Then, R software was used for single-sample gene set enrichment analysis (ssGSEA) and immune infiltration analysis on the co-expressed genes in the two datasets., Therefore, a logistic regression model was constructed to predict PTSD and MDD using the R language. Ultimately, this study employed PTSD and MDD models to assess alterations in the expression of target genes within the mouse hippocampus. Four core genes (GNAQ, DPEP3, ICAM2, PACSIN2) were obtained through different analyses, and these genes had predictive validity for PTSD and MDD, playing an important role in the common mechanism of PTSD and MDD. The study findings reveal decreased expression levels of DPEP3, GNAQ, and PACDIN2 in PTSD samples, accompanied by an increased expression of ICAM2. In MDD samples, the expression of DPEP3 and ICAM2 is reduced, whereas GNAQ and PACDIN2 show an increase in expression. This study provides a new perspective on the common molecular mechanisms of PTSD and MDD. These common pathways and core genes may provide promising clues for further experimental studies. • Four hub genes were obtained through different analyses, and these genes had predictive validity for PTSD and MDD. • This study provides a new perspective on the common molecular mechanisms of PTSD and MDD. • These common pathways and hub genes may provide promising clues for further experimental studies. [ABSTRACT FROM AUTHOR]

The cell cycle is a highly regulated process in which proteins involved in cell cycle progression exhibit periodic expression patterns, controlled by specific mechanisms such as transcription, translation, and degradation. However, the precise mechanisms underlying the oscillations of mRNA levels in cell cycle regulators are not fully understood. In this study, we observed that the stability of cyclin D1 (CCND1) mRNA fluctuates during the cell cycle, with increased stability during interphase and decreased stability during the M phase. Additionally, we identified a key RNA binding protein, positive coactivator 4 (PC4), which plays a crucial role in stabilizing CCND1 mRNA and regulating its periodic expression. Moreover, the binding affinity of PC4 to CCND1 mRNA is modulated by two cell cycle-specific posttranslational modifications: ubiquitination of K68 enhances binding and stabilizes the CCND1 transcript during interphase, while phosphorylation of S17 inhibits binding during the M phase, leading to degradation of CCND1 mRNA. Remarkably, PC4 promotes the transition from G1 to S phase in the cell cycle, and depletion of PC4 enhances the efficacy of CDK4/6 inhibitors in hepatocellular carcinoma, suggesting that PC4 could serve as a potential therapeutic target. These findings provide valuable insights into the intricate regulation of cell cycle dynamics. [ABSTRACT FROM AUTHOR]

Although the gut microbiota has been well reported to contribute to the pest insecticidal activity of Bacillus thuringiensis (Bt) toxin, the underlying mechanism remains largely unknown. Here, bioassay, RNA-seq, and 16S rRNA sequencing were employed to explore the potential mechanism by which gut microbiota enhance the virulence of Bt maize to Mythimna separata. Two groups of neonate larvae were fed with the leaves of conventional maize (CK group) and insect-resistant transgenic maize (Bt group), respectively. The results indicated that body weight, body length, and survival rate of M. separata in the Bt group were significantly reduced. Additionally, the induced growth retardation further led to normal mating failure and fecundity deprivation of M. separata in Bt group. The 16S rRNA sequencing results indicated that exposure to insect-resistant transgenic maize significantly decreased the diversity of the bacterial community and increased the relative abundance of Enterobacter cloacae and Enterococcus mundtii by 153.02-folds and 2.08-folds, respectively. Reintroduction of these two bacteria significantly increased the sensitivity of M. separata to Bt toxin. Transcriptome results revealed that numerous genes related to Notch, Hippo, Wnt, amino acid synthesis, and fatty acid metabolism pathways were significantly down-regulated in the Bt group, whereas almost all Bt toxin receptor aminopeptidase N genes were up-regulated. This study revealed that exposure to insect-resistant transgenic maize reduced gut bacterial diversity and altered the gene expression of M. separata. Furthermore, E. cloacae and E. mundtii enhanced the susceptibility of M. separata to Bt toxin. Our findings on the interaction between Bt toxins, gut microbiota, and the host insect will contribute to the development of pest management strategies and the promotion of transgenic crops in China. [ABSTRACT FROM AUTHOR]

Summary: The chilling stress induced by the global climate change harms rice production, especially at seedling and booting stage, which feed half the population of the world. Although there are key quantitative trait locus genes identified in the individual stage, few genes have been reported and functioned at both stages.Utilizing chromosome segment substitution lines (CSSLs) and a combination of map‐based cloning and phenotypes of the mutants and overexpression lines, we identified the major gene Chilling‐tolerance in Geng/japonica rice 3 (COG3) of q chilling‐tolerance at the booting and seedling stage 11 (qCTBS11) conferred chilling tolerance at both seedling and booting stages.COG3 was significantly upregulated in Nipponbare under chilling treatment compared with its expression in 93‐11. The loss‐of‐function mutants cog3 showed a reduced chilling tolerance. On the contrary, overexpression enhanced chilling tolerance. Genome evolution and genetic analysis suggested that COG3 may have undergone strong selection in temperate japonica during domestication. COG3, a putative calmodulin‐binding protein, physically interacted with OsFtsH2 at chloroplast. In cog3‐1, OsFtsH2‐mediated D1 degradation was impaired under chilling treatment compared with wild‐type.Our results suggest that COG3 is necessary for maintaining OsFtsH2 protease activity to regulate chilling tolerance at the booting and seedling stage. [ABSTRACT FROM AUTHOR]

