Expression Correlation Analysis Research Articles

Estrogen-Related Receptors Gene Expression and Copy Number Alteration Association With the Clinicopathologic Characteristics of Breast Cancer

Purpose:It has been suggested that dysregulation of transcription factors expression or activity plays significant roles in breast cancer (BC) severity and poor prognosis. Therefore, our study aims to thoroughly evaluate the estrogen-related receptor isoforms (ESRRs) expression and copy number alteration (CNA) status and their association with clinicopathologic characteristics in BC.Methods:A METABRIC dataset consist of 2509 BC patients’ samples was obtained from the cBioPortal public domain. The gene expression, putative CNA, and relevant tumor information of ESRRs were retrieved. ESRRs messenger RNA (mRNA) expression in BC cell lines was obtained from the Cancer Cell Line Encyclopedia (CCLE). Association and correlation analysis of ESRRs expression with BC clinicopathologic characteristics and molecular subtype were performed. Kaplan–Meier survival analysis was conducted to evaluate the prognostic value of ESRRs expression on patient survival.Results:ESRRα expression correlated negatively with patients’ age and overall survival, whereas positively correlated with tumor size, the number of positive lymph nodes, and Nottingham prognostic index (NPI). Conversely, ESRRγ expression was positively correlated with patients’ age and negatively correlated with NPI. ESRRα and ESRRγ expression were significantly associated with tumor grade, expression of hormone receptors, human epidermal growth factor receptor 2 (HER2), and molecular subtype, whereas ESRRβ was only associated with tumor stage. A significant and distinct association of each of ESRRs CNA with various clinicopathologic and prognostic factors was also observed. Kaplan–Meier survival analysis demonstrated no significant difference for survival curves among BC patients with high or low expression of ESRRα, β, or γ. On stratification, high ESRRα expression significantly reduced survival among premenopausal patients, patients with grade I/II, and early-stage disease. In BC cell lines, only ESRRα expression was significantly higher in HER2-positive cells. No significant association was observed between ESRRβ expression and any of the clinicopathologic characteristics examined.Conclusions:In this clinical dataset, ESRRα and ESRRγ mRNA expression and CNA show a significant correlation and association with distinct clinicopathologic and prognostic parameters known to influence treatment outcomes; however, ESRRβ failed to show a robust role in BC pathogenesis. ESRRα and ESRRγ can be employed as therapeutic targets in BC-targeted therapy. However, the role of ESRRβ in BC pathogenesis remains unclear.

Family with sequence similarity 153 member B as a potential prognostic biomarker of gastric cancer.

Gastric cancer (GC) is one of the most common digestive tumors in Northwest China. Previous sequencing analysis revealed that family with sequence similarity 153 member B (FAM153B) might be the primary driver gene of GC. In this study, we aim to explore the potential roles of FAM153B in GC. Microarray data were firstly obtained from public databases with the aim to evaluate the genetic expression of FAM153B between GC and normal tissues. The results were verified in immunohistochemistry (IHC). We also performed the co-expression network analysis and enrichment analysis to identify underlying mechanisms. A correlation analysis of FAM153B expression and immune infiltration was performed then. Furthermore, two GC cell lines were used to evaluate the effect of FAM153B on gastric cell proliferation by employing MTT and Edu assays. Our findings suggest that FAM153B is downregulated in tumoral tissue, and positively associated with unfavorable survival. The enrichment pathways of FAM153B were regulation of signaling receptor activity, DNA replication, cell cycle transition, chromosomal regulation, and so on. Besides, from the perspective of bioinformatics, the protein expression level of FAM153B is related to the degree of immune cell infiltration. In vitro, overexpression of FAM153B inhibit the proliferation of two cell lines. In summary, this study demonstrates that FAM153B might serve as an effective prognostic and therapeutic biomarker in GC.

