Focal Adhesion Signaling Pathways Research Articles

The enhanced generation of motor neurons from mESCs by MgAl layered double hydroxide nanoparticles

The committed differentiation of stem cells into neurons is a promising therapeutic strategy for neurological diseases. Predifferentiation of transplanted stem cells into neural precursors could enhance their utilization and control the direction of differentiation. Embryonic stem cells with totipotency can differentiate into specific nerve cells under appropriate external induction conditions. Layered double hydroxide (LDH) nanoparticles have been proven to regulate the pluripotency of mouse ESCs (mESCs), and LDH could be used as carrier in neural stem cells for nerve regeneration. Hence, we sought to study the effects of LDH without loaded factors on mESCs neurogenesis in this work. A series of characteristics analyses indicated the successful construction of LDH nanoparticles. LDH nanoparticles that may adhere to the cell membranes had insignificant effect on cell proliferation and apoptosis. The enhanced differentiation of mESCs into motor neurons by LDH was systematically validated by immunofluorescent staining, quantitative real-time PCR analysis and western blot analysis. In addition, transcriptome sequencing analysis and mechanism verification elucidated the significant regulatory roles of focal adhesion signaling pathway in the enhanced mESCs neurogenesis by LDH. Taken together, the functional validation of inorganic LDH nanoparticles promoting motor neurons differentiation provide a novel strategy and therapeutic prospect for the clinical transition of neural regeneration.

Focal adhesion signaling pathway involved in skin immune response of tongue sole Cynoglossus semilaevis to Vibrio vulnificus infection

Focal adhesion (FA) plays a key role in cell adhesion, migration and antibacterial immune, but it remained unclear in fish. In this study, half-smooth tongue sole Cynoglossus semilaevis were infected with Vibrio vulnificus, and then immune-related protein in the skin, especially for FA signaling pathway were screened and identified by iTRAQ analysis. Results showed that the differentially expressed proteins (DEPs) in skin immune response (eg., ITGA6, FN, COCH, AMBP, COL6A1, COL6A3, COL6A6, LAMB1, LAMC1, FLMNA) were firstly found in FA signaling pathway. Furthermore, the validation analysis of FA-related genes were basically consistent with the iTRAQ data at 36 hpi (r = 0.678, p < 0.01), and their spatio-temporal expressions were confirmed by qPCR analysis. The molecular characterization of vinculin of C. semilaevis was described. This study will provide a new perspective for understanding the molecular mechanism of FA signaling pathway in the skin immune response in marine fish.

Key circRNAs from goat: discovery, integrated regulatory network and their putative roles in the differentiation of intramuscular adipocytes

BackgroundThe procession of preadipocytes differentiation into mature adipocytes involves multiple cellular and signal transduction pathways. Recently. a seirces of noncoding RNAs (ncRNAs), including circular RNAs (circRNAs) were proved to play important roles in regulating differentiation of adipocytes.ResultIn this study, we aimed to identificate the potential circRNAs in the early and late stages of goat intramuscular adipocytes differentiation. Using bioinformatics methods to predict their biological functions and map the circRNA-miRNA interaction network. Over 104 million clean reads in goat intramuscular preadipocytes and adipocytes were mapped, of which16 circRNAs were differentially expressed (DE-circRNAs). Furthermore, we used real-time fluorescent quantitative PCR (qRT-PCR) technology to randomly detect the expression levels of 8 circRNAs among the DE-circRNAs, and our result verifies the accuracy of the RNA-seq data. From the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the DE-circRNAs, two circRNAs, circ_0005870 and circ_0000946, were found in Focal adhesion and PI3K-Akt signaling pathway. Then we draw the circRNA-miRNA interaction network and obtained the miRNAs that possibly interact with circ_0005870 and circ_0000946. Using TargetScan, miRTarBase and miR-TCDS online databases, we further obtained the mRNAs that may interact with the miRNAs, and generated the final circRNA-miRNA-mRNA interaction network. Combined with the following GO (Gene Ontology) and KEGG enrichment analysis, we obtained 5 key mRNAs related to adipocyte differentiation in our interaction network, which are FOXO3(forkhead box O3), PPP2CA (protein phosphatase 2 catalytic subunit alpha), EEIF4E (eukaryotic translation initiation factor 4), CDK6 (cyclin dependent kinase 6) and ACVR1 (activin A receptor type 1).ConclusionsBy using Illumina HiSeq and online databases, we generated the final circRNA-miRNA-mRNA interaction network that have valuable functions in adipocyte differentiation. Our work serves as a valuable genomic resource for in-depth exploration of the molecular mechanism of ncRNAs interaction network regulating adipocyte differentiation.

DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens

BackgroundThe quality of poultry eggshells is closely related to the profitability of egg production. Eggshell speckles reflect an important quality trait that influences egg appearance and customer preference. However, the mechanism of speckle formation remains poorly understood. In this study, we systematically compared serum immune and antioxidant indices of hens laying speckled and normal eggs. Transcriptome and methylome analyses were used to elucidate the mechanism of eggshell speckle formation.ResultsThe results showed that seven differentially expressed genes (DEGs) were identified between the normal and speckle groups. Gene set enrichment analysis (GSEA) revealed that the expressed genes were mainly enriched in the calcium signaling pathway, focal adhesion, and MAPK signaling pathway. Additionally, 282 differentially methylated genes (DMGs) were detected, of which 15 genes were associated with aging, including ARNTL, CAV1, and GCLC. Pathway analysis showed that the DMGs were associated with T cell-mediated immunity, response to oxidative stress, and cellular response to DNA damage stimulus. Integrative analysis of transcriptome and DNA methylation data identified BFSP2 as the only overlapping gene, which was expressed at low levels and hypomethylated in the speckle group.ConclusionsOverall, these results indicate that aging- and immune-related genes and pathways play a crucial role in the formation of speckled eggshells, providing useful information for improving eggshell quality.

Transcriptome Analysis Revealed Osmoregulation Related Regulatory Networks and Hub Genes in the Gills of Hilsa shad, Tenualosa ilisha, during the Migratory Osmotic Stress

Tenualosa ilisha (Hilsa shad), an anadromous fish, usually inhabits coastal and estuarine waters, and migrates to freshwater for spawning. In this study, large-scale gill transcriptome analyses from three salinity regions, i.e., fresh, brackish and marine water, revealed 3277 differentially expressed genes (DEGs), out of which 232 were found to be common between marine vs freshwater and brackish vs freshwater. These genes weremapped into 54 KEGG Pathways, and the most significant of thesewere focal adhesion, adherens junction, tight junction, and PI3K-Akt signaling pathways. A total of 24 osmoregulatory genes were found to be differentially expressed in different habitats. The gene members of slc16 and slc2 families showed a dissimilar pattern of expressions, while two claudin genes (cldn11 & cldn10), transmembrane tm56b, and voltage-gated potassium channel gene kcna10 were downregulated in freshwater samples, as compared to that of brackish and marine environment. Protein-protein interaction (PPI) network analysis of 232 DEGs showed 101 genes to beinvolved in PPI, while fn1 gene was found to be interacting with the highest number of genes (36). Twenty-five hub genes belonged to 12 functional groups, with muscle structure development with seven genes, forming the major group. These results provided valuable information about the genes, potentially involved in the molecular mechanisms regulating water homeostasis in gills, during migration for spawning and low-salinity adaptation in Hilsa shad. These genes may form the basis for the bio-marker developmentfor adaptation to the stress levied by major environmental changes, due to hatchery/culture conditions.

In Silico Analysis of MicroRNA Expression Data in Liver Cancer.

Abnormal miRNA expression has been evidenced to be directly linked to HCC initiation and progression. This study was designed to detect possible prognostic, diagnostic, and/or therapeutic miRNAs for HCC using computational analysis of miRNAs expression. Methods: miRNA expression datasets meta-analysis was performed using the YM500v2 server to compare miRNA expression in normal and cancerous liver tissues. The most significant differentially regulated miRNAs in our study undergone target gene analysis using the mirWalk tool to obtain their validated and predicted targets. The combinatorial target prediction tool; miRror Suite was used to obtain the commonly regulated target genes. Functional enrichment analysis was performed on the resulting targets using the DAVID tool. A network was constructed based on interactions among microRNAs, their targets, and transcription factors. Hub nodes and gatekeepers were identified using network topological analysis. Further, we performed patient data survival analysis based on low and high expression of identified hubs and gatekeeper nodes, patients were stratified into low and high survival probability groups. Results: Using the meta-analysis option in the YM500v2 server, 34 miRNAs were found to be significantly differentially regulated (P-value ⩽ .05); 5 miRNAs were down-regulated while 29 were up-regulated. The validated and predicted target genes for each miRNA, as well as the combinatorially predicted targets, were obtained. DAVID enrichment analysis resulted in several important cellular functions that are directly related to the main cancer hallmarks. Among these functions are focal adhesion, cell cycle, PI3K-Akt signaling, insulin signaling, Ras and MAPK signaling pathways. Several hub genes and gatekeepers were found that could serve as potential drug targets for hepatocellular carcinoma. POU2F1 and PPARA showed a significant difference between low and high survival probabilities (P-value ⩽ .05) in HCC patients. Our study sheds light on important biomarker miRNAs for hepatocellular carcinoma along with their target genes and their regulated functions.