Objective: To investigate the role and mechanisms of SOCS3 protein in IL-10 inhibiting the expression of inflammatory factors in Chlamydia-infected cells. Methods: The activation of STAT3 protein were examined in Chlamydia-infected cells by Western blot, and the activation of p38 and ERK1/2 were also examined in infected cells treated with socs3 siRNA. The expression of socs3 gene was examined in Chlamydia-infected cells treated with IL-10 or Stattic by RT-PCR. IL-6 and IL-12 were measured in infect-ed cells treated with socs3 siRNA using ELISA kits. Results: Socs3 expression was up-regulated by IL-10 through activation of STAT3 protein. IL-6 and IL-12 induced by Chlamydia were down-regulated by IL-10 through induction of socs3. The activation of p38 and ERK1/2 signalling pathways were inhibited by SOCS3. Conclusion: IL-10 inhibits the production of pro-inflammatory cytokines through induction of SOCS3 and inhibition p38 and ERK1/2 signalling pathways. [ABSTRACT FROM AUTHOR]

Necroptosis is a recently identified caspase-independent form of cell death which plays a significant role in the onset and progression of cancer. MicroRNAs (miRNAs) are vital for the development of uterine corpus endometrial carcinoma (UCEC) because they are an important regulatory component in necroptosis. This study developed a new necroptosis-related miRNAs profile to predict the prognosis of patients with UCEC. The TCGA-UCEC cohort's RNA sequencing data, consisting of 534 tumor samples and 33 normal samples, was downloaded. Ten differentially expressed miRNAs related to necroptosis were identified. A prediction model for necroptosis-related miRNAs was then created through COX regression and nomograms analysis. Clinical and pathological parameters were integrated to construct a nomogram and evaluate the model. Prognosis-related miRNAs were further used to predict target genes, and functional analysis was conducted to explore the potential mechanisms of these target genes. Subsequently, immune infiltration analysis was performed using transcriptome data to identify immune genes associated with prognosis, and the expression levels of target gene was validated using UCEC tissues. We identified 7 up-regulated miRNAs (hsa-miR-577, hsa-miR-7-5p, hsa-miR-210-3p, hsa-miR-210-5p, hsa-miR-200a-5p, hsa-miR-141-3p, hsa-miR-425-5p) and 3 down-regulated miRNAs (hsa-miR-7-2-3p, hsa-miR-383-5p, hsa-miR-29a-3p). The risk signature was based on univariate and multivariate COX analyses, constructed using 2 independent prognostic factors and miRNAs (hsa-miR-425-5p, hsa-miR-7-5p) associated with necroptosis. Nomograms demonstrated the prognostic value of risk level, age, FIGO stage, and histological type. Kaplan–Meier analysis revealed significant differences in overall survival (OS) outcomes associated with the expression of hsa-miR-425-5p (P < 0.001) and hsa-miR-7-5p (P = 0.015). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) investigations indicated that these miRNAs play crucial roles in tumor development, metastasis, and prognosis. Immune infiltration analysis showed decreased infiltration of CD8+ T cells, CD8+ T cells, NK cells, and M1 macrophages in normal tissues. Subsequently, a necroptosis-related immune gene significantly associated with prognosis (THRB) was identified, western blot and immunohistochemical staining confirmed the differential expression of THRB in normal endometrial tissues and tumor. Our findings demonstrate a close association between necroptosis and UCEC. The two necroptosis-related miRNAs used in this study may serve as valuable prognostic markers for UCEC patients, and are associated with immune cell infiltration. This suggests that necroptosis may be involved in the development of UCEC through its interaction with immune responses. [ABSTRACT FROM AUTHOR]

Diabetic retinopathy (DR) is a severe microvascular complication of diabetes and is one of the primary causes of blindness in the working-age population in Europe and the United States. At present, no cure is available for DR, but early detection and timely intervention can prevent the rapid progression of the disease. Several treatments for DR are known, primarily ophthalmic treatment based on glycemia, blood pressure, and lipid control, which includes laser photocoagulation, glucocorticoids, vitrectomy, and antivascular endothelial growth factor (anti-VEGF) medications. Despite the clinical efficacy of the aforementioned therapies, none of them can entirely shorten the clinical course of DR or reverse retinopathy. MicroRNAs (miRNAs) are vital regulators of gene expression and participate in cell growth, differentiation, development, and apoptosis. MicroRNAs have been shown to play a significant role in DR, particularly in the molecular mechanisms of inflammation, oxidative stress, and neurodegeneration. The aim of this review is to systematically summarize the signaling pathways and molecular mechanisms of miRNAs involved in the occurrence and development of DR, mainly from the pathogenesis of oxidative stress, inflammation, and neovascularization. Meanwhile, this article also discusses the research progress and application of miRNA-specific therapies for DR. [ABSTRACT FROM AUTHOR]