Identification of SHCBP1 as a potential biomarker involving diagnosis, prognosis, and tumor immune microenvironment across multiple cancers

Shc SH2-domain binding protein 1 (SHCBP1), a protein specific binding to SH2 domain of Src homolog and collagen homolog (Shc), takes part in the regulation of various signal transduction pathways, which has been reported to be associated with tumorigenesis and progression. However, the pathological mechanisms are not completely investigated. Thus, this study aimed to comprehensively elucidate the potential functions of SHCBP1 in multiple cancer types. The comprehensive analyses for SHCBP1 in various tumors, including gene expression, diagnosis, prognosis, immune-related features, genetic alteration, and function enrichment, were conducted based on multiple databases and analysis tools. SHCBP1 was upregulated in most types of cancers. The results of qRT-PCR had confirmed that SHCBP1 mRNA was significantly upregulated in lung adenocarcinoma (LUAD) and liver hepatocellular carcinoma (LIHC) cell lines. Based on the receiver operating characteristic (ROC) and survival analysis, SHCBP1 was considered as a potential diagnostic and prognostic biomarker. Furthermore, SHCBP1 expression was linked with tumor immunity and immunosuppressive microenvironment according to the correlation analysis of SHCBP1 expression with immune cells infiltration, immune checkpoint genes, and immune-related genes (MHC genes, chemokines, and chemokines receptors). Moreover, SHCBP1 expression correlated with tumor mutational burden (TMB), microsatellite instability (MSI), and neoantigens. The feature of SHCBP1 mutational landscape in pan-cancer was identified. Finally, we focused on investigating the clinical significance and the potential biological role of SHCBP1 in LUAD. Our study comprehensively uncovered that SHCBP1 could be identified as an immune-related biomarker for cancer diagnosis and prognosis, and a potential therapeutic target for tumor immunotherapy.

Tsp2 Facilitates Tumor-associated Fibroblasts Formation and Promotes Tumor Progression in Retroperitoneal Liposarcoma.

Retroperitoneal liposarcoma (RLPS) is the most common subtype of retroperitoneal soft tissue sarcoma, characterized by a high recurrence rate and insensitivity to radiotherapy and chemotherapy. The function of tumor microenvironmental components, especially tumor-associated fibroblasts (TAFs), remains unclear in RLPS. The crosstalk between tumor cells and stromal cells should be clarified for therapy target discovery in RLPS. In this study, we demonstrated that TAFs from dedifferentiated liposarcoma (DDLPS) could attract LPS cells and promote their proliferation and migration. However, although α-SMA is positively expressed in RLPS, its expression does not indicate prognosis. By screening differentially expressed genes, performing Oncomine visualization, TCGA gene expression correlation analysis and qPCR verification, we determined that thrombospondin-2 (THBS2) gene expression was related to TAFs. The expression of Tsp2 protein, which was encoded by THBS2, was correlated with α-SMA expression, and it was an independent predictive factor for disease-free survival and recurrence-free survival in patients with RLPS. In vitro, Tsp2 facilitated the transformation of bone marrow-derived fibroblasts (BMFs) to TAFs and promoted the malignant biological behaviors of LPS cells by activating the MAPK/MEK/ERK pathway. Therefore, suppression of Tsp2 is expected to be a promising treatment method for RLPS patients.

Correlation Analysis of Protein Expression of 10 HDAC/Sirtuin Isoenzymes with Sensitivities of 23 Anticancer Drugs in 17 Cancer Cell Lines and Potentiation of Drug Activity by Co-Treatment with HDAC Inhibitors.

Simple SummaryProtein expression profiles of 10 HDAC/Sirtuin isoenzymes in two panels of human cancer cell lines were compared with each other and with the potencies of various anticancer drugs by Pearson and Spearman correlation analysis to identify patterns of enzyme expression and anticancer activity. Furthermore, the NCI COMPARE database was used to identify possible correlations between the mRNA expression in a 60 cancer cell panel and the potency of the same anticancer drugs. While several interesting correlations were found within both data sets, none of these correlations were identical in the two sets of data, suggesting that protein and mRNA expression profiles are not comparable. Combination treatments with several HDAC inhibitors with a number of the anticancer drugs revealed interesting synergistic effects that were in keeping with some of the correlations predicted by our protein expression analysis.Inhibiting the activity of histone deacetylase (HDAC) is an ongoing strategy in anticancer therapy. However, to our knowledge, the relationships between the expression of HDAC proteins and the antitumor drug sensitivity of cancer cells have not been studied until now. In the current work, we investigated the relative expression profiles of 10 HDAC isoenzymes comprising the classes I–III (HDAC1/2/4/6; Sirt1/2/3/5/6/7) in a panel of 17 cancer cell lines, including the breast, cervix, oesophageal, lung, oral squamous, pancreas, as well as urinary bladder carcinoma cells. Correlations between the data of mRNA expression for these enzymes obtained from the National Cancer Institute (NCI) 60 cancer cell line program were also examined. Next, we performed univariate analysis between the expression patterns of HDAC/Sirt isoenzymes with the sensitivity of a 16 cell panel of cancer cell lines towards several antitumor drugs. In a univariate correlation analysis, we found a strong relation between Sirt2 expression and cytotoxicity caused by busulfan, etoposide, and hydroxyurea. Moreover, it was identified that Sirt5 correlates with the effects exerted by oxaliplatin or topotecan, as well as between HDAC4 expression and these two drugs. Correlations between the data of mRNA expression for enzymes with the potencies of the same anticancer agents obtained from the NCI 60 cancer cell line program were also found, but none were the same as those we found with our protein expression data. Additionally, we report here the effects upon combination of the approved HDAC inhibitor vorinostat and one other known inhibitor trichostatin A as well as newer hetero-stilbene and diazeno based sirtuin inhibitors on the potency of cisplatin, lomustine, and topotecan. For these three anticancer drugs, we found a significantly enhanced cytotoxicity when co-incubated with HDAC inhibitors, demonstrating a potentially beneficial influence of HDAC inhibition on anticancer drug treatment.