Periplaneta americana extract promotes osteoblast differentiation of human alveolar bone marrow mesenchymal stem cells.

This study aims to investigate the effects of Traditional Chinese medicine, Periplaneta americana extract (PAE), on osteoblast differentiation of human alveolar bone marrow-derived mesenchymal stem cells (hABMMSCs). Human alveolar bone marrow-derived mesenchymal stem cells were treated with different concentrations of PAE. Cell Counting Kit-8 (CCK-8) assay and transwell migration assay were conducted to evaluate cell proliferation and migration, respectively. Alkaline phosphatase (ALP) staining, ALP activity assay, and Alizarin red S staining were performed to detect osteogenesis in hABMMSCs. In addition, real-time quantitative polymerase chain reaction (RT-qPCR) and western blot (WB) assay were performed to evaluate expression levels of osteogenic markers. Finally, RNA sequencing analysis and WB were carried out to elucidate the underlying mechanism. A total of 0.1 mg/ml PAE promoted cell proliferation and migration. PAE also increased ALP activity and mineralized nodule formation of hABMMSCs. In addition, PAE upregulated the expression of osteogenesis-related genes (RUNX2, COL1A1, and BGLAP). RNA-sequencing analysis revealed that PAE activated the focal adhesion signaling pathway. Treatment with Defactinib, an inhibitor of FAK, attenuated the effects induced by PAE. PAE could enhance osteoblast differentiation of hABMMSCs through focal adhesion signaling pathway, suggesting a therapeutic potential for the alveolar bone defect.

MiRNA profiling in intrauterine exosomes of pregnant cattle on day 7.

Intrauterine exosomes have been identified to be involved in the embryo development and implantation. The aim of this study was to explore the role of miRNAs in intrauterine exosomes in bovine pregnancy. Intrauterine exosomes were collected from uterine flushing fluids of three donor and three recipient Xianan cows 7 days after fertilization. Intrauterine exosomes miRNAs were extracted and the exosomal miRNAs expression levels were analyzed. Sixty miRNAs differed significantly in their amounts between donors and recipients (p-value < 0.05, |log2(FoldChange)| > 1). Twenty-two miRNAs were upregulated and 38 downregulated in the group of donor cows. The bta-miR-184 was the most significant (P Benjamini-Hochberg < 0.001). A total of 9,775 target genes were predicted using the 60 miRNAs. GO and KEGG analysis showed that the target genes were enriched in several biological processes or pathways associated with embryo implantation and endometrial development, such as cell adhesion, cell junction, focal adhesion, and Rap1 signaling pathway. Our findings suggest that, in cattle early pregnancy stage, these differently expressed miRNAs in intrauterine exosomes involved in embryo implantation and endometrial development, which may exert a significant effect and influence the uterine microenvironment for embryo implantation. These results could provide reference for screening and exploring the intrauterine exosomal miRNA affecting embryo implantation.

Identification of key genes of anti-programmed death ligand 1 for meningioma immunotherapy by bioinformatic analysis

Meningioma is one of the most common primary tumors in the central nervous system (CNS). A deeper understanding of its molecular characterization could provide potential therapeutic targets to reduce recurrence. In this study, we attempted to identify specific gene mutations in meningioma for immunotherapy. One GSE43290 dataset was obtained from the Gene Expression Omnibus (GEO) database to find differentially expressed genes (DEGs) between meningioma tissues and normal meninges. In total, 420 DEGs were identified, including 15 up-regulated and 405 down-regulated genes. Functional enrichment analysis showed that these DEGs were mainly enriched in PI3K-Akt signaling pathway, Focal adhesion, and MAPK signaling pathway. We identified 20 hub genes by protein–protein interaction (PPI) analysis. Among the hub genes, the expression of FLT1, CXCL8, JUN, THBS1, FECAM1, CD34, and FGF13 were negatively correlated with Programmed Death Ligand-1 (PD-L1). Additionally, the expression of those genes was co-regulated by miR‐155‐5p. The findings suggest that miR-155-5p play an important role in the pathogenesis of meningioma and may represent potential therapeutic targets for its anti-PD-L1 immunotherapy.