Background: Epithelial ovarian cancer (EOC) is insensitive to immunotherapy due to its poor immunogenicity; thus, suitable biomarkers need to be identified for better prognostic stratification and individualized treatment. CD47 is a novel immunotherapy target; however, its impact on EOC prognosis is controversial and correlation with genetic features is unclear. The aim of this study was to investigate the prognostic significance of CD47 and its correlations with biological behaviors and genetic features of EOC. Methods: Immunohistochemistry (IHC) and next-generation sequencing (NGS) were performed to examine expressions of CD47, PD-L1, and genomic mutations in the tissue samples of 75 EOC patients. Various clinicopathologic and genomic features were then evaluated to determine their correlation with CD47 expression. Kaplan–Meier analysis and Cox regression analysis were used to identify independent prognostic factors. Risk score modeling was then established, and the predictive capacity of this model was further confirmed by nomogram analysis. Results: CD47 was mainly expressed in the tumor cell membrane and cytoplasm, and the rate of high CD47 expression was 63.7%. CD47 expression was associated with various clinicopathological factors, including FIGO stage, CA125 and HE4 value, presence of multidisciplinary surgeries, presence and volume of ascites, lymph-node metastasis, Ki-67 index and platinum-resistant, as well as genetic characteristics like BRCA mutation, HRD status, and TP53 mutation in EOC. Patients with high CD47 expression showed worse prognosis than the low-expression group. Cox regression analysis demonstrated that CA125, CD47, and BRCA mutation were independent factors for EOC prognosis. Patients were then categorized into high-risk and low-risk subgroups based on the risk score of the aforementioned independent factors, and the prognosis of the high-risk group was worse than those of the low-risk group. The nomogram showed adequate discrimination with a concordance index of 0.777 (95% CI, 0.732–0.822). The calibration curve showed good consistency. Conclusion: CD47 correlated with various malignant biology and genetic characteristics of EOC and may play pivotal and multifaceted roles in the tumor microenvironment of EOC Finally, we constructed a reliable prediction model centered on CD47 and integrated CA125 and BRCA to better guide high-risk population management. [ABSTRACT FROM AUTHOR]

Diabetic nephropathy(DN) remains a significant risk factor for cardiovascular and all-cause mortality, and end-stage renal disease (ESRD) associated with it is growing in prevalence.However, there is absolutely no curative strategy for DN. We subjected db/db and control mouse kidneys to transcriptional sequencing analysis to obtain transcriptome expression profile data in the diabetic nephropathy.We next performed differential analysis of db/db and control mice kidney sequencing data to obtain differentially expressed genes. The differential expressed genes were intersected with the oxidative stress and inflammatory response related genes derived from the MGI/MsiDB gene set to yield oxidative stress inflammatory response related differential 122 genes (OIRDEGs). To further clarify the biological functions of DEGs, we conducted GOKEGG analysis and obtained the top 20 genes by five computational algorithms of the cytohubba plugin via cytoscape, respectively. The genes obtained by the five algorithms were intersected and the intersection genes were considered as key genes,including Cd40lg, Il2rb, Lck, Il2rg, Zap70, Serpinb1a. Also,we used GSEA and immune infiltration analysis to clarify the biological signaling pathways and immune cell infiltration that are substantial in the diabetic nephropathy.Correlation studies of key genes with immune cell infiltration revealed that they were correlated with the majority types of T cells while only with two types of B cells.Then, we predicted miRNA and TF for the key genes and constructed the interaction network. Finally, the expression differences of key genes were examined by validation dataset and RT-PCR experiment.In conclusion,we have identified key genes associated with T cell immune response in a diabetic nephropathy model, which bear significance in the etiopathogenesis of immunological injury in diabetic nephropathy and provide an innovative proposal for the recognition and management of DN. • Diabetic nephropathy is a major cause of end-stage renal disease. • Pathogenesis of diabetic nephropathy is undefined and key genes have essential contributions. • Key genes in diabetic nephropathy are associated with T cell development and signaling pathways. • T cell-associated immune-inflammatory responses may be a novel target for intervention in diabetic nephropathy. [ABSTRACT FROM AUTHOR]

