Gene Expression Research Articles

Unveiling the Protective Role of Hypoxia - Inducible Factor-1 Alpha Gene Polymorphisms (rs11549465 and rs11549467) in Psoriasis

Unveiling the Protective Role of Hypoxia - Inducible Factor-1 Alpha Gene Polymorphisms (rs11549465 and rs11549467) in Psoriasis

Integrated metabolomic and transcriptomic strategies to reveal adaptive mechanisms in barley plant during germination stage under waterlogging stress.

Barley (Hordeum vulgare L.) is an important cereal crop used in animal feed, beer brewing, and food production. Waterlogging stress is one of the prominent abiotic stresses that has a significant impact on the yield and quality of barley. Seed germination plays a critical role in the establishment of seedlings and is significantly impacted by the presence of waterlogging stress. However, there is a limited understanding of the regulatory mechanisms of gene expression and metabolic processes in barley during the germination stage under waterlogging stress. This study aimed to investigate the metabolome and transcriptome responses in germinating barley seeds under waterlogging stress. The findings of the study revealed that waterlogging stress sharply decreased seed germination rate and seedling growth. The tolerant genotype (LLZDM) exhibited higher levels of antioxidase activities and lower malondialdehyde (MDA) content in comparison to the sensitive genotype (NN). In addition, waterlogging induced 86 and 85 differentially expressed metabolites (DEMs) in LLZDM and NN, respectively. Concurrently, transcriptome analysis identified 1776 and 839 differentially expressed genes (DEGs) in LLZDM and NN, respectively. Notably, the expression of genes associated with redox reactions, hormone regulation, and other biological processes were altered in response to waterlogging stress. Furthermore, the integrated transcriptomic and metabolomic analyses revealed that the DEGs and DEMsimplicated in mitigating waterlogging stress primarily pertained to the regulation of pyruvate metabolism and flavonoid biosynthesis. Moreover, waterlogging might promote flavonoid biosynthesis by regulating 15 flavonoid-related genes and 10 metabolites. The present research provides deeper insights into the overall understanding of waterlogging-tolerant mechanisms in barley during the germination process.

Exploring the dual roles of sec-dependent effectors from Candidatus Liberibacter asiaticus in immunity of citrus plants.

The three SDEs of CLas were expressed in citrus leaves by AuNPs-PEI mediated transient expression system, and promoted the proliferation of CLas and inhibited citrus immunity. Huanglongbing (HLB) is the most severe bacterial disease of citrus caused by Candidatus Liberibacter asiaticus (CLas). CLas suppress host immune responses and promote infection by sec-dependent effectors (SDEs), thus insight into HLB pathogenesis is urgently needed to develop effective management strategies. In this study, we focused on the roles of SDE4310, SDE4435 and SDE4955 in citrus. We found that the expression of SDE4310, SDE4435 and SDE4955 to increase with increasing citrus immune genes CsPR1, CsPR2, CsPR5, CsNPR1, CsRBOHD, CsMAP3K and CsBIK1, suggesting that the level of citrus immunity could be judged by the expression of SDE. To further explore the relationship between these three SDEs and citrus immunity, we established a transient expression system in citrus leaves, using gold nanoparticle-polyethyleneimine (AuNPs-PEI) to deliver recombinant plasmid containing SDE4310, SDE4435 or SDE4955 respectively into citrus leaves. Results showed that SDE4310, SDE4435 and SDE4955 were successfully expressed in citrus leaves using this transient expression system, and found that SDE4310, SDE4435 and SDE4955 could promote the CLas proliferation by decreasing the immune gene expression of the citrus. Additionally, we used AuNPs-PEI to deliver siRNA4310 to citrus cells, significantly reducing the expression of SDE4310 within 3days. Although the suppression of SDE4310 expression did not inhibit the CLas proliferation, it increased the expression level of CsPR1, CsNPR1 and CsBIK1. This is also the first time that AuNPs-PEI has been found to be able to deliver exogenous plasmids into citrus cells and express the target protein, providing a new method for future studies on citrus HLB.