Serum bone remodeling parameters and transcriptome profiling reveal abnormal bone metabolism associated with keel bone fractures in laying hens

Keel bone fractures affect welfare, health, and production performance in laying hens. A total of one hundred and twenty 35-wk-old Hy-line Brown laying hens with normal keel (NK) bone were housed in furnished cages and studied for ten weeks to investigate the underlying mechanism of keel bone fractures. At 45 wk of age, the keel bone state of birds was assessed by palpation and X-ray, and laying hens were recognized as NK and fractured keel (FK) birds according to the presence or absence of fractures in keel bone. The serum samples of 10 NK and 10 FK birds were collected to determine bone metabolism-related indexes and slaughtered to collect keel bones for RNA-sequencing (RNA-seq), Micro-CT, and histopathological staining analyses. The results showed that the concentrations of Ca, phosphorus, calcitonin, 25-hydroxyvitamin D3, and osteocalcin and activities of alkaline phosphatase and tartrate-resistant acid phosphatase (TRAP) in serum samples of FK birds were lower than those of NK birds (P < 0.05), but the concentrations of parathyroid hormone, osteoprotegerin, and corticosterone in serum samples of FK birds were higher than those of NK birds (P < 0.05). TRAP staining displayed that FK bone increased the number of osteoclasts (P < 0.05). Micro-CT analysis indicated that FK bone decreased bone mineral density (P < 0.05). Transcriptome sequencing analysis of NK and FK bones identified 214 differentially expressed genes (DEGs) (|log2FoldChange| > 1, P < 0.05), among which 88 were upregulated and 126 downregulated. Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis indicated that 14 DEGs related to skeletal muscle movement and bone Ca transport (COL6A1, COL6A2, COL6A3, PDGFA, MYLK2, EGF, CAV3, ADRA1D, BDKRB1, CACNA1S, TNN, TNNC1, TNNC2, and RYR3) were enriched in focal adhesion and Ca signaling pathway, regulating bone quality. This study suggests that abnormal bone metabolism related to keel bone fractures is possibly responded to fracture healing in laying hens.

Identification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans

Suicide is a leading cause of death; however, the molecular genetic basis of suicidal thoughts and behaviors (SITB) remains unknown. To identify novel, replicable genomic risk loci for SITB. This genome-wide association study included 633 778 US military veterans with and without SITB, as identified through electronic health records. GWAS was performed separately by ancestry, controlling for sex, age, and genetic substructure. Cross-ancestry risk loci were identified through meta-analysis. Study enrollment began in 2011 and is ongoing. Data were analyzed from November 2021 to August 2022. SITB. A total of 633 778 US military veterans were included in the analysis (57 152 [9%] female; 121 118 [19.1%] African ancestry, 8285 [1.3%] Asian ancestry, 452 767 [71.4%] European ancestry, and 51 608 [8.1%] Hispanic ancestry), including 121 211 individuals with SITB (19.1%). Meta-analysis identified more than 200 GWS (P < 5 × 10-8) cross-ancestry risk single-nucleotide variants for SITB concentrated in 7 regions on chromosomes 2, 6, 9, 11, 14, 16, and 18. Top single-nucleotide variants were largely intronic in nature; 5 were independently replicated in ISGC, including rs6557168 in ESR1, rs12808482 in DRD2, rs77641763 in EXD3, rs10671545 in DCC, and rs36006172 in TRAF3. Associations for FBXL19 and AC018880.2 were not replicated. Gene-based analyses implicated 24 additional GWS cross-ancestry risk genes, including FURIN, TSNARE1, and the NCAM1-TTC12-ANKK1-DRD2 gene cluster. Cross-ancestry enrichment analyses revealed significant enrichment for expression in brain and pituitary tissue, synapse and ubiquitination processes, amphetamine addiction, parathyroid hormone synthesis, axon guidance, and dopaminergic pathways. Seven other unique European ancestry-specific GWS loci were identified, 2 of which (POM121L2 and METTL15/LINC02758) were replicated. Two additional GWS ancestry-specific loci were identified within the African ancestry (PET112/GATB) and Hispanic ancestry (intergenic locus on chromosome 4) subsets, both of which were replicated. No GWS loci were identified within the Asian ancestry subset; however, significant enrichment was observed for axon guidance, cyclic adenosine monophosphate signaling, focal adhesion, glutamatergic synapse, and oxytocin signaling pathways across all ancestries. Within the European ancestry subset, genetic correlations (r > 0.75) were observed between the SITB phenotype and a suicide attempt-only phenotype, depression, and posttraumatic stress disorder. Additionally, polygenic risk score analyses revealed that the Million Veteran Program polygenic risk score had nominally significant main effects in 2 independent samples of veterans of European and African ancestry. The findings of this analysis may advance understanding of the molecular genetic basis of SITB and provide evidence for ESR1, DRD2, TRAF3, and DCC as cross-ancestry candidate risk genes. More work is needed to replicate these findings and to determine if and how these genes might impact clinical care.