Background: Inflammatory bowel disease (IBD) and psoriasis (Ps) are common immune‐mediated diseases that exhibit clinical comorbidity, possibly due to a common genetic structure. However, the exact mechanism remains unknown. Methods: The study population consisted of IBD and Ps genome‐wide association study (GWAS) data. Genetic correlations were first evaluated. Then, the overall evaluation employed LD score regression (LDSC), while the local assessment utilized heritability estimation from summary statistics (HESS). Causality assessment was conducted through two‐sample Mendelian randomization (2SMR), and genetic overlap analysis utilized the conditional false discovery rate/conjunctional FDR (cond/conjFDR) method. Finally, LDSC applied to specifically expressed genes (LDSC‐SEG) was performed at the tissue level. For IBD and Ps‐specific expressed genes, genetic correlation, causality, shared genetics, and trait‐specific associated tissues were methodically examined. Results: At the genomic level, both overall and local genetic correlations were found between IBD and Ps. MR analysis indicated a positive causal relationship between Ps and IBD. The conjFDR analysis with a threshold of < 0.01 identified 43 loci shared between IBD and Ps. Subsequent investigations into disease‐associated tissues indicated a close association of IBD and Ps with whole blood, lung, spleen, and EBV‐transformed lymphocytes. Conclusion: The current research offers a novel perspective on the association between IBD and Ps. It contributes to an enhanced comprehension of the genetic structure and mechanisms of comorbidities in both diseases. [ABSTRACT FROM AUTHOR]

Annexins (ANNs) are a structurally conserved protein family present in almost all plants. In the present study, 27 GhANNs were identified in cotton and were unevenly distributed across 14 chromosomes. Transcriptome data and RT-qPCR results revealed that multiple GhANNs respond to at least two abiotic stresses. Similarly, the expression levels of GhANN4 and GhANN11 were significantly upregulated under heat, cold, and drought stress. Using virus-induced gene silencing (VIGS), functional characterization of GhANN4 and GhANN11 revealed that, compared with those of the controls, the leaf wilting of GhANN4-silenced plants was more obvious, and the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) were lower under NaCl and PEG stress. Moreover, the expression of stress marker genes (GhCBL3, GhDREB2A, GhDREB2C, GhPP2C, GhRD20-2, GhCIPK6, GhNHX1, GhRD20-1, GhSOS1, GhSOS2 and GhSnRK2.6) was significantly downregulated in GhANN4-silenced plants after stress. Under cold stress, the growth of the GHANN11-silenced plants was significantly weaker than that of the control plants, and the activities of POD, SOD, and CAT were also lower. However, compared with those of the control, the elasticity and orthostatic activity of the GhANN11-silenced plants were greater; the POD, SOD, and CAT activities were higher; and the GhDREB2C, GhHSP, and GhSOS2 expression levels were greater under heat stress. These results suggest that different GhANN family members respond differently to different types of abiotic stress. [ABSTRACT FROM AUTHOR]

MnSOD is a ubiquitous metalloenzyme that constitutes the first line of antioxidant defense against oxidative stress. In this study, full length sequence of MnSOD was identified from hybrid crucian carp (WR, Carassius cuvieri ♀ × Carassius auratus red var ♂). Tissue-specific analysis revealed that the highest expression of WR-MnSOD was detected in kidney. Aeromonas hydrophila challenge could dramatically enhance WR-MnSOD mRNA expression in tissues. In vivo administration of purified WR-MnSOD peptide could maintain gut mucosal barrier function, rescue redox balance as well as decrease apoptotic cell death in midgut upon bacterial infection, suggesting that WR-MnSOD is playing a crucial role in gut mucosal barrier function and could be used as feed additive to improve gut immunity in fish. [ABSTRACT FROM AUTHOR]

T-2 toxin and selenium deficiency are considered important etiologies of Kashin–Beck disease (KBD), although the exact mechanism is still unclear. To identify differentially expressed microRNAs (DE-miRNAs) in the articular cartilage of rats exposed to T-2 toxin and selenomethionine (SeMet) supplementation, thirty-six 4-week-old Sprague Dawley rats were divided into a control group (gavaged with 4% anhydrous ethanol), a T-2 group (gavaged with 100 ng/g·bw/day T-2 toxin), and a T-2 + SeMet group (gavaged with 100 ng/g·bw/day T-2 toxin and 0.5 mg/kg·bw/day SeMet), respectively. Toluidine blue staining was performed to detect the pathological changes of articular cartilage. Three rats per group were randomly selected for high-throughput sequencing of articular cartilage. Target genes of DE-miRNAs were predicted using miRanda and RNAhybrid databases, and the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway were enriched. The network map of miRNA-target genes was constructed using Cytoscape software. The expression profiles of miRNAs associated with KBD were obtained from the Gene Expression Omnibus database. Additionally, the DE-miRNAs were selected for real-time quantitative PCR (RT-qPCR) verification. Toluidine blue staining demonstrated that T-2 toxin damaged articular cartilage and SeMet effectively alleviated articular cartilage lesions. A total of 50 DE-miRNAs (28 upregulated and 22 downregulated) in the T-2 group vs. the control group, 18 DE-miRNAs (6 upregulated and 12 downregulated) in the T-2 + SeMet group vs. the control group, and 25 DE-miRNAs (5 upregulated and 20 downregulated) in the T-2 + SeMet group vs. the T-2 group were identified. Enrichment analysis showed the target genes of DE-miRNAs were associated with apoptosis, and in the MAPK and TGF-β signaling pathways in the T-2 group vs. the control group. However, the pathway of apoptosis was not significant in the T-2 + SeMet group vs. the control group. These results indicated that T-2 toxin induced apoptosis, whereas SeMet supplementation antagonized apoptosis. Apoptosis and autophagy occurred simultaneously in the T-2 + SeMet group vs. T-2 group, and autophagy may inhibit apoptosis to protect cartilage. Compared with the GSE186593 dataset, the evidence of miR-133a-3p involved in apoptosis was more abundant. The results of RT-qPCR validation were consistent with RNA sequencing results. Our findings suggested that apoptosis was involved in articular cartilage lesions induced by T-2 toxin, whereas SeMet supplementation antagonized apoptosis, and that miR-133a-3p most probably played a central role in the apoptosis process. [ABSTRACT FROM AUTHOR]