Pro-cumulin addition in a biphasic in vitro oocyte maturation system modulates human oocyte and cumulus cell transcriptomes.

Biphasic in vitro oocyte maturation (IVM) can be offered as a patient-friendly alternative to conventional ovarian stimulation in in vitro fertilization (IVF) patients predicted to be hyper-responsive to ovarian stimulation. However, cumulative live birth rates after IVM per cycle are lower than after conventional ovarian stimulation for IVF. In different animal species, supplementation of IVM media with oocyte-secreted factors (OSFs) improves oocyte developmental competence through the expression of pro-ovulatory genes in cumulus cells. Whether the addition of OSFs in human biphasic IVM culture impacts the transcriptome of oocytes and cumulus cells retrieved from small antral follicles in minimally stimulated non-hCG-triggered IVM cycles remains to be elucidated. To answer this, human cumulus oocyte complexes (COCs) that were fully surrounded by cumulus cells or partially denuded at the time of retrieval were cultured in a biphasic IVM system either without or with the addition of pro-cumulin, a GDF9: BMP15 heterodimer. Oocytes and their accompanying cumulus cells were collected separately, and single-cell RNA-seq libraries were generated. The transcriptomic profile of cumulus cells revealed that pro-cumulin upregulated the expression of genes involved in cumulus cell expansion and proliferation while downregulating steroidogenesis, luteinization and apoptosis pathways. Moreover, pro-cumulin modulated the immature oocyte transcriptome during the prematuration step, including regulating translation, apoptosis and mitochondria remodeling pathways in the growing germinal vesicle (GV) oocytes. The addition of pro-cumulin also restored the transcriptomic profile of matured metaphase II (MII) oocytes that were partially denuded at collection. These results suggest that cumulus cell and oocyte transcriptome regulation by pro-cumulin may increase the number of developmentally competent oocytes after biphasic IVM treatment. Future studies should assess the effects of pro-cumulin addition in human biphasic IVM at the proteomic level and the embryological outcomes, particularly its potential to enhance outcomes of oocytes that are partially denuded at COC collection.

Identification of Novel Biomarkers for Ischemic Stroke Through Integrated Bioinformatics Analysis and Machine Learning.

Ischemic stroke leads to permanent damage to the affected brain tissue, with strict time constraints for effective treatment. Predictive biomarkers demonstrate great potential in the clinical diagnosis of ischemic stroke, significantly enhancing the accuracy of early identification, thereby enabling clinicians to intervene promptly and reduce patient disability and mortality rates. Furthermore, the application of predictive biomarkers facilitates the development of personalized treatment plans tailored to the specific conditions of individual patients, optimizing treatment outcomes and improving prognoses. Bioinformatics technologies based on high-throughput data provide a crucial foundation for comprehensively understanding the biological characteristics of ischemic stroke and discovering effective predictive targets. In this study, we evaluated gene expression data from ischemic stroke patients retrieved from the Gene Expression Omnibus (GEO) database, conducting differential expression analysis and functional analysis. Through weighted gene co-expression network analysis (WGCNA), we characterized gene modules associated with ischemic stroke. To screen candidate core genes, three machine learning algorithms were applied, including Least Absolute Shrinkage and Selection Operator (LASSO), random forest (RF), and support vector machine-recursive feature elimination (SVM-RFE), ultimately identifying five candidate core genes: MBOAT2, CKAP4, FAF1, CLEC4D, and VIM. Subsequent validation was performed using an external dataset. Additionally, the immune infiltration landscape of ischemic stroke was mapped using the CIBERSORT method, investigating the relationship between candidate core genes and immune cells in the pathogenesis of ischemic stroke, as well as the key pathways associated with the core genes. Finally, the key gene VIM was further identified and preliminarily validated through four machine learning algorithms, including generalized linear model (GLM), Extreme Gradient Boosting (XGBoost), RF, and SVM-RFE. This study contributes to advancing our understanding of biomarkers for ischemic stroke and provides a reference for the prediction and diagnosis of ischemic stroke.