Exploration of the relationship between gut microbiota and fecal microRNAs in patients with major depressive disorder

Microbiota-gut-brain axis signaling plays a pivotal role in mood disorders. The communication between the host and the gut microbiota may involve complex regulatory networks. Previous evidence showed that host-fecal microRNAs (miRNAs) interactions partly shaped gut microbiota composition. We hypothesized that some miRNAs are correlated with specific bacteria in the fecal samples in patients with major depressive disorder (MDD), and these miRNAs would show enrichment in pathways associated with MDD. MDD patients and healthy controls were recruited to collect fecal samples. We performed 16S ribosome RNA sequence using the Illumina MiSeq sequencers and analysis of 798 fecal miRNAs using the nCounter Human-v2 miRNA Panel in 20 subjects. We calculated the Spearman correlation coefficient for bacteria abundance and miRNA expressions, and analyzed the predicted miRNA pathways by enrichment analysis with false-discovery correction (FDR). A total of 270 genera and 798 miRNAs were detected in the fecal samples. Seven genera (Anaerostipes, Bacteroides, Bifidobacterium, Clostridium, Collinsella, Dialister, and Roseburia) had fold changes greater than one and were present in over 90% of all fecal samples. In particular, Bacteroides and Dialister significantly differed between the MDD and control groups (p-value < 0.05). The correlation coefficients between the seven genera and miRNAs in patients with MDD showed 48 pairs of positive correlations and 36 negative correlations (p-value < 0.01). For miRNA predicted functions, there were 57 predicted pathways with a p-value < 0.001, including MDD-associated pathways, axon guidance, circadian rhythm, dopaminergic synapse, focal adhesion, long-term potentiation, and neurotrophin signaling pathway. In the current pilot study, our findings suggest specific genera highly correlated with the predicted miRNA functions, which might provide clues for the interaction between host factors and gut microbiota via the microbiota-gut-brain axis. Follow-up studies with larger sample sizes and refined experimental design are essential to dissect the roles between gut microbiota and miRNAs for depression.

Therapeutic targets and signaling mechanisms of dasatinib activity against radiation skin ulcer.

To reveal the potential targets and signaling pathways of dasatinib in the treatment of radiation ulcers through network pharmacology and molecular docking technology. Pathological targets of radiation ulcers were screened using GeneCards database. At the same time, the pharmacological targets of dasatinib were obtained through SwissTargetPrediction (STP), Binding DB and Drugbank databases. Subsequently, the potential targets of dasatinib for anti-radiation ulcers were obtained after intersection by Venn diagram. Next, a protein-protein interaction (PPI) network was constructed through the STRING database and core targets were screened. Finally, the identified core targets were subjected to GO and KEGG enrichment analysis, co-expression network analysis, and molecular docking technology to verify the reliability of the core targets. A total of 76 potential targets for anti-radiation ulcer with dasatinib were obtained, and 6 core targets were screened, including EGFR, ERBB2, FYN, JAK2, KIT, and SRC. These genes were mainly enriched in Adherens junction, EGFR tyrosine kinase inhibitor resistance, Focal adhesion, Bladder cancer and PI3K-Akt signaling pathway. Molecular docking results showed that dasatinib binds well to the core target. Dasatinib may play a role in the treatment of radiation ulcers by regulating EGFR, ERBB2, FYN, JAK2, KIT, and SRC. These core targets may provide new insights for follow-up studies of radiation ulcers.

