Expression Correlation Analysis Research Articles

Systematic analysis identifies REST as an oncogenic and immunological biomarker in glioma

The repressor element 1 silencing transcription factor (REST) has been proposed to function as a transcription factor to silence gene transcription by binding to repressor element 1 (RE1), a highly conserved DNA motif. The functions of REST in various tumors have been studied, but its role and correlation with immune cell infiltration remains uncertain in gliomas. REST expression was analyzed in datasets of The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) and validated by the Gene Expression Omnibus and Human Protein Atlas databases. The clinical prognosis of REST was evaluated by clinical survival data of TCGA cohort and validated by Chinese Glioma Genome Atlas cohort. MicroRNAs (miRNAs) contributing to REST overexpression in glioma were identified by a combination of a series of in silico analyses, including expression analysis, correlation analysis, and survival analysis. The correlations between immune cell infiltration level and REST expression were analyzed by TIMER2 and GEPIA2 tools. Enrichment analysis of REST was performed using STRING and Metascape tools. The expression and function of predicted upstream miRNAs at REST and their association with glioma malignancy and migration were also confirmed in glioma cell lines. REST was highly expressed and associated with poorer overall survival and disease-specific survival in glioma and some other tumors. MiR-105-5p and miR-9-5p were identified as the most potential upstream miRNAs of REST in glioma patient cohort and experiments in vitro. REST expression was positively correlated with infiltration of immune cells and the expression of immune checkpoints such as PD1/PD-L1 and CTLA-4 in glioma. Furthermore, histone deacetylase 1 (HDAC1) was a potential REST-related gene in glioma. Enrichment analysis of REST found chromatin organization and histone modification were the most significant enriched terms, and Hedgehog-Gli pathway might be involved in the effect of REST on the pathogenesis of glioma. Our study suggests REST to be an oncogenic gene and the biomarker of poor prognosis in glioma. High REST expression might affect the tumor microenvironment of glioma. More basic experiments and large clinical trials aimed at the carcinogenetic study of REST in glioma will be needed in the future.

Effect of VEGF on neurological impairment and prognosis of acute cerebral infarction patients: A retrospective case-control study.

Due to the complex pathological mechanism of acute cerebral infarction, the role of vascular endothelial growth factor (VEGF) on the disease is not clear. Therefore, a retrospective case-control study was performed to explore the effect of VEGF on neurological impairment and prognosis of acute cerebral infarction patients. A total of 100 patients with acute cerebral infarction admitted to our hospital from April 2021 to April 2022 were selected. Blood samples from all patients would be routinely collected to detect the expression of serum VEGF. Pearson chi-square, Spearman correlation and univariate Logistic regression were used to analyze the clinical data to explore the relationship between VEGF expression and basic information, stroke degree, quality of life, and prognosis of patients. To determine whether VEGF can provide relevant basis for the early prevention and prognostic treatment of acute cerebral infarction. And multivariate logistic regression was used to calculate the odds ratio between each variable and VEGF expression. Pearson chi-square test and Spearman correlation coefficient showed that sex, degree of stroke, limb convulsions, loss of consciousness, hemiplegia, aphasia, mental functioning score, overall quality of life score, and short-term prognosis were significantly correlated with VEGF expression in 100 patients. Univariate logistic regression was used to describe the ORs and 95% confidence interval of subjects at the univariate level, and the degree of stroke (OR = 83.333, P < 0.001), tic of limbs (OR = 26.316, P < 0.001), loss of consciousness (OR = 23.256, P < 0.001), hemiplegia (OR = 62.500, P < 0.001), aphasia (OR = 76.923, P < 0.001), mental functioning score (OR = 7.937, P < 0.001), overall quality of life score (OR = 5.464, P < 0.001), short-term prognosis (OR = 37.037, P < 0.001) was significantly correlated with the high expression of VEGF. The level of serum VEGF was positively correlated with neurological impairment degree and prognosis in patients with acute cerebral infarction, the more severe the degree of stroke and the worse the prognosis.

High GNG4 predicts adverse prognosis for osteosarcoma: Bioinformatics prediction and experimental verification.