Metabogenomic analysis to functionally annotate the regulatory role of long non-coding RNAs in the liver of cows with different nutrient partitioning phenotype

Long non-coding RNAs (lncRNAs) hold gene regulatory potential, but require substantial further functional annotation in livestock. Applying two metabogenomic approaches by combining transcriptomic and metabolomic analyses, we aimed to identify lncRNAs with potential regulatory function for divergent nutrient partitioning of lactating crossbred cows and to establish metabogenomic interaction networks comprising metabolites, genes and lncRNAs. Through correlation analysis of lncRNA expression with transcriptomic and metabolomic data, we unraveled lncRNAs that have a putative regulatory role in energy and lipid metabolism, the urea and tricarboxylic acid cycles, and gluconeogenesis. Especially FGF21, which correlated with a plentitude of differentially expressed genes, differentially abundant metabolites, as well as lncRNAs, suggested itself as a key metabolic regulator. Notably, lncRNAs in close physical proximity to coding-genes as well as lncRNAs with natural antisense transcripts appear to perform a fine-tuning function in gene expression involved in metabolic pathways associated with different nutrient partitioning phenotypes.

Influence of seasonal migration on the development of the insecticide resistance of oriental armyworm (Mythimna separata) to λ-cyhalothrin.

The seasonal long-distance migration of pests amongst different seasonal habitats may encounter different degrees of insecticide selection pressure, but knowledge of the evolution of resistance and the underlying mechanisms remains sparse. Here, we show that the development of resistance of the oriental armyworm Mythimna separata (Walker), a notorious agricultural pest that migrates between northern and northeast China seasonally across the Bohai Gulf, is influenced by seasonal migration. There are two conspicuous migrations of M. separata, the northeastwards population in the second half of May and the returning population in the second half of August, between northern and northeast China per year, and the abundance values of migrants from April to October are significantly different. The resistance levels of seasonal migratory populations to λ-cyhalothrin vary in different months, and the resistance levels and estimated frequency of the resistance allele of the first northeastward population (second half of May, May.-2) in spring are significantly higher than those of the returning populations in autumn. Moreover, resistance decline was observed in migrating population Jul.-2, with the resistance levels in the F1 progeny higher than those in their F2 progeny. Synergism tests indicate that cytochrome P450 monooxygenases (P450s) play a major role in resistance. Enzymatic assays show that P450 activity is significantly correlated with resistance levels in migratory populations, indicating that increased P450 activity is the main mechanism of resistance. The expression levels and correlation analysis of the relative expression of P450s with resistance levels show that three (CYP9A144, CYP9G40, and CYP6B79) out of 23 genes from CYP6 and CYP9 subfamilies are potentially involved in resistance to λ-cyhalothrin. Our results show that the resistance of M. separata to λ-cyhalothrin is unstable and likely to be metabolically driven by enhanced P450 activity mediated by the overexpression of multiple P450 genes. Notably, the development of resistance is probably affected by seasonal migration.

Bioinformatic Analysis of Potential Biomarker for hsa-miR-196b-5p in Mesothelioma.