Genome-wide characterization of circRNA expression profile in overexpression of RIP2 chicken macrophages associated with avian pathogenic E.coli infection

ABSTRACT Avian pathogenic E. coli (APEC) can cause localized and systemic diseases in poultry, threatening human health via meat or egg contamination and resulting in considerable economic losses to the poultry industry globally. Increasing evidence shows circRNAs were widely involved in various biological processes. However, the role of circRNAs in the host response against APEC infection, especially correlated with the regulation of RIP2, remains unclear. Herein, the RNAseq technology was used to identify the circRNA expression profiles in the overexpression of RIP2 macrophages with or without APEC infection. A total of 256 and 287 differentially expressed (DE) circRNAs were identified in the overexpression of RIP2 group (oeRIP2) vs. the wild-type group (WT) and oeRIP2 + APEC vs. APEC, respectively, whose parental genes were involved in MAPK signalling pathway, Wnt signalling pathway, focal adhesion, tight junction, and VEGF signalling pathways. Specifically, the key circRNAs, such as 5:814443-825127, 10:18922360-18928461, 2:8746306-8750639, and 2:124177751-124184063 might play a critical role in APEC infection and the regulation of RIP2. As a whole, these findings will facilitate understanding the molecular mechanism underlying circRNAs, especially related to the regulation of the RIP2 gene. Meanwhile, the study may offer new ideas to improve host immune and inflammatory response against APEC infection.

Construction of a novel immune-related prognostic-predicting model of gastric cancer

Gastric cancer (GC) is a common primary stomach tumor of the central nervous system with a poor prognosis. In this study, 274 differentially expressed immune-related genes (DEIRGs) were identified among six cell subpopulations in GSE112302 single-cell RNA sequencing (scRNA-seq) data of GC. Those DEIRGs were able to divide GC patients into three distinct subtypes with different overall survivals and tumor microenvironment. By univariate Cox and LASSO regression analyses, eight immune-related genes, including CTGF, CXCL3, CXCR4, NRP1, OAS1, SP1, STC1 and TAP1, were identified as GC prognostic signatures. Accordingly, a risk score model for predicting GC prognosis was constructed in TCGA-GC training cohort and validated in the external GSE66229 dataset. Moreover, a nomogram for predicting the survival of GC patients was also established based on independent prognostic factors (age, grade, cancer status and risk score) identified by univariate and multivariate Cox regression analyses. In addition, Gene Set Variation Analysis (GSVA) analysis indicated that the prognostic immune signatures may regulate GC via inflammation and cell proliferation related pathways, such as DNA replication, complement and coagulation cascades, focal adhesion and TGF-β signaling pathway.

Identification of Histone Acetylation Regulator KAT2A As a Potential Prognostic Biomarker in Diffuse Large B-Cell Lymphoma

Introduction Diffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous lymphoid neoplasm with variations in the expression of genes and genetic alterations. Epigenetic alterations are associated with lymphoma pathogenesis, one of which is histone acetylation. Ferroptosis is a novel type of cell death with distinct properties and recognizing functions involved in physical conditions or various cancers. However, the functions of histone acetylation and ferroptosis in DLBCL remain unclear. Our study assesses the significance and mechanisms of ferroptosis-related genes (FRG) and histone acetylation regulators (HAG). Methods Using consensus clustering, we categorized DLBCL patients based on histone acetylation regulators and ferroptosis-related genes (HFGs) expression. The WGCNA identified genes and mechanisms that affect HF clusters. LASSO Cox regression was used to calculate risk scores. To assess the accuracy of this model, Kaplan-Meier survival analysis, univariate and multivariate Cox regression analysis, and ROC curve analysis were performed. qRT-PCR was used to validate the expression of four HFGs in DLBCL cell lines. Results A total of 38 HA regulators were evaluated for mutations. According to the study, CREBBP had the highest mutation frequency. Based on CREBBP mutations, patients were divided into mutant and wild groups, and several histone acetylation regulators were overexpressed in the mutant group. There was a high rate of copy number variation (CNV) in some genes. To demonstrate the potential malignant mechanisms of HFGs in DLBCL development and their prognostic value. A significant positive self-correlation was observed in HAGs and FRGs. A negative correlation was found between KAT2A, the HA writer, and the majority of FRGs (Fig. 1A). 36 genes were selected (P < 0.05) by univariate regression correlations with clinical prognosis. Consensus clustering was used to categorize the expression of DLBCL patients. K-M survival analysis showed that HFcluster B had a worse prognosis. To investigate the underlying mechanisms, WGCNA was used to divide genes into different modules. Afterwards, we selected the blue and green modules to analyze their functions. KEGG enrichment emphasized oncological pathways like PI3K-Akt, focal adhesion, Hippo, and MAPK signaling pathway. Based on HFGs and their corresponding signatures, we developed a high-quality and high-accuracy gene signature prediction model. Following LASSO Cox regression, a four-gene signature model was identified. Patients with DLBCL in the high-risk group had a significantly shorter OS (P < 0.001, Fig. 1B). ROC curves, univariate and multivariate Cox regression analyses also revealed that riskScore served as an independent indicator for patients with DLBCL (P < 0.001). GSEA enrichment analysis identified JAK-STAT, P53, and APOPTOSIS as the most differentially enriched genes for malignant mechanisms. Analyses revealed that molecular mechanisms mediate histone acetylation and ferroptosis. The results of PCR in CD19+ B cells and DLBCL cell lines also confirmed the accuracy of the model. Due to its close relationship to ferroptosis-related genes, KAT2A was explored in greater depth. Further study revealed that KAT2A was significantly correlated with age (P = 0.028) and IPI (P = 0.016). In univariate analysis, KAT2A was an independent indicator of DLBCL patients (P < 0.001). The expression level of KAT2A was negatively correlated with OS in DLBCL patients (P = 0.003). Conclusions There were significant correlations among these HFGs, indicating their potential role in DLBCL development and predictive value for prognosis. Additionally, our study shows that KAT2A is associated with prognosis in patients with DLBCL. Further study of the mechanisms of KAT2A in DLBCL may help clinicians to individualize the treatment of this patient population. Keywords: histone acetylation, ferroptosis, mechanism, DLBCL Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