Guanine nucleotide binding (G) protein subunit γ 4 (GNG4) is closely related to the malignant progression and poor prognosis of various tumours. However, its role and mechanism in osteosarcoma remain unclear. This study aimed to elucidate the biological role and prognostic value of GNG4 in osteosarcoma. Osteosarcoma samples in the GSE12865, GSE14359, GSE162454 and TARGET datasets were selected as the test cohorts. The expression level of GNG4 between normal and osteosarcoma was identified in GSE12865 and GSE14359. Based on the osteosarcoma single-cell RNA sequencing (scRNA-seq) dataset GSE162454, differential expression of GNG4 among cell subsets was identified at the single-cell level. As the external validation cohort, 58 osteosarcoma specimens from the First Affiliated Hospital of Guangxi Medical University were collected. Patients with osteosarcoma were divided into high- and low-GNG4 groups. The biological function of GNG4 was annotated using Gene Ontology, gene set enrichment analysis, gene expression correlation analysis and immune infiltration analysis. Kaplan-Meier survival analysis was conducted and receiver operating characteristic (ROC) curves were calculated to determine the reliability of GNG4 in predicting prognostic significance and diagnostic value. Functional in vitro experiments were performed to explore the function of GNG4 in osteosarcoma cells. GNG4 was generally highly expressed in osteosarcoma. As an independent risk factor, high GNG4 was negatively correlated with both overall survival and event-free survival. Furthermore, GNG4 was a good diagnostic marker for osteosarcoma, with an area under the receiver operating characteristic curve (AUC) of more than 0.9. Functional analysis suggested that GNG4 may promote the occurrence of osteosarcoma by regulating ossification, B-cell activation, the cell cycle and the proportion of memory B cells. In in vitro experiments, silencing of GNG4 inhibited the viability, proliferation and invasion of osteosarcoma cells. Through bioinformatics analysis and experimental verification, high expression of GNG4 in osteosarcoma was identified as an oncogene and reliable biomarker for poor prognosis. This study helps to elucidate the significant potential of GNG4 in carcinogenesis and molecular targeted therapy for osteosarcoma.

Transcriptome analysis constructed the necroptosis associated prognostic signature in endometrial cancer and identified EZH2 as a potential biomarker

Endometrial cancer (EC) is one of the most common malignancies of the female reproductive system, but our understanding of the tumor microenvironment of EC remains unclear. Programmed cell death (PCD) plays an important role in the genesis and progression of tumors. Necroptosis is a novel form of PCD that does not rely on the caspase system. However, the role of necroptosis in EC is unclear. Transcriptome data of endometrial cancer were downloaded from The Cancer Genome Atlas (TCGA) database and log2 conversion was performed. Expression analysis and correlation analysis were performed to explore necroptosis gene expression and interaction in EC. Lasso regression was used to construct necroptosis-related prognostic signature. Finally, immunocorrelation analysis and single cell sequencing analysis were used to explore the significance of this signature in EC tumor microenvironment. A total of 15 of the 17 necroptosis genes were differentially expressed in EC. Subsequently, necroptosis related prognostic signature was constructed through Lasso regression. Riskscore = (−0.0999) × Toll-likereceptor4 (TLR4) + (−0.0528) × tumor necrosis factor receptor superfamily member 1A (TNFRSF1A) + (0.1208) × Enhancer of Zeste Homolog 2 (EZH2) + (−0.004) × N-myc Down-stream Regulated Gene 2 (NDRG2). EC patients can be divided into high-risk group and low-risk group based on the median riskscore and the high-risk group has a worse prognosis. Survival analysis showed a worse prognosis for patients in the high-risk group (p &lt; 0.05). Immunomicroenvironment analysis showed a significant negative correlation between risk score and infiltration levels of B cells, CD4+ T cells, CD8+ T cells, Endothelial cells, macrophages, and NK cells. Subsequent cell experiments showed that knockdown of the key gene EZH2 in signature significantly reduced the invasion, migration and healing abilities of EC cell lines, proving that EZH2 is a promising marker of EC.