The Arabidopsis eATP receptor, DORN1 and CNGC19 channel act in tandem to regulate plant defense upon Spodoptera litura herbivory.

Plants deploy cellular Ca2+ elevation as a signal for environmental stress signaling. Extracellular ATP (eATP) is released into the extracellular matrix when cells are wounded. DOES NOT RESPOND TO NUCLEOTIDES 1 (DORN1), a key legume-type lectin receptor, senses and binds eATP and activates Ca2+ signaling. No evidence directly links calcium-mediated eATP signaling to resistance against insect herbivores. Here, we report upregulation of DORN1 transcripts upon wounding and Spodoptera litura feeding in Arabidopsis. Loss-of-function of DORN1 resulted in increased S. litura feeding compared to that on wildtype. Plant immunity is compromised in dorn1 mutants as they show reduced S. litura oral secretion mediated Ca2+ elevation, jasmonic acid accumulation, and expression of jasmonate responsive genes. The herbivory-induced calcium channel, CYCLIC NUCLEOTIDE GATED CHANNEL 19 (CNGC19), co-expresses with DORN1. We found that eATP-induced Ca2+ elevation requires functional CNGC19. Loss-of-function of DORN1 and CNGC19 highly increased the susceptibility to S. litura, mediated by reduced accumulation of jasmonates. We also demonstrate a plausible interaction of CNGC19 with DORN1. The data implicate the role of damage-released eATP and its receptor DORN1 in herbivory-induced defense signaling. DORN1 together with the Ca2+ channel CNGC19 generate the eATP-induced Ca2+ elevation, leading to the activation of immune signaling.

Construction and application of an inducible transcriptional regulatory tool from Medicago truncatula in Saccharomyces cerevisiae

Transcriptional regulation based on transcription factors is an effective regulatory method widely used in microbial cell factories. Currently, few naturally transcriptional regulatory elements have been discovered from Saccharomyces cerevisiae and applied. Moreover, the discovered elements cannot meet the demand for specific metabolic regulation of exogenous compounds due to the high background expression or narrow dynamic ranges. There are abundant transcriptional regulatory elements in plants. However, the sequences and functions of most elements have not been fully characterized and optimized. Particularly, the applications of these elements in microbial cell factories are still in the infancy stage. In this study, natural regulatory elements from Medicago truncatula were selected, including the transcription factors MtTASR2 and MtTASR3, along with their associated promoter ProHMGR1, for functional characterization and engineering modification. We constructed an inducible transcriptional regulation tool and applied it in the regulation of heterologous β-carotene synthesis in S. cerevisiae, which increased the β-carotene production by 7.31 folds compared with the original strain. This study demonstrates that plant-derived transcriptional regulatory elements can be used to regulate the expression of multiple genes in S. cerevisiae, providing new strategies and ideas for the specific regulation and application of these elements in microbial cell factories.

Doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.

Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface. doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/. Supplementary data are available at Bioinformatics online and at https://github.com/almeidasilvaf/doubletrouble_paper.

Mapping organism-wide single cell mRNA expression linked to extracellular vesicle biogenesis, secretion and cargo.

Extracellular vesicles (EVs) are functional lipid-bound nanoparticles trafficked between cells and found in every biofluid. It is widely claimed that EVs can be secreted by every cell, but the quantity and composition of these EVs can differ greatly among cell types and tissues. Defining this heterogeneity has broad implications for EV-based communication in health and disease. Recent discoveries have linked single-cell EV secretion to the expression of genes encoding EV machinery and cargo. To gain insight at single-cell resolution across an entire organism, we compared the abundance, variance and co-expression of 67 genes involved in EV biogenesis and secretion, or carried as cargo, across >44,000 cells obtained from 117 cell populations in the Tabula Muris.

CHAF1B promotes the progression of lung squamous-cell carcinoma by inhibiting SETD7 expression.