[Display omitted] Rice (Oryza sativa L.) production is threatened by global warming associated with extreme high temperatures, and rice heat sensitivity is differed when stress occurs between daytime and nighttime. However, the underlying molecular mechanism are largely unknown. We show here that two glycine-rich RNA binding proteins, OsGRP3 and OsGRP162, are required for thermotolerance in rice, especially at nighttime. The rhythmic expression of OsGRP3 / OsGRP162 peaks at midnight, and at these coincident times, is increased by heat stress. This is largely dependent on the evening complex component OsELF3-2. We next found that the double mutant of OsGRP3 /Os GRP162 is strikingly more sensitive to heat stress in terms of survival rate and seed setting rate when comparing to the wild-type plants. Interestingly, the defect in thermotolerance is more evident when heat stress occurred in nighttime than that in daytime. Upon heat stress, the double mutant of OsGRP3 / OsGRP162 displays globally reduced expression of heat-stress responsive genes, and increases of mRNA alternative splicing dominated by exon-skipping. This study thus reveals the important role of OsGRP3/OsGRP162 in thermotolerance in rice, and unravels the mechanism on how OsGRP3/OsGRP162 regulate thermotolerance in a diurnal manner. [ABSTRACT FROM AUTHOR]

The evolution of insect vector‐pathogen relationships has long been of interest in the field of molecular ecology. One system of special relevance, due to its economic impacts, is that between Diaphorina citri and 'Candidatus Liberibacter asiaticus' (CLas), the cause of the severe Asian form of huanglongbing. CLas‐positive D. citri are more fecund than their CLas‐negative counterparts, boosting opportunities for pathogens to acquire new vector hosts. The molecular mechanism behind this life‐history shift remains unclear. Here, we found that CLas promoted ovarian development and increased the expression of the vitellogenin receptor (DcVgR) in ovaries. DcVgR RNAi significantly decreased fecundity and CLas titer in ovaries, extended the preoviposition period, shortened the oviposition period and blocked ovarian development. Given their importance in gene regulation, we explored the role of miRNAs in shaping these phenotypes and their molecular triggers. Our results showed that one miRNA, miR‐275, suppressed DcVgR expression by binding to its 3' UTR. Overexpression of miR‐275 knocked down DcVgR expression and CLas titer in ovaries, causing reproductive defects that mimicked DcVgR knockdown phenotypes. We focused, further, on roles of the Juvenile Hormone (JH) pathway in shaping the observed fecundity phenotype, given its known impacts on ovarian development. After CLas infection, this pathway was upregulated, thereby increasing DcVgR expression. From these combined results, we conclude that CLas hijacks the JH signalling pathway and miR‐275, thereby targeting DcVgR to increase D. citri fecundity. These changes simultaneously increase CLas replication, suggesting a pathogen‐vector host mutualism, or a seemingly helpful, but cryptically costly life‐history manipulation. [ABSTRACT FROM AUTHOR]

Profiling spatial variations of cellular composition and transcriptomic characteristics is important for understanding the physiology and pathology of tissues. Spatial transcriptomics (ST) data depict spatial gene expression but the currently dominating high-throughput technology is yet not at single-cell resolution. Single-cell RNA-sequencing (SC) data provide high-throughput transcriptomic information at the single-cell level but lack spatial information. Integrating these two types of data would be ideal for revealing transcriptomic landscapes at single-cell resolution. We develop the method STEM (SpaTially aware EMbedding) for this purpose. It uses deep transfer learning to encode both ST and SC data into a unified spatially aware embedding space, and then uses the embeddings to infer SC-ST mapping and predict pseudo-spatial adjacency between cells in SC data. Semi-simulation and real data experiments verify that the embeddings preserved spatial information and eliminated technical biases between SC and ST data. We apply STEM to human squamous cell carcinoma and hepatic lobule datasets to uncover the localization of rare cell types and reveal cell-type-specific gene expression variation along a spatial axis. STEM is powerful for mapping SC and ST data to build single-cell level spatial transcriptomic landscapes, and can provide mechanistic insights into the spatial heterogeneity and microenvironments of tissues. STEM is a transfer-learning-based method that integrates spatial transcriptomics and scRNA-seq data to reconstruct localization at the single-cell level and reveal gene expression variation within cell types in tissues. [ABSTRACT FROM AUTHOR]