Genome-wide identification of the plant U-box (&lt;i&gt;PUB&lt;/i&gt;) gene family and their global expression analysis in tomato (&lt;i&gt;Solanum lycopersicum&lt;/i&gt;)

Plant ubiquitination plays an important role in proteins post-translational changes that occurs in a wide variety of eukaryotic organisms and regulating a broad range of biological processes. However, little is known about the evolutionary relationships, gene duplication, and functional evolution of <italic>PUB</italic> genes in tomato. Herein, we explored 48 <italic>PUB</italic> genes in the tomato genome and were further classified into 7 major groups based on their sequences and relative genetic similarities with <italic>Arabidopsis</italic>. Gene structure analysis suggested that most of the PUBs carry similar features and with slight differentiation in their sources of functions during the process of evolution. Collinear analysis showed a high degree of conservation among SlPUBs, with a total of ten pairs identified as collinear with potential interactions with each other and another family. Based on their duplication forms, a total of 23 pairs were chosen for <italic>Ka/Ks</italic> calculation: 13 pairs of dispersed, 1 tandem, and 9 pairs of WGD or segmental. The majority of the gene pairs from the three forms of duplication had a <italic>Ka/Ks</italic> ratio of less than 1.00, indicating purifying selection and reduced divergence after duplication. Only 3 pairs i.e., <italic>SlPUB16-SlPUB22, SlPUB30-SlPUB32,</italic> and <italic>SlPUB36-SlPUB37</italic> were perceived by higher than 1.00 values, signifying positive selection. In addition, three major RNA-seq datasets analyses from the cultivated and its relatives, as well as Micro-Tom (MT), revealed their highly tissue-specific role, with the expression correlation analysis of duplicated pairs indicating highly putative neo-functionalization as compared to functional conservation or sub-functionalization after duplication. <italic>SlPUB10</italic> was screened out and preliminary verified as a key gene in salt and cold stress response with validation of transgenic strains. These results are indicative of their response during the gene duplication and evolution process, while further functional validation step is required to determine their specific role.

Correlation Analysis of Ki67 Expression and EGFR Mutation on the Risk of Recurrence and Metastasis in Postoperative Patients with Stage I Lung Adenocarcinoma

The prognosis of stage I non-small cell lung cancer (NSCLC) is generally good. However, some of the stage I NSCLC patients still may have early recurrence and metastasis, and there is no standard method to screen this part of the population. The aim of this study is to investigate the relationship between Ki67 expression as well as epidermal growth factor receptor (EGFR) mutation and the risk of recurrence in postoperative patients with stage I lung adenocarcinoma. We retrospectively enrolled 118 postoperative patients with stage I lung adenocarcinoma. EGFR mutation was tested using amplification refractory mutation system polymerase chain reaction (ARMS-PCR) , and Ki67 level was detected by immunohistochemistry (IHC), followed by the collection of the patients' clinical characteristics. Kaplan-Meier method, Log-rank test, and Cox proportional hazards regression model were used for the prognostic statistical analysis. Among the 118 patients, the rate of high Ki67 expression was 43.22% (51/118), which is related to gender, smoking status, surgical method, differentiation degree, and postoperative stage (P<0.05). Meanwhile, EGFR mutation rate was 61.02% (72/118), of which EGFR exon 19 deletion mutation rate was 19.49% (23/118), and the EGFR exon 21 L858R mutation rate was 41.53% (49/118). However, Ki67 expression was not associated with EGFR mutation status (χ2=1.412, P=0.235). Survival analysis showed that high Ki67 expression was inversely associated with disease-free survival (DFS) and overall survival (OS) in stage I lung adenocarcinoma (P<0.05), but EGFR mutation status was not significantly associated with DFS and OS (P>0.05). In the subgroup analysis, the DFS of the EGFR exon 19 deletion group was significantly decreased compared with the EGFR exon 21 L858R mutation group (P=0.031), but there was no significant difference in OS (P=0.308). Multivariate analysis showed that there was statistical significance between Ki67 expression (P=0.001) and DFS in stage I lung adenocarcinoma; Ki67 expression (P=0.03) and gender (P=0.015) were associated with OS in stage I lung adenocarcinoma. Ki67 expression is an independent influencing factor for postoperative recurrence and OS of stage I lung adenocarcinoma and it is not significantly associated with EGFR mutation. There is no significant difference between EGFR mutation status and the prognostis of stage I lung adenocarcinoma. However, the prognosis differed in EGFR mutation types; the patients with EGFR exon 19 deletion are at higher risk of recurrence than EGFR exon 21 L858R mutation.

Significance of Identifying Key Genes Involved in HBV-Related Hepatocellular Carcinoma for Primary Care Surveillance of Patients with Cirrhosis.