The p60 subunit of the chromatin assembly factor-1 complex, that is, chromatin assembly factor-1 subunit B (CHAF1B), is a histone H3/H4 chaperone crucial for the transcriptional regulation of cell differentiation and self-renewal. CHAF1B is overexpressed in several cancers and may represent a potential target for cancer therapy. However, its expression and clinical significance in lung squamous-cell carcinoma (LUSC) remain unclear. In this study, we performed weighted gene correlation network analysis to analyze the Gene Expression Omnibus GSE68793 LUSC dataset and identified CHAF1B as one of the most important driver gene candidates. Immunohistochemical analysis of 126 LUSC tumor samples and 80 adjacent normal lung tissues showed the marked upregulation of CHAF1B in tumor tissues and the negative association of its expression level with patient survival outcomes. Silencing of CHAF1B suppressed LUSC proliferation in vitro and LUSC tumor growth in vivo. Furthermore, bulk RNA sequencing of CHAF1B knockdown cells indicated SET domain containing 7 (SETD7) as a significant CHAF1B target gene. In addition, CHAF1B competitively binds to the SETD7 promoter region and represses its transcription. Altogether, these results imply that CHAF1B plays a vital role in LUSC tumorigenesis and may represent a potential molecular target for this deadly disease.

MicroRNAs' Significance in Retinoblastoma Diagnosis and Treatment: The Little Heroes.

One in 16, 000 live births is affected by the retinal tumor RB (retinoblastoma), which is frequently found in a child's early years. Both of the RB1 alleles that have been locally mutated in the affected retina are present in 60 percent of cases. Retinoblastoma (RB) can be detected using a variety of techniques, including imaging of the brain and orbits, eye examinations under anesthesia (EUAs), and the discovery of cell-free tumor DNA in samples of aqueous humor or plasma. In addition to the conventional surgical, chemotherapy, and radiotherapy approaches to treating retinoblastoma, new approaches have also been developed. Oncogenes, genes of tumor suppressors, and other molecular elements involved in cell growth and division interact complexly during the pathogenesis of retinoblastoma. The development of new therapies depends on comprehending the function of these molecular components. As a small class of non-coding RNAs capable of altering gene expression, microRNAs (miRNA) are understood to represent potential targets for the treatment of cancer. This study aimed to describe the changes in microRNA expression in some types of cancer, with a particular focus on retinoblastoma.

Telomerase in cancer- ongoing quest and future discoveries.

Telomerase, constituted by the dynamic duo of telomerase reverse transcriptase (TERT), the catalytic entity, and an integral RNA component (TERC), is predominantly suppressed in differentiated human cells due to postnatal transcriptional repression of the TERT gene. Dysregulation of telomerase significantly contributes to cancer development via telomere-dependent and independent mechanisms. Telomerase activity is often elevated in advanced cancers, with TERT reactivation and upregulation of TERC observed in early tumorigenesis. Beyond their primary function of telomere maintenance, TERT and TERC exhibit multifaceted roles in regulating gene expression, signal transduction pathways, and cellular metabolism. The presence of the enzymatic component TERT in both the nucleus and mitochondria underscores its non-canonical roles. Cell death is prevented in TERT-upregulated cells regardless of the DNA damage events and safeguards mitochondrial DNA from oxidative damage. This highlights its protective role in cancer cells where it intersects with glucose metabolism and epigenetic regulation, shaping tumor phenotypes. Oncogenic viruses exploit various strategies to manipulate telomerase activity, aiding cancer progression. The perpetual cell proliferation facilitated by telomerase is a hallmark of cancer, making it an attractive therapeutic target. Inhibitors targeting the catalytic subunit of telomerase, nutraceutical-based compounds, and telomerase-based vaccines represent promising avenues for cancer therapy. Considering the pivotal roles played by the complete enzyme telomerase and TERT component in cancer initiation, substantial endeavors have been dedicated to unravel the mechanisms driving telomerase activation and TERT induction. This review also explores how computational modeling can be leveraged to uncover new insights in telomere research, and efficient targeted therapies.