Simple Summary: In order to investigate the effects of low oxygen stress on the survival rate, antioxidant, anaerobic metabolic enzymes, and related genes of crayfish during aquaculture. This experiment conducted a 24-h low oxygen stress experiment on juvenile and subadult crayfish, and the results showed that the higher the degree of low oxygen stress, the higher the antioxidant and anaerobic metabolic enzyme activity and gene expression levels of juvenile crayfish and subadult crayfish. Compared with subadult crayfish, the antioxidant system of crayfish larvae is more sensitive to hypoxic environments. The red swamp crayfish Procambarus clarkii is the most reared shrimp in China, but it is often affected by hypoxia stress in the process of seedling culture and adult crayfish culture. The oxygen consumption rate and asphyxiation point of juvenile crayfish (1.17 ± 0.03 g) and subadult crayfish (11.68 ± 0.11 g) at different temperatures (20, 22, 24, 26, and 28 °C) were studied. The survival, glycolysis, and expression of antioxidant genes were compared under 24 h acute hypoxia stress (1, 2, and 3 mg/L) and normal dissolved oxygen (7.5 mg/L). The results showed that the oxygen consumption rate and asphyxiation point of juvenile and subadult crayfish increased with increasing temperatures (20–28 °C). At the same temperature, the oxygen consumption rate and asphyxiation point of juvenile crayfish were significantly higher than those of subadult crayfish (p < 0.05). Within 24 h, the three hypoxia stress environments did not lead to the death of crayfish, indicating that P. clarkii has a strong ability to adapt to hypoxia. Hypoxia stress significantly affected the activities of antioxidant and anaerobic metabolic enzymes and gene expression in juvenile and subadult crayfish. The activities of the superoxide dismutase (SOD), catalase (CAT), and lactate dehydrogenase (LDH) and the content of lactic acid (LD) in the hepatopancreas of juvenile and subadult crayfish in the hypoxia stress groups increased significantly. The expression levels of SOD mRNA, CAT mRNA, Hsp70 mRNA, and crustin 4 mRNA in the hepatopancreas of juvenile and subadult crayfish in the hypoxia stress groups were significantly higher than those in the control group (p < 0.05), and the higher the degree of hypoxia stress, the higher the expression of each gene. The results showed that the antioxidant system of juvenile crayfish was more sensitive to hypoxia environments, and hypoxia stress resulted in increased stress levels in juvenile crayfish and subadult crayfish. [ABSTRACT FROM AUTHOR]

Cupriavidus necator is a versatile microbial chassis to produce high-value products. Blocking the poly-β-hydroxybutyrate synthesis pathway (encoded by the phaC1AB1 operon) can effectively enhance the production of C. necator, but usually decreases cell density in the stationary phase. To address this problem, we modified the hexose utilization pathways of C. necator in this study by implementing strategies such as blocking the Entner–Doudoroff pathway, completing the phosphopentose pathway by expressing the gnd gene (encoding 6-phosphogluconate dehydrogenase), and completing the Embden–Meyerhof–Parnas pathway by expressing the pfkA gene (encoding 6-phosphofructokinase). During heterotrophic fermentation, the OD600 of the phaC1AB1-knockout strain increased by 44.8% with pfkA gene expression alone, and by 93.1% with gnd and pfkA genes expressing simultaneously. During autotrophic fermentation, gnd and pfkA genes raised the OD600 of phaC1AB1-knockout strains by 19.4% and 12.0%, respectively. To explore the effect of the pfkA gene on the production of C. necator, an alanine-producing C. necator was constructed by expressing the NADPH-dependent L-alanine dehydrogenase, alanine exporter, and knocking out the phaC1AB1 operon. The alanine-producing strain had maximum alanine titer and yield of 784 mg/L and 11.0%, respectively. And these values were significantly improved to 998 mg/L and 13.4% by expressing the pfkA gene. The results indicate that completing the Embden–Meyerhof–Parnas pathway by expressing the pfkA gene is an effective method to improve the growth and production of C. necator. [ABSTRACT FROM AUTHOR]

Purpose: Recurrent implantation failure (RIF) affects up to 10% of in vitro fertilization (IVF) patients worldwide. However, the pathogenesis of RIF remains unclear. This study was aimed at identifying hub transcription factors (TFs) of RIF in bioinformatics approaches. Methods: The GSE111974 (mRNA), GSE71332 (miRNA), and GSE103465 (mRNA) datasets were downloaded from the Gene Expression Omnibus database from human endometrial tissue using R version 4.2.1 and used to identify differentially expressed TFs (DETFs), differentially expressed miRNAs, and differentially expressed genes for RIF, respectively. DETFs were subjected to functional enrichment analysis and the protein–protein interaction network analysis using the Search Tool for the Retrieval of Interacting Genes (version 11.5) database. Hub TFs were identified using the cytoHubb plug-in, after which a hub TF–miRNA–mRNA network was constructed using Cytoscape v3.8.2. Results: Fifty-seven DETFs were identified, in which Gene Ontology analysis revealed to be mainly involved in the regulation of transcription. Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that DETFs were enriched in transcriptional misregulation in cancer, aldosterone synthesis and secretion, AMPK signaling pathway, and cGMP-PKG signaling pathway. EOMES, NKX2-1, and POU5F1 were identified as hub TFs, and a hub TF–miRNA–mRNA regulatory network was constructed using these three hub TFs, four miRNAs, and four genes. Conclusion: Collectively, we identified three promising molecular biomarkers for the diagnosis of RIF, which may further be potential therapeutic targets. This study provides novel insights into the molecular mechanisms underlying RIF. However, further experiments are required to verify these results. [ABSTRACT FROM AUTHOR]