Purpose: Malignant pleural mesothelioma is a rare neoplasia with a poor prognosis, and the majority of patients have advanced disease at the time of presentation. Exposure to asbestos is the most important risk factor for malignant pleural mesothelioma. Materials and Methods: To determine the cytotoxicity of geldanamycin in mesothelioma H28 cells, the MTT assay was used. To determine changes in microRNA (miRNA) expression in geldanamycin-treated H28 cells, miRNA microarray analysis was performed. To determine the function of miR-196b-5p, we performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of miR-196b-5p targets predicted by miRwalk. Results: Our data showed that geldanamycin treatment reduced H28 cell viability in a dose-dependent manner. MicroRNA array analyses showed that expression of hsa-miR-196b-5p was downregulated in geldanamycin-treated H28 cells. Geldanamycin regulated miRNAs with roles in processes such as aging, angiogenesis, apoptosis, cell cycle, cell differentiation, cell proliferation, DNA repair, and secretion. Survival analysis showed that decreased expression of hsa-miR-196b-5p was significantly associated with a better outcome in mesothelioma patients. Expression of miR-196b-5p was also significantly associated with the developmental stages of mesothelioma. To narrow down the target genes of miR-196b-5p, we determined the overlap between the predicted target genes of miR-196b-5p and downregulated mRNAs in ovarian cancer based on the Gene Expression Omnibus dataset GSE12345. PDE1A, LAMA4, and PAPPA were identified as both miR-196b-5p targets and downregulated genes in GSE12345 and were thus considered targets of miR-196b-5p. Gene-miRNA expression correlation analysis showed that PDE1A, LAMA4, and PAPPA expression was negatively correlated with miR-196b-5p expression. Conclusions: We suggest that geldanamycin has potential for the treatment of mesothelioma via regulating miR-196b-5p. Furthermore, miR-196b-5p may be a potential biomarker for mesothelioma.

Abstract PO-115: Effects of mesothelin exert on tumor microenvironment in pancreatic ductal adenocarcinoma

Abstract Background: High mesothelin (MSLN) expression has been associated with poor prognosis in patients with pancreatic ductal adenocarcinoma (PDAC); however, the effect of MSLN exert on PDAC tumor microenvironment (TME) is largely unknown. Methods: MSLN over-expressed (MSLN-OE) and knocked-down (MSLN-KD) PDAC cells were established to investigate the MSLN-PD-L1 relationship in PDAC. Using an MSLN overexpressed Panc02 (Panc02-MSLN) cell line, we established an orthotopic PDAC mouse model. All mice were euthanized on day 27 after cell inoculation and the tumor-infiltrating leukocytes (TILs) were isolated for mass cytometry (CyTOF) study. The gene expression correlation between MSLN and a panel of immune cell markers was assessed by using a dataset that includes149 PDAC patients in the TCGA-PAAD cohort. Results: MSLN upregulated PD-L1 expression at both mRNA and protein levels in PDAC. MSLN was able to enhance PD-L1 transcription by recruitment of NF-kB P65 to the PD-L1 promoter. The Orthotopic implanted Panc02-MSLN group showed significantly increased tumor size, tumor weight, upregulated PD-L1, and reduced survival when compared with the vector control group. CyTOF analysis of the total CD45+ hematopoietic cells infiltrated to the TME revealed 13 distinct cell subsets. In MSLN-high tumors, there is a significant expansion of neutrophils, eosinophils, PD-1+CD8+, and CD8+NK cells. In addition, pan T cells, regulatory T cells (Treg), CD8+, and PD-1+CD4+ cells were increased. A considerable decrease of tumor-associated macrophages (TAM), dendritic cells, B cells, NK cells, and a trend towards decreased Ly6C+CD8+ cells was also found. Within the TAM subset, a decreased iNOS+M1 to Relm-a+M2 ratio was detected. Furthermore, although there were increased CD8+NK cells, we found more immunosuppressive markers such as PD-1, CTLA4, LAG3, KLRG1, and TIM3, and a decreased activation marker CD69 and transcription factor T-bet. Intriguingly, gene expression correlation analysis with 149 PDAC patients cohort in TCGA dataset showed that MSLN expression negatively correlates with the mRNA levels of the B220 marker of B cells, the F4/80 marker of macrophages, as well as the CD4, CD8, CD69, granzyme B, IL-2 and IFN-γ markers of T-cell activation. Conclusions: We showed here that MSLN could significantly modulate the TME, possibly through the upregulation of PD-L1 expression. Compared with MSLN-low PDAC tumors, MSLN-high tumors recruit diverse immunosuppressive rather than immunoreactive leukocytes into tumor tissues to constitute an immunologically cold TME. Since targeting MSLN or PD-L1 as a monotherapy exhibited only modest objective response rates in the clinic, our findings may provide an alternative strategy by combining the depletion of MSLN with immune checkpoint inhibitors, which could result in improved treatment efficacy in PDAC. Citation Format: Dongliang Liu, Ethan Poteet, Zhengdong Liang, Emily Laplante, Lisa Brubaker, Sadhna Dhingra, Aleksandar Milosavljevic, Changyi Chen, Qizhi Cathy Yao. Effects of mesothelin exert on tumor microenvironment in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-115.