Directed Evolution of AAV9 for Efficient Gene Expression in Cardiomyocytes In Vitro and In Vivo.

Adeno-associated viral (AAV) vectors are increasingly used for preclinical and clinical cardiac gene therapy approaches. However, gene transfer to cardiomyocytes poses a challenge due to differences between AAV serotypes in terms of expression efficiency in vitro and invivo. For example, AAV9 vectors work well in rodent heart muscle cells invivo but not in cultivated neonatal rat ventricular cardiomyocytes (NRVCMs), necessitating the use of AAV6 vectors for in vitro studies. Therefore, we aimed to develop an AAV that could efficiently express genes in NRVCMs, human engineered heart tissue (hEHT), and mammalian hearts. The production of AAV6 vectors results in lower yields compared with AAV9. Hence, we used random AAV9 peptide libraries and selected variants on NRVCMs at the vector genome and RNA levels in parallel. The enriched library variants were characterized using high-throughput analysis of barcoded variants, followed by individual validation of the most promising candidates. Interestingly, we found striking differences in NRVCM transduction and gene expression patterns of the AAV capsid variants depending on the selection strategy. AAV variants selected based on the vector genome level enabled the highest transduction but were outperformed by AAVs selected on the RNA level in terms of expression efficiency. In addition, we identified a new AAV9 capsid variant that not only allowed significantly higher gene expression in NRVCMs compared with AAV6 but also enabled similar gene expression in murine hearts as AAV9 wild-type vectors after being intravenously injected into mice. Moreover, the novel variant facilitated significantly higher gene expression in hEHT compared with AAV9. Therefore, this AAV variant could streamline preclinical gene therapy studies of myocardial diseases by eliminating the need for using different AAVs for NRVCMs, hEHT, and mice.

A Sox2 Enhancer Cluster Regulates Region-Specific Neural Fates from Mouse Embryonic Stem Cells.

Sex-determining region Y box 2 (Sox2) is a critical transcription factor for embryogenesis and neural stem and progenitor cell (NSPC) maintenance. While distal enhancers control Sox2 in embryonic stem cells (ESCs), enhancers closer to the gene are implicated in Sox2 transcriptional regulation in neural development. We hypothesize that a downstream enhancer cluster, termed Sox2 regulatory regions 2-18 (SRR2-18), regulates Sox2 transcription in neural stem cells and we investigate this in NSPCs derived from mouse ESCs. Using functional genomics and CRISPR-Cas9 mediated deletion analyses we investigate the role of SRR2-18 in Sox2 regulation during neural differentiation. Transcriptome analyses demonstrate that loss of even one copy of SRR2-18 disrupts the region-specific identity of NSPCs, reducing the expression of genes associated with more anterior regions of the embryonic nervous system. Homozygous deletion of this Sox2 neural enhancer cluster causes reduced SOX2 protein, less frequent interaction with transcriptional machinery, and leads to perturbed chromatin accessibility genome-wide further affecting the expression of neurodevelopmental and anterior-posterior regionalization genes. Furthermore, homozygous NSPC deletants exhibit self-renewal defects and impaired differentiation into cell types found in the brain. Altogether, our data define a cis-regulatory enhancer cluster controlling Sox2 transcription in NSPCs and highlight the sensitivity of neural differentiation processes to decreased Sox2 transcription, which causes differentiation into posterior neural fates, specifically the caudal neural tube. This study highlights the importance of precise Sox2 regulation by SRR2-18 in neural differentiation.

Dissecting the Genetic Basis of Preharvest Sprouting in Rice Using a Genome-Wide Association Study.