Cirrhosis is frequently the final stage of disease preceding the development of hepatocellular carcinoma (HCC) and is one of the risk factors for HCC. Preventive surveillance for early HCC in patients with cirrhosis is advantageous for achieving early HCC prevention and diagnosis, thereby enhancing patient prognosis and reducing mortality. However, there is no highly sensitive diagnostic marker for the clinical surveillance of HCC in patients with cirrhosis, which significantly restricts its use in primary care for HCC. To increase the accuracy of illness diagnosis, the study of the effective and sensitive genetic biomarkers involved in HCC incidence is crucial. In this study, a set of 120 significantly differentially expressed genes (DEGs) was identified in the GSE121248 dataset. A protein-protein interaction (PPI) network was constructed among the DEGs, and Cytoscape was used to extract hub genes from the network. In TCGA database, the expression levels, correlation analysis, and predictive performance of hub genes were validated. In total, 15 hub genes showed increased expression, and their positive correlation ranged from 0.80 to 0.90, suggesting they may be involved in the same signaling pathway governing HBV-related HCC. The GSE10143, GSE25097, GSE54236, and GSE17548 datasets were used to investigate the expression pattern of these hub genes in the progression from cirrhosis to HCC. Using Cox regression analysis, a prediction model was then developed. The ROC curves, DCA, and calibration analysis demonstrated the superior disease prediction accuracy of this model. In addition, using proteomic analysis, we investigated whether these key hub genes interact with the HBV-encoded oncogene X protein (HBx), the oncogenic protein in HCC. We constructed stable HBx-expressing LO2-HBx and Huh-7-HBx cell lines. Co-immunoprecipitation coupled with mass spectrometry (Co-IP/MS) results demonstrated that CDK1, RRM2, ANLN, and HMMR interacted specifically with HBx in both cell models. Importantly, we investigated 15 potential key genes (CCNB1, CDK1, BUB1B, ECT2, RACGAP1, ANLN, PBK, TOP2A, ASPM, RRM2, NEK2, PRC1, SPP1, HMMR, and DTL) participating in the transformation process of HBV infection to HCC, of which 4 hub genes (CDK1, RRM2, ANLN, and HMMR) probably serve as potential oncogenic HBx downstream target molecules. All these findings of our study provided valuable research direction for the diagnostic gene detection of HBV-related HCC in primary care surveillance for HCC in patients with cirrhosis.

High VSX1 expression promotes the aggressiveness of clear cell renal cell carcinoma by transcriptionally regulating FKBP10

BackgroundClear cell renal cell carcinoma (ccRCC), the most common urological malignancy, has an unfavorable prognosis and an unknown mechanism of progression. Through survival analyses screening of The Cancer Genome Atlas (TCGA) dataset, we identified Visual system homeobox1 (VSX1) as a novel potential prognostic biomarker in ccRCC and subsequently investigated the oncogenic role of VSX1 in ccRCC.MethodsThe differential expression of VSX1 in human tumors and the clinical prognoses were analyzed in the TCGA dataset and Gene Expression Omnibus. Spearman’s correlation coefficient was determined for the correlation analysis of VSX1 expression and other genes of interest. The roles of VSX1 in cell proliferation, invasion, and migration of ccRCC cells were evaluated via the CCK-8 assay, colony formation assay, and Transwell assay, respectively. Further results were demonstrated by western blotting, immunohistochemistry, qRT-PCR, tumor sphere formation, flow cytometry, and the dual‑luciferase reporter assay.ResultsVSX1 mRNA upregulation was generally observed in multiple human malignancies from the TCGA database and was confirmed in ccRCC clinical specimens from our department. High VSX1 expression usually indicated that overall and disease-free survival were unfavorable for patients with ccRCC. In terms of mechanism, knockdown or overexpression of VSX1 affected ccRCC aggressiveness in vitro. The dual-luciferase reporter gene assay implied that VSX1 overexpression significantly increased the luciferase activity of TMEM44, FKBP10, and TRIB3, which indicated that VSX1 promoted ccRCC invasiveness via transcriptional regulation of these genes. The significantly enhanced growth in vitro that was induced by stable VSX1 overexpression was almost restored to normal by the knockdown of FKBP10.ConclusionsThis study demonstrated that VSX1 was a novel prognostic biomarker in ccRCC and that high VSX1 expression promoted cell proliferation, invasion, and migration in ccRCC via transcriptional activation of downstream target genes.