KANK3 mediates the p38 MAPK pathway to regulate the proliferation and invasion of lung adenocarcinoma cells

BackgroundLung adenocarcinoma (LUAD) is one of the major subtypes of lung cancer and is the most common cause of cancer deaths globally. The Kank (kidney or KN motif and ankyrin repeat domain-containing) family of proteins has been characterized as critical for regulating the capacity of cells to migrate and their anti-tumor drug sensitivity. The current research designs to explore the specific effects and potential regulatory molecular mechanism of KANK3 on LUAD cells. MethodTwo datasets (TCGA-LUAD and GSE116959) were analyzed to confirm the differently expressed genes. qRT-PCR was carried out to measure KANK3 level in LUAD tissue samples and adjacent non-cancerous tissue samples. Western blot assay was utilized to investigate the KANK3, p-p38 and p38 protein levels. MTT assay were employed to investigate the cell proliferation. Cell invasion and migration were assessed using Transwell and wound healing assay. ResultKANK3 was down-regulated in LUAD tissues and the expressions of KANK3 had a strong influence on prognosis of LUAD patients. Overexpression of KANK3 significantly inhibited， whereas KANK3 silencing observably enhanced the capacity of NCI-H1975 and PC-9 cells to proliferate, invade and migrate. GSEA showed that, differentially expressed genes which regulated by KANK3 enriched in cell adhesion, chemokine, focal adhesion or MAPK signaling pathway. Further experiments proved that KANK3 regulated LUAD cells proliferation and metastasis through p38 MAPK pathway. ConclusionKANK3 exerts antitumor effect in LUAD through regulation of p38 MAPK signaling pathway. These outcomes foreboded that KANK3 could be a novel therapeutic target for further study of LUAD.

Single-cell and bulk RNA sequencing reveal ligands and receptors associated with worse overall survival in serous ovarian cancer