Unravelling lncRNA mediated gene expression as potential mechanism for regulating secondary metabolism in Citrus limon

Plant long non-coding RNAs (lncRNAs) are emerging as important regulators of gene expression through various mechanisms viz. binding to double-stranded DNA (dsDNA), physically targeting mRNAs and also act as microRNA (miRNA) sponges. Characteristic secondary metabolites and their content determine the market value of Citrus plant products for culinary and industrial uses. Though lncRNAs are emerging as important molecular players that regulate secondary metabolites in plants but the roles of lncRNAs are yet unknown for the regulation of secondary metabolites in Citrus limon. In this study, a total of 11814 lncRNAs were identified from four RNA-seq datasets comprising of data from four different tissues of C. limon viz. leaf, bud, fruit and peel. Co-expression analysis of whole set of genes with identified lncRNAs revealed a total of 632 lncRNAs correlating with 5810 genes. Functional annotation of genes correlating with lncRNAs unveiled the association of 379 genes with the biosynthesis of secondary metabolite pathways and among them, 36 and 12 genes are from terpenoids and flavonoids metabolism/biosynthesis pathways respectively. Expression correlation analysis unfolded the possible role of 113 lncRNAs in terpenoids metabolism and 29 lncRNAs in the flavonoids metabolic pathway. Seventy nine lncRNAs were predicted to take part in miRNA-mediated gene regulation, out of which 10 lncRNAs were predicted to act as endogenous target mimics (eTMs) for miRNAs and 74 lncRNAs were found to act as miRNA targets. Expression of six predicted lncRNAs and seven correlated genes involved in terpenoids and flavonoids metabolism were validated using semi-quantitative RT- PCR.

Intronic Architecture Links DNA Methylation to Gene Expression and Helps Drive Subtype-Specific Transcriptional Landscapes in DNMT3A- and IDH1/2-Mutant Acute Myeloid Leukemias (AML)

Mutations in DNMT3A and IDH1/2 are each found in ~20% of AML patients. 10-15% of AMLs carry mutations in both genes (herein, double mutants), resulting in a unique methylation landscape and upregulation of a signaling signature. In murine models, the presence of both mutations results in greater leukemogenic potential. However, the specific mechanism through which DNA methylation (DNAme) drives gene expression programs in double mutants remains unclear. We hypothesized that the link between DNAme and gene expression would be explained by more than simple proximity, and that the genomic architecture of the affected genes would play a key role.To test this, we first performed an unbiased correlation analysis of gene expression with DNAme at all CpG sites (mCs) located within the same topologically associated domain (TAD). We identified 406 genes with significant (FDR> 5% and absolute rho > 0.5) expression-methylation correlations with mCs proximal to the respective genes (herein the E-M gene set). In addition, another 2,088 genes (the L E-M set) were identified with long-range correlations (>2Kb from the gene body) with mCs in the respective TAD (median distance = 451 Kb). As a set, the E-M genes significantly overlapped (P < 10 -2) with genes identified as either differentially expressed (DE; n=890) or differentially methylated (DM; n= 4,006) between IDH1/2 and DNMT3A mutant AMLs. Notably, a simple overlap analysis of DE and DM genes showed no significant overlap between them, thus demonstrating that correlation analysis performed better in bridging the epigenome with the transcriptome. DAVID and Gene Set Enrichment Analysis on the genes ranked by correlation strength revealed that signaling, fructose and lipid metabolism pathways are enriched in the E-M gene set (FDR < 5%) but not in the L E-M set. Analysis of transcription factor (TF) binding profiles did not reveal a common set of TF(s) binding to the mCs proximal to the genes of the identified pathways. Thus, we hypothesized that the E-M genes have other structural characteristics in common that drive regulation through DNAme, for which we focused on their genomic architecture. This analysis revealed that introns of genes in both the E-M and L E-M sets are significantly denser in Mammalian Interspersed Repeats (MIR) than expected by random chance (P < 10 -2). Additionally, E-M genes were significantly sparser in endogenous retroviruses (ERVL) and primate-specific Alu elements. mCs with significant correlations were also enriched at MIR and depleted from Alu elements (P < 10 -2), thus creating a regulatory network between mCs and genes with MIR sequences as the common denominator. Genome-wide, CpGs within retrotransposons that were differentially methylated among the three AML subtypes were enriched at enhancer regions or coding genes, particularly the E-M genes. Furthermore, the Dnmt3a knock-out (KO) or Idh2 R140Q knock-in mouse models display the same architectural biases at genes correlated with DNAme as the E-M genes identified in the human samples. Next, we sought to put our findings in the context of normal hematopoiesis and found that genes upregulated during normal hematopoietic differentiation are significantly denser in MIR elements and sparser of Alu elements than expected (P < 10 -2). Alignment of the leukemic samples within normal differentiation trajectories revealed that double mutants resembled differentiated cell types more closely, while DNMT3A and IDH1/2 single mutants resembled hematopoietic stem cells. The E-M and L E-M sets significantly overlapped (P < 10 -2) with those genes upregulated during myeloid but not erythroid or lymphoid differentiation, demonstrating that genes regulated by DNAme are at the core of the biology of these AMLs.In summary, our integrative work sheds light on a novel mechanism in which epigenetic modifications can regulate gene expression through MIR sequences within introns of hematopoietic-relevant genes and we posit that overlapping CpG dinucleotides may act as recruiters or substrates of DNMT3A and/or TET proteins. This mechanism seems to also be active in normal hematopoiesis and thus, is hijacked by leukemic cells. Therefore, our findings identify retrotransposons as a missing link in the understanding of epigenetic regulation of gene expression, reveal a previously uncharacterized role for these elements in leukemogenesis, and point to different cells of origin for each AML subtype. DisclosuresNo relevant conflicts of interest to declare.