Specific lncRNA signatures discriminate childhood acute leukaemias: a pilot study

BackgroundLong non-coding RNAs are RNAs longer than 200 bps that do not encode any proteins and are able to alter gene expression by acting on different steps of regulation, including DNA methylation and chromatin structure. They represent a class of biomarkers of crescent interest in the hematologic and oncologic fields. Recent studies showed that the expression levels of specific lncRNAs correlate with the prognosis of paediatric patients with Acute Lymphoblastic Leukaemia.MethodsWe used NGS approaches to analyse the transcriptome of 9 childhood B-ALL patients and 6 childhood T-ALL patients, in comparison with B and T healthy lymphocytes from cord blood. We validate our findings both ex vivo, in a different cohort of 10 B-ALL and 10 T-ALL patients, and in silico using public datasets.ResultsWe characterised the lncRNA landscape for B-ALL, T-ALL, healthy B, and T cell progenitors. From the characterised signature, we selected candidate lncRNAs able to discriminate not only B-ALL and T-ALL from healthy subjects but also between the two types of leukaemia, and subsequently validated their potential as a diagnostic tool in an additional cohort of paediatric patients. We confirmed our finding with open access transcriptomic data, comparing ALL lncRNAs with AML lncRNA landscape as well. Finally, expression correlation analyses of T-ALL selected lncRNA biomarkers suggested a possible role in lymphocyte activation and the β-catenin signalling pathway for AC247036.1 and involvement in hedgehog signalling for HHIP-AS1.ConclusionsOur work identified a lncRNA signature discriminating paediatric B-ALL and T-ALL from healthy subjects, between them and from AML. This study provides the keystone to future clinical studies determining the theragnostic value of the characterised long non coding transcriptome panorama in a clinical setting for childhood patient management.

Correlation analysis of serum CTRP3 and PGC-1α expression with traumatic fracture healing

To investigate the relationship between serum C1q/tumor necrosis factor-related protein-3(CTRP3) and peroxisome proliferator-activated receptor γ coactivator-1α(PGC-1α) on predictive value of expression level on fracture healing. From January 2019 to January 2020, 80 patients with traumatic tibial plateau fractures were treated by internal fixation with support plates through the posterior approach of the knee joint. The patients were followed up for 12 months. According to the criteria for delayed fracture healing, the patients were divided into two groups:54 patients in fracture healing group included 24 males and 30 females, aged 29 to 75 years old with an average of (52.36±13.17) years;In the delayed healing group, there were 26 cases, 13 males and 13 females, aged from 29 to 75 with an average od (53.82±13.52) years. The serum levels of CTRP3, PGC-1αand 25 hydroxyvitamin D3[25(OH)D3] in patients with traumatic fracture were detected by enzyme-linked immunosorbent assay(ELISA);Blood phosphorus and calcium levels were measured by automatic biochemical analyzer, and the product of calcium and phosphorus was calculated;Pearson's method was used to analyze the correlation between serum CTRP3, PGC-1αand bone biochemical indexes in patients with delayed union one week after operation;The predictive value of serum levels of CTRP3 and PGC-1αon traumatic fracture healing was analyzed by receiver operating characteristic curve(ROC curve). PGC-1α, calcium phosphorus product and 25(OH)D3 in the fracture healing group were higher than those in the delayed healing group at 1 and 4 weeks after operation(P<0.05). Serum CTRP3 was positively correlated with PGC-1α(r=0.637, P<0.05) and positively correlated with calcium phosphorus product and 25(OH)D3(P<0.05). The areas under the curve(AUC) of serum ctrp3 and PGC-1α levels in predicting traumatic fracture healing were 0.845 and 0.855, respectively. The cutoff values were 188.678 pg/ml and 2.697 ng/ml, respectively. The specificity was 96.2% and 80.8%, and the sensitivity was 53.7% and 77.8%;The predicted AUC was 0.904, the specificity was 88.5%, and the sensitivity was 81.5%. The serum levels of CTRP3 and PGC-1 in patients with delayed union of traumatic fracture at 1 and 4 weeks after operation α The expression level is of certain reference value to predict the fracture healing status of patients.

The role of YAP1 in survival prediction, immune modulation, and drug response: A pan-cancer perspective.