Preharvest sprouting (PHS) is an unfavorable trait in cereal crops that significantly reduces grain yield and quality. However, the regulatory mechanisms underlying this complex trait are still largely unknown. Here, 276 rice accessions from the 3000 Rice Genomes Project were used to perform a genome-wide association study. In total, seven PHS-associated quantitative trait loci (QTLs) were identified, including two novel QTLs and five previously reported QTLs. Among them, four QTLs were identified in 2020 and 2021, and rice accessions carrying at least two favorable alleles exhibited significantly improved PHS resistance. Within these four stable QTLs, five candidate genes were identified based on haplotype and gene expression analyses, including two genes in qPhs-1.1, one gene in qPhs-3, one gene in qPhs-6, and one gene in qPhs-7. Notably, the novel QTL qPhs-6 was found to contain the candidate gene Pi starvation-induced transcription factor 1 (OsPTF1). We discovered that OsPTF1 plays a novel role in negatively regulating PHS in rice and identified two elite haplotypes of OsPTF1 associated with low PHS. Our results provide future insight into the genetic basis of PHS and will prove useful in the future studies on the role of OsPTF1 in PHS in rice.

Optimising Age-Specific Insulin Signalling to Slow Down Reproductive Ageing Increases Fitness in Different Nutritional Environments.

The developmental theory of ageing proposes that age-specific decline in the force of natural selection results in suboptimal levels of gene expression in adulthood, leading to functional senescence. This theory explicitly predicts that optimising gene expression in adulthood can ameliorate functional senescence and improve fitness. Reduced insulin/IGF-1 signalling (rIIS) extends the reproductive lifespan of Caenorhabditis elegans at the cost of reduced reproduction. Here, we show that adulthood-only rIIS improves late-life reproduction without any detrimental effects on other life-history traits in both benign and stressful conditions. Remarkably, we show that rIIS additively extends late-life reproduction and lifespan when animals are exposed to a fluctuating food environment-intermittent fasting (IF)-resulting in reduced food intake in early adulthood. Full factorial genome-wide RNA-Seq across the life course demonstrated that IF and rIIS modulate the age-specific expression of pro-longevity genes. IF, rIIS and combined IF + rIIS treatment downregulated genes involved in biosynthesis in early life and differentially regulated immunity genes in later life. Importantly, combined IF + rIIS treatment uniquely regulated a large cluster of genes in mid-life that are associated with immune response. These results suggest that optimising gene expression in adulthood can decelerate reproductive ageing and increase fitness.

A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals.

Small non-coding RNAs can be categorized into two main classes: structural RNAs and regulatory RNAs. Structural RNAs, which are abundant and ubiquitously expressed, have essential roles in the maturation of pre-mRNAs, modification of rRNAs and the translation of coding transcripts. By contrast, regulatory RNAs are often expressed in a developmental-specific, tissue-specific or cell-type-specific manner and exert precise control over gene expression. Reductions in cost and improvements in the accuracy of high-throughput RNA sequencing have led to the identification of many new small RNA species. In this Review, we provide a broad discussion of the genomic origins, biogenesis and functions of structural small RNAs, including tRNAs, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), vault RNAs (vtRNAs) and Y RNAs as well as their derived RNA fragments, and of regulatory small RNAs, such as microRNAs (miRNAs), endogenous small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs), in animals.

Hypoxia-Inducible Factor Prolyl Hydroxylase Inhibitor Roxadustat Accelerates Wound Healing in a Mouse Hind limb Lymphedema Model.

Objective: Drugs regulating hypoxia-inducible factor (HIF)-1α have not been investigated for wound healing in lymphedema. Therefore, we examined the effects of drug modulation of HIF-1α activity for wound healing in our previously developed mouse model of nonirradiated hind limb lymphedema. Approach: Mouse hind limb lymphedema models (n = 17) and a sham group (n = 6) were created using 8- to 10-week-old male C57BL/6N mice. Mice with hind limb lymphedema were randomized into experimental groups receiving roxadustat, 3-(5'-hydroxymethyl-2'-furyl)-1-benzylindazole (YC-1), or dimethyl sulfoxide and were given intraperitoneal injections every 2 days for up to 2 weeks. Four days after the surgery, an 8-mm diameter full-thickness skin wound was created in the hind limb. The number of days required for wound closure and the percentage of wounds closed were measured. Skin samples taken at wound creation were evaluated by histological and molecular analysis. Results: Administration of roxadustat accelerated wound healing, whereas YC-1 delayed it, with a significant decrease and increase in skin thickness, respectively. The relative mRNA expression of Hif1α, matrix metalloproteinase-3, and interleukin-6 was significantly higher in the roxadustat group and that of metalloproteinase-9 was significantly lower in the roxadustat group compared with the control group. Innovation: This study is the first to demonstrate delayed wound healing in a mouse model of hind limb lymphedema and the first to demonstrate the promotion of significant wound healing through the use of roxadustat. Conclusion: Roxadustat exerts wound-healing effects and may promote the regulation of extracellular matrix remodeling via gene expression in hind limb lymphedema wound models.