Strawberry is a major fruit crop worldwide because its nutritional and health benefits to human health, but its productivity is limited by Botrytis cinerea. Sucrose nonfermentation 1-related protein kinase 1 (SnRK1) has a defense function against pathogens, but the function of SnRK1 in the defense response to B. cinerea in plants is still unclear. In this study, FaSnRK1α-OE and RNAi fruits were constructed and then inoculated with B. cinerea. The result reveals a positive role of FaSnRK1α in the regulation of resistance to gray mold. FaSnRK1α affects SA content by regulating FaPAL1 and FaPAL2 expressions. The genes related to the SA signaling pathway (FaTGA1 and FaTGA2.1) were significantly increased/decreased in FaSnRK1α-OE or FaSnRK1α-RNAi fruit, respectively. FaSnRK1α interacted with the FaWRKY33.2 protein and negatively regulated FaWRKY33.2 expression, and FaWRKY33.2 acts as a repressor of disease resistance to B. cinerea. Finally, FaSnRK1a regulates the expression of six PR genes and the activities of antioxidant enzymes to boost defense response after B. cinerea inoculation. Our findings showed that FaSnRK1a increases the resistance of strawberry fruit to B. cinerea via SA signaling pathway and interaction with the FaWRKY33.2 transcription factor. [ABSTRACT FROM AUTHOR]

Objective To investigate the effects of long non-coding ribonucleic acid (LncRNA) repulsive guidance molecules B-antisense chain (RGMB-AS1) on the proliferation, migration and invasion of human prostate cancer cells (DU145), and explore its targeting effect on miR-574-3p. Methods Human prostate cancer cells (DU145) were cultured and used in the study. Cell tests were divided into 9 groups including RGMB-AS1 upregulation group (transfected with pcDNA3. 1-RGMB-AS1), RGMB-AS1 upregulation control group (transfected with pcDNA3. 1 control), RGMB-AS1 downregulation group (transfected with si-RGMB-ASl), RGMB-AS1 downregulation control group (transfected with si-NC), miR-574-3p upregulation group (transfected with miR-574-3p mimics), miR-574-3p upregulation control group (transfected with miR mimics NC ), miR-574-3p downregulation group (transfected with miR-574-3 p inhibitor), miR-574-3p downregulated control group (transfected with miR inhibitor NC) and blank group, and 3 wells in each group. After 48 hours culture, cell proliferation activity was detected by CCK-8 assay. Cell migration ability was evaluated by wound healing assay. Cell invasive ability was assessed by Matrigel invasion assay (Transwell chamber). The expression of LncRNA RGMB-AS1, the expression of miR-574-3p, and the gene expressions of Cyclin D1, P21, ZEB1, N-cadherin, E-cadherin, and Vimentin were detected by LncRNA-RT-qPCR, miRNA-RT-qPCR and RT-qPCR, respectively. The protein expressions of Cyclin Dl, P21, ZEB1, N-cadherin, E-cadherin, and VIM were measured by western blot. The dual luciferase gene reporter assay was used to determine whether LncRNA RGMB-AS1 targets miR-574-3p. Results Compared with those in the blank group, RGMB-AS1 up-regulated control group, RGMB-AS1 down-regulated control group, miR-574-3p up-regulated control group, and miR-574-3p down-regulated control group, the D value, scratch healing rates, invasive cell counts, Cyclin Dl, ZEB1, N-cadherin, and VIM expressions in the RGMB-AS1 up-regulated group and miR-574-3p up-regulated group were all decreased (P <0. 05), while the proliferation inhibition rates, P21, and E-cadherin expressions were all increased (P <0.05). Simultaneously, the D value, scratch healing rates, invasive cell counts, Cyclin Dl, ZEB1, N-cadherin, and VIM expressions in the RGMB-AS1 down-regulated group and miR-574-3p down-regulated group were all increased (P <0. 05), while the proliferation inhibition rates, P21, and E-cadherin expressions were all decreased (P<0.05). Compared with the miR-NC group, the miR-574-3p mimics group showed a decrease in Wt-RGMR-AS1 luciferase activity (P<0. 05), but little change in Mut RGMB-AS1-luciferase activity (P > 0. 05). Conclusion Upregulation of LncRNA RGMB-AS1 can target upregulation of miR-574-3p to inhibit the proliferation, migration, and invasion of human prostate cancer cells, which may be attributed to downregulation of Cyclin D1, ZEB1, N-cadherin, VIM expressions, and upregulation of P21 and E-cadherin expressions. [ABSTRACT FROM AUTHOR]