Dysregulation of the Hippo signaling pathway has been implicated in multiple pathologies, including cancer, and YAP1 is the major effector of the pathway. In this study, we assessed the role of YAP1 in prognostic value, immunomodulation, and drug response from a pan-cancer perspective. We compared YAP1 expression between normal and cancerous tissues and among different pathologic stages survival analysis and gene set enrichment analysis were performed. Additionally, we performed correlation analyses of YAP1 expression with RNA modification-related gene expression, tumor mutation burden (TMB), microsatellite instability (MSI), immune checkpoint regulator expression, and infiltration of immune cells. Correlations between YAP1 expression and IC50s (half-maximal inhibitory concentrations) of drugs in the CellMiner database were calculated. We found that YAP1 was aberrantly expressed in various cancer types and regulated by its DNA methylation and post-transcriptional modifications, particularly m6A methylation. High expression of YAP1 was associated with poor survival outcomes in ACC, BLCA, LGG, LUAD, and PAAD. YAP1 expression was negatively correlated with the infiltration of CD8+ T lymphocytes, CD4+ Th1 cells, T follicular helper cells, NKT cells, and activated NK cells, and positively correlated with the infiltration of myeloid-derived suppressor cells (MDSCs) and cancer-associated fibroblasts (CAFs) in pan-cancer. Higher YAP1 expression showed upregulation of TGF-β signaling, Hedgehog signaling, and KRAS signaling. IC50s of FDA-approved chemotherapeutic drugs capable of inhibiting DNA synthesis, including teniposide, dacarbazine, and doxorubicin, as well as inhibitors of hypoxia-inducible factor, MCL-1, ribonucleotide reductase, and FASN in clinical trials were negatively correlated with YAP1 expression. In conclusion, YAP1 is aberrantly expressed in various cancer types and regulated by its DNA methylation and post-transcriptional modifications. High expression of YAP1 is associated with poor survival outcomes in certain cancer types. YAP1 may promote tumor progression through immunosuppression, particularly by suppressing the infiltration of CD8+ T lymphocytes, CD4+ Th1 cells, T follicular helper cells, NKT cells, and activated NK cells, as well as recruiting MDSCs and CAFs in pan-cancer. The tumor-promoting activity of YAP1 is attributed to the activation of TGF-β, Hedgehog, and KRAS signaling pathways. AZD2858 and varlitinib might be effective in cancer patients with high YAP1 expression.

Disturbing effect of cepharanthine on valve interstitial cells calcification via regulating glycolytic metabolism pathways.

Osteogenic differentiation of valve interstitial cells (VICs) directly leads to aortic valve calcification, which is a common cardiovascular disease caused by inflammation and metabolic disorder. There is still no ideal drug for its treatment and prevention. The purpose of this study was to explore the effect and molecular mechanism of cepharanthine (CEP), a natural product, on inhibiting the osteogenic differentiation of VICs. First, CCK8 assay was used to evaluate cell viability of CEP on VICs. CEP concentration of 10μM was the effective dose with slight cytotoxicity, which was used for further study. The alizarin red staining analysis showed that CEP significantly inhibited calcium deposition caused by osteogenic medium related calcification induction. In order to explore the anti-calcification molecular mechanism of CEP, transcriptome and metabolome were synchronously used to discover the possible molecular mechanism and target of CEP. The results showed that CEP inhibited valve calcification by regulating the glycolytic pathway. The molecular docking of CEP and selected key factors in glycolysis showed significant binding energies for GLUT1 (-11.3kcal/mol), ENO1 (-10.6kcal/mol), PKM (-9.8kcal/mol), HK2 (-9.2kcal/mol), PFKM (-9.0kcal/mol), and PFKP (-8.9kcal/mol). The correlation analysis of RUNX2 expression and cellular lactate content showed R2 of 0.7 (p < 0.001). In conclusion, this study demonstrated that CEP inhibited osteoblastic differentiation of VICs by interfering with glycolytic metabolisms via downregulation of the production of lactate and glycolysis-associated metabolites.

Biological relevance of ZNF224 expression in chronic lymphocytic leukemia and its implication IN NF-kB pathway regulation.