Spleen tyrosine kinase aggravates intestinal inflammation through regulating inflammatory responses of macrophage in ulcerative colitis.

Ulcerative colitis (UC) is a persistent chronic, non-specific inflammatory disease, and macrophages play a crucial role in its pathogenesis. Spleen tyrosine kinase (Syk) is strongly associated with the pathogenesis of several inflammatory diseases. However, the role of Syk in the pathogenesis of UC is still obscure. Syk expression was analyzed in peripheral blood mononuclear cells (PBMCs) and colonic tissues of UC patients using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and immunofluorescence. A public database was used to analyze the expression of selected signature genes of interest in UC patients with different expressions of Syk. R788, a small molecule inhibitor of Syk, was used to treat macrophages from mice. The functions of macrophages were assessed using qRT-PCR, flow cytometry, and fluorescence microscopy. Dextran sodium sulfate (DSS)-induced colitis mice model was established to determine the role of Syk in UC. The Syk levels were markedly increased in PBMCs, colonic tissues, and colonic mucosa lamina propria macrophages from UC patients, and positively related to disease activity. Inhibition of Syk with R788 decreased pro-inflammatory genes expression and increased anti-inflammatory genes expression in peritoneal macrophages and bone marrow macrophages. Blockade of Syk enhanced phagocytosis and bactericidal ability of macrophages. Syk promoted the production of reactive oxygen species of macrophages and M1-type macrophage polarization. Furthermore, inhibition of Syk alleviated intestinal mucosal inflammation in DSS-induced colitis model. Syk plays a vital role in intestinal inflammation by regulating inflammatory responses of macrophages in UC. Targeting Syk may be a promising therapeutic approach for UC.

Transcriptomic insights into the anti-inflammatory mechanisms of Protaetia brevitarsis seulensis larvae in IL-1β-driven chondrosarcoma cells.

Osteoarthritis (OA) is a complex, degenerative, multi-factorial joint disease. Because of the difficulty in treating OA, developing new targeting strategies that can be used to understand its molecular mechanisms is critical. Protaetia brevitarsis seulensis larvae offer much therapeutic value; however, the presence of various active compounds and the multi-factorial risk factors for OA render the precise mechanisms of action unclear. A systematic transcriptome analysis was used to investigate the key mechanisms of action of P. brevitarsis seulensis larvae aqueous extract (PBSL) and its compounds on OA. Major mechanisms and transcription factors of PBSL were analyzed by profiling gene expression changes in interleukin (IL)-1β-induced human chondrosarcoma cell (SW1353) treated with PBSL. An in vitro assay was performed to validate the efficacy of the novel mechanism and targets of PBSL. PBSL exerted anti-inflammatory effects on SW1353 cells by regulating many molecular pathways. The IL-6/JAK/STAT3 pathway was significantly downregulated by PBSL, and STAT3 was identified as a major transcription factor regulating PBSL-induced target gene expression. Of the six PBSL compounds, the major compound was regulated by the IL-6/JAK/STAT3 pathway. This study provided potential novel mechanisms and transcription factors for PBSL and its active compounds against OA and indicated that inhibiting the IL-6/JAK/STAT3 pathway is a therapeutic target for treating OA.