The aim of the work described here was to investigate the relative contribution of subtotal ultrasound-guided percutaneous microwave ablation (MWA) to amplifying programmed cell death protein-1 (PD-1) inhibition in advanced hepatocellular carcinoma (HCC). Between April 2019 and December 2021, advanced HCC patient demographics, tumor response, survival data, neutrophil-to-lymphocyte ratio (NLR) and peripheral lymphocyte profiles were retrospectively collected and analyzed. In hepa1–6 tumor-bearing C57BL/6J mice, RNA sequencing, flow cytometry, immunohistochemistry staining and cytokine tests were also performed. Twenty-nine HCC patients were enrolled, with a median follow-up duration of 15.1 mo. Compared with the ablation rate (AR) ≤50% group (n = 10), the AR >50% group (n = 19) had a higher disease control rate, a longer time to progression and a longer overall survival. More patients in the AR >50% group had an early decrease in NLR and better immune activation. RNA sequencing of murine tumors subjected to MWA >50% AR showed that immune-related gene expression upregulated. CD8+ T cells, interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α) were also increased, indicating that MWA >50% AR boosted the immunomodulatory effect of PD-1 inhibitors. More MWA could induce superior antitumor immunity by enhancing immune-related gene expression, priming CD8+ T cells and thereby boosting PD-1 inhibition. It is advisable that eradication of tumors to the degree possible should be considered within technical access to obtain a better prognosis. [ABSTRACT FROM AUTHOR]

SUMMARY: Chromatin in eukaryotes folds into a complex three‐dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low‐Pi treatment led to greater chromatin volume. Furthermore, low‐Pi stress increased the insulation score and the number of TAD‐like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD‐like boundaries, whereas RdDM peak levels at conserved TAD‐like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome‐wide RdDM sites near TAD‐like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low‐Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low‐Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP‐seq results revealed that ZmDDM1A could bind to Pi‐ and root development‐related genes. Strong associations were found between interacting genes in significantly different chromatin‐interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low‐Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics. Significance Statement: This study is a pioneering study in the field of plant nutrient utilization. For the first time, this study discovered that the plant's low‐Pi response was closely linked to the RdDM pathway and chromatin spatial structure, and the low‐Pi response was validated by a mutant of chromatin remodeling gene ZmDDM1a (RdDM pathway gene). In addition, the results of ChIP‐seq and multi‐point GWAS for 2 years revealed the interaction of a large number of candidate genes related to Pi and roots with ZmDDM1A. We believe that the results presented in this article will have a great influence in this field and will be concerned and cited by many researchers. [ABSTRACT FROM AUTHOR]

Recent experimental evidence strongly supports that three-dimensional (3D) long-range enhancer-promoter (E-P) interactions have important influences on gene-expression dynamics, but it is unclear how the interaction information is translated into gene expression over time (4D). To address this question, we developed a general theoretical framework (named as a 4D nucleome equation), which integrates E-P interactions on chromatin and biochemical reactions of gene transcription. With this equation, we first present the distribution of mRNA counts as a function of the E-P genomic distance and then reveal a power-law scaling of the expression level in this distance. Interestingly, we find that long-range E-P interactions can induce bimodal and trimodal mRNA distributions. The 4D nucleome equation also allows for model selection and parameter inference. When this equation is applied to the mouse embryonic stem cell smRNA-FISH data and the E-P genomic-distance data, the predicted E-P contact probability and mRNA distribution are in good agreement with experimental results. Further statistical inference indicates that the E-P interactions prefer to modulate the mRNA level by controlling promoter activation and transcription initiation rates. Our model and results provide quantitative insight into both spatiotemporal gene-expression determinants (i.e., long-range E-P interactions) and cellular fates during development. Author summary: Gene expression is an essential biological process in all organisms. Numerous experimental studies have reported that the long-range enhancer-promoter (E-P) interaction on three-dimensional (3D) chromatin architecture plays important roles in regulating gene expression and cell functions, but the quantitative and qualitative impact of E-P interaction on gene expression over time is unclear. We develop a theoretically and numerically efficient model (called the 4D nucleome equation) to couple E-P interaction with gene expression and use this equation to characterize dynamic behavior. Then, we obtain the theoretical distribution of mRNAs and predict the gene expression profiles under E-P regulations. Interestingly, we find that E-P interactions can induce bimodal and trimodal shapes of mRNA distribution. When applying this framework to mouse embryonic stem cell data to investigate the dynamical behaviors of E-P interaction and gene expression, we reproduce the experimentally measured E-P contact frequencies and mRNA distribution under different E-P interactions. Our results support the picture of an essential mechanism for explaining phenotypic diversity and cellular decision-making. [ABSTRACT FROM AUTHOR]