Chronic lymphocytic leukemia (CLL) is a heterogeneous disease, whose presentation and clinical course are highly variable. Identification of novel prognostic factors may contribute to improving the CLL classification and providing indications for treatment options. The zinc finger protein ZNF224 plays a key role in cell transformation, through the control of apoptotic and survival pathways. In this study, we evaluated the potential application of ZNF224 as a novel marker of CLL progression and therapy responsiveness. To this aim, we analyzed ZNF224 expression levels in B lymphocytes from CLL patients at different stages of the disease and in patients showing different treatment outcomes. The expression of ZNF224 was significantly increased in disease progression and dramatically decreased in patients in complete remission after chemotherapy. Gene expression correlation analysis performed on datasets of CLL patients revealed that ZNF224 expression was well correlated with that of some prognostic and predictive markers. Moreover, bioinformatic analysis coupled ZNF224 to NF-κB pathway, and experimental data demonstrated that RNA interference of ZNF224 reduced the activity of the NF-κB survival pathway in CLL cells. Consistently with a pro-survival role, ZNF224 knockdown raised spontaneous and drug-induced apoptosis and inhibited the proliferation of peripheral blood mononuclear cells from CLL patients. Our findings provide evidence for the involvement of ZNF224 in the survival of CLL cells via NF-κB pathway modulation, and also suggest ZNF224 as a prognostic and predictive molecular marker of CLL disease.

The Expression Characteristics and Correlation Analysis of Bone Mineral Density and Bone Turnover Biomarkers in CKD Patients

The Expression Characteristics and Correlation Analysis of Bone Mineral Density and Bone Turnover Biomarkers in CKD Patients

Effects of UVA disappearance and presence on the acylated anthocyanins formation in grape berries

Ultraviolet A (UVA), the major component of the UV, plays a crucial role in formatting the characteristics of color in wine grapes by influencing its anthocyanin composition and contents. Results showed that anthocyanin biosynthesis was suppressed by UVA screening and enhanced by irradiation. The acetylation and p-coumaroylation of anthocyanins were more pronounced and showed positive correlation with a* and negative correlation with L*, b*, C*, and h, thereby leading to changes in color. Weighted gene co-expression network analysis showed that two modules (red and turquoise) were significantly related to the acetylation and p-coumaroylation of peonidin. In addition, relative gene expression assays and correlation analysis also indicated that VvMYBA1 might influence anthocyanin accumulation by directly regulating VvOMT expression and increasing the flux to the vacuole through VvGST4. In conclusion, the results helped in improving our understanding of the role of UVA in skin color formation.

Aberrantly hypermethylated ARID1B is a novel biomarker and potential therapeutic target of colon adenocarcinoma.

Background and Objective: Understanding the tumor microenvironment (TME) and immune cell infiltration (ICI) may help guide immunotherapy efforts for colon cancer (COAD). However, whether ARID1B is truly regulated by hypermethylation or linked to immune infiltration remains unknown. The current work focused on the ARID1B gene expression and methylation in COAD, as well as its relation with ICI. Methods and Results: Multiple tools based on TCGA were used to analyze the differences in the expression of the ARID1B gene, DNA methylation, and its association with various clinicopathological features, somatic mutations, copy number variation, and the prognosis of patients with COAD. According to the analysis results, patients with high mRNA, low methylation levels showed better overall survival than patients with low mRNA, high methylation levels. The correlation analysis of immune cell infiltration and immune checkpoint gene expression showed that the infiltration rates of the main ICI subtypes, cancer-associated fibroblast, and myeloid cells were significantly enriched and correlated with ARID1B in COAD. An association between ARID1B expression and immune infiltration in COAD was found by correlating ICI indicators with ARID1B expression in the immune cell composition of the COAD microenvironment. Notably, M2 chemokines were related to ARID1B expression, while M1 chemokines were not. Conclusion: This study provided evidence that ARID1B may have a role in the pathogenesis of COAD. The specific underlying mechanisms that could be responsible for ARID1B’s downregulation in COAD will need to be investigated in the future.

Transcriptome and Metabolome Analyses Provide Insights into the Flavonoid Accumulation in Peels of Citrus reticulata 'Chachi'.

The quality of Chinese medicinal materials depends on the content of bioactive components, which are affected by the environmental factors of different planting regions. In this research, integrated analysis of the transcriptome and metabolome of C. reticulata ‘Chachi’ was performed in two regions, and three orchards were included in the analysis. In total, only 192 compounds were found in fresh peels, and among 18 differentially accumulated flavonoid metabolites, 15 flavonoids were enriched in peels from the Xinhui planting region. In total, 1228 genes were up-regulated in peels from Xinhui, including the CHS and GST genes, which are involved in the salt stress response. Overall, based on the correlation analysis of flavonoid content and gene expression in peels of C. reticulata ‘Chachi’, we concluded that the authenticity of the GCRP from Xinhui may be closely related to the higher content of naringin and narirutin, and the increase in the content of these may be due to the highly saline environment of the Xinhui region.