BackgroundSerous ovarian carcinoma is the most frequent histological subgroup of ovarian cancer and the leading cause of death among gynecologic tumors. The tumor microenvironment and cancer-associated fibroblasts (CAFs) have a critical role in the origin and progression of cancer. We comprehensively characterized the crosstalk between CAFs and ovarian cancer cells from malignant fluids to identify specific ligands and receptors mediating intercellular communications and disrupted pathways related to prognosis and therapy response.MethodsMalignant fluids of serous ovarian cancer, including tumor-derived organoids, CAFs-enriched (eCAFs), and malignant effusion cells (no cultured) paired with normal ovarian tissues, were explored by RNA-sequencing. These data were integrated with single-cell RNA-sequencing data of ascites from ovarian cancer patients. The most relevant ligand and receptor interactions were used to identify differentially expressed genes with prognostic values in ovarian cancer.ResultsCAF ligands and epithelial cancer cell receptors were enriched for PI3K-AKT, focal adhesion, and epithelial-mesenchymal transition signaling pathways. Collagens, MIF, MDK, APP, and laminin were detected as the most significant signaling, and the top ligand-receptor interactions THBS2/THBS3 (CAFs)—CD47 (cancer cells), MDK (CAFs)—NCL/SDC2/SDC4 (cancer cells) as potential therapeutic targets. Interestingly, 34 genes encoding receptors and ligands of the PI3K pathway were associated with the outcome, response to treatment, and overall survival in ovarian cancer. Up-regulated genes from this list consistently predicted a worse overall survival (hazard ratio > 1.0 and log-rank P < 0.05) in two independent validation cohorts.ConclusionsThis study describes critical signaling pathways, ligands, and receptors involved in the communication between CAFs and cancer cells that have prognostic and therapeutic significance in ovarian cancer.AKQp7fCjRyS9LmaGP7R5S5Video abstract

Identifying Diagnostic and Prognostic Differentially Expressed Genes of Gastric Cancer Based on Bioinformatics Analyses of RNA-seq Data.

Background: The abnormal expression of genes in serum may be associated with early diagnosis of patients with malignant tumors. This study was designed to screen for significantly differentially expressed genes (DEGs) that may be associated with gastric cancer using bioinformatic methods. Methods: RNA-seq data from gastric cancers were downloaded from the TCGA and GEO databases, and 1903 secretory genes were downloaded from the HPA database. The diagnostic secretory RNAs of gastric cancer were screened using least absolute shrinkage and selection operator regression analysis. Univariate Cox regression analysis was used to evaluate the prognostic significance of the results. Biological functions were performed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Then, 640 cases of gastric cancer and paracancerous tissues were collected, and immunohistochemistry (IHC) was used to detect the expression of COL4A1. Results: In total, 25 upregulated differentially expressed genes (DEGs) were identified, which were secreted mainly in the blood and cell matrices. Six secretory genes (OLFM4, CEMIP, APOC1, CST1, COL4A1, and CD55) with diagnostic significance were identified, and the enrichment scores of these six genes were significantly associated with tumor stage. In addition, we found that increased COL4A1 expression might be associated with a poor prognosis in patients with gastric cancer. Based on GO and KEGG analyses, we found COL4A1-related DEGs were mainly enriched in connective tissue development, collagen fibrous tissue-related processes, extracellular structure, extracellular matrix (ECM) tissue, and related to the ECM receptor-related pathway, focal adhesion, and PI3K-Akt signaling pathway. Moreover, the results of immunohistochemical analyses showed that the COL4A1 protein level in gastric cancers was also higher than in the matched paracancerous tissues. Conclusions: In this study, we found six upregulated secretory genes, including OLFM4, CEMIP, APOC1, CST1, COL4A1, and CD55 which we hypothesized to be significant DEGs for the diagnosis of gastric cancer. Our data also suggest that COL4A1 may play an important role in the diagnosis and prognosis of gastric cancer.

DUSP5P1 promotes gastric cancer metastasis and platinum drug resistance

We elucidated the functional significance and molecular mechanisms of DUSP5P1 lncRNA (dual specificity phosphatase 5 pseudogene 1) in gastric carcinogenesis. We demonstrated that gastric cancer (GC) patients with high DUSP5P1 expression had shortened survival in two independent cohorts. DUSP5P1 promoted GC cell migration and invasion in vitro and metastasis in vivo. Mechanistically, DUSP5P1 activated ARHGAP5 transcription by directly binding to the promoter of ARHGAP5 with a binding motif of TATGTG. RNA-seq revealed that ARHGAP5 activated focal adhesion and MAPK signaling pathways to promote GC metastasis. DUSP5P1 also dysregulated platinum drug resistance pathway. Consistently, DUSP5P1 overexpression in GC cells antagonized cytotoxic effect of Oxaliplatin, and shDUSP5P1 plus Oxaliplatin exerted synergistic effect on inhibiting GC metastasis in vitro and in vivo. DUSP5P1 depletion also suppressed the growth of platinum drug-resistant PDO models. In conclusion, DUSP5P1 promoted GC metastasis by directly modulating ARHGAP5 expression to activate focal adhesion and MAPK pathways, serves as therapeutic target for platinum drug resistant GC, and is an independent prognostic factor in GC.