Expression patterns and correlation analyses of muscle-specific genes in the process of sheep myoblast differentiation.

The purpose of this study was to establish a system for the isolation, culture, and differentiation of sheep myoblasts, and to explore the expression patterns as well as mutual relationships of muscle-specific genes. Sheep fetal myoblasts (SFMs) were isolated by two-step enzymatic digestion, purified by differential adhesion and identified using immunofluorescence techniques. Two percent horse serum was used to induce differentiation in SFMs. Real-time quantitative and Western blot analyses were respectively used to detect the mRNA and protein expressions of muscle-specific genes including MyoD, MyoG, Myf5, Myf6, PAX3, PAX7, myomaker, desmin, MYH1, MYH2, MYH4, MYH7, and MSTN during the differentiation of SFMs. Finally, the correlation between muscle-specific genes was analyzed by the Pearson correlation coefficient method. The results showed that the isolated and purified SFMs could form myotubes after the induction for differentiation. The marker factors including MyoD, MyoG, myomaker, desmin, and MyHC were positively stained in SFMs. The mRNA expressions of MyoD, MyoG, and myomaker increased and then decreased, while Myf5, PAX3, and PAX7 decreased; Myf6, desmin, MYH1, MYH2, MYH4, and MYH7 increased; and MSTN fluctuated up and down during the differentiation of SFMs. The expression patterns of protein were basically consistent with those of mRNA except MSTN. There existed significant or highly significant correlations at mRNA or protein level among some genes. Some transcription factor proteins (MyoD, Myf5, Myf6, PAX3, PAX7) showed significant or highly significant correlations with the mRNA level of some other genes and/or themselves. In conclusion, SFMs with good myogenic differentiation ability were successfully isolated, and the expression patterns and correlations of muscle-specific genes during SFM differentiation were revealed, which laid an important foundation for elucidating the gene regulation mechanism of sheep myogenesis.

XDec-CHI reveals immunosuppressive interactions in pancreatic ductal adenocarcinoma

SummaryMost cancers harbor a diverse collection of cell types including a typically heterogeneous cancer cell fraction. To reconstruct cell-intrinsic and heterotypic interactions driving tumor progression, we combine the XDec deconvolution method with cell-type-specific gene expression correlation analysis into the XDec-CHI method. XDec-CHI identifies intra- and inter-cellular pathways using correlation and places them in the context of specific tumor subtypes, as defined by the state of constituent cancer cells. We make the method web-accessible for analysis of publicly accessible pancreatic ductal adenocarcinoma, breast, head and neck, glioblastoma, and glioma tumors. We apply the method to TCGA and ICGC datasets to identify immune-suppressive interactions within PDAC tumors that are relevant for immunotherapies targeting PD-L1. Subtype-specific interactions derived from correlative analyses validated in co-culture experiments suggest PDAC subtypes have distinct therapeutic weaknesses, with Basal-like and MSLN-high Classical B tumors most likely to respond to therapies targeting PD-L1.

Serine protease PRSS23 drives gastric cancer by enhancing tumor associated macrophage infiltration via FGF2.

Serine proteases has been considered to be closely associated with the inflammatory response and tumor progression. As a novel serine protease, the biological function of PRSS23 is rarely studied in cancers. In this study, the prognostic significance of PRSS23 was analyzed in two-independent gastric cancer (GC) cohorts. PRSS23 overexpression was clinically correlated with poor prognosis and macrophage infiltration of GC patients. Loss-of-function study verified that PRSS23 plays oncogenic role in GC. RNA-seq, qRT-PCR, western blotting and ELISA assay confirmed that serine protease PRSS23 positively regulated FGF2 expression and secretion. Single-cell analysis and gene expression correlation analysis showed that PRSS23 and FGF2 were high expressed in fibroblasts, and highly co-expressed with the biomarkers of tumor associated macrophages (TAMs), cancer-associated fibroblasts (CAFs) and mesenchymal cells. Functional analysis confirmed PRSS23/FGF2 was required for TAM infiltration. Rescue assay further verified that PRSS23 promotes GC progression and TAM infiltration through FGF2. Survival analysis showed that high infiltration of M1-macrophage predicted favorable prognosis, while high infiltration level of M2-macrophage predicted poor prognosis in GC. Our finding highlights that PRSS23 promotes TAM infiltration through regulating FGF2 expression and secretion, thereby resulting in a poor prognosis.