Comprehensive Secretome Profiling Elucidates Novel Disease Biology and Identifies Pre-Infusion Candidate Biomarkers to Predict the Development of Severe Cytokine Release Syndrome in Pediatric Patients Receiving CART19

Comprehensive Secretome Profiling Elucidates Novel Disease Biology and Identifies Pre-Infusion Candidate Biomarkers to Predict the Development of Severe Cytokine Release Syndrome in Pediatric Patients Receiving CART19

Gene expression analysis of MAOA and the clock gene ARNTL in individuals with bipolar disorder compared to healthy controls

Introduction Circadian rhythms are associated with bipolar disorder (BD). This cross-sectional study aimed at investigating ARNTL and MAOA gene expression differences (1) between individuals with BD and controls, (2) between affective episodes, and (3) the relationship between ARNTL and MAOA expression. Methods ARNTL and MAOA gene expression in peripheral mononuclear blood cells were analysed from fasting blood samples (BD n = 81, controls n = 54) with quantitative real-time PCR operating on TaqMan® assays (normalised to 18S RNA expression). ANCOVAs corrected for age, sex, body mass index, and medication was used to evaluate expression differences and correlation analyses for the relation between ARNTL and MAOA expression. Results ARNTL gene expression differed between affective episodes (F(2,78) = 3.198, p = 0.047, Partial Eta2= 0.083), but not between BD and controls (n.s.). ARNTL and MAOA expression correlated positively in BD (r = 0.704, p < 0.001) and in controls (r = 0.932, p < 0.001). MAOA expression differed neither between BD and controls nor between affective episodes (n.s.). Discussion Clock gene expression changes were observed in different affective states of BD. More precisely, ARNTL gene expression was significantly higher in euthymia than in depression. ARNTL and MAOA gene expression correlated significantly in BD and in controls, which emphasises the strong concatenation between circadian rhythms and neurotransmitter breakdown.

Comprehensive Analyses Identify APOBEC3A as a Genomic Instability-Associated Immune Prognostic Biomarker in Ovarian Cancer.

Ovarian cancer (OC) is one of the most malignant tumors whose mortality rate ranks first in gynecological tumors. Although immunotherapy sheds new light on clinical treatments, the low response still restricts its clinical use because of the unique characteristics of OC such as immunosuppressive microenvironment and unstable genomes. Further exploration on determining an efficient biomarker to predict the immunotherapy response of OC patients is of vital importance. In this study, integrative analyses were performed systematically using transcriptome profiles and somatic mutation data from The Cancer Genome Atlas (TCGA) based on the immune microenvironment and genomic instability of OC patients. Firstly, intersection analysis was conducted to identify immune-related differentially expressed genes (DEGs) and genomic instability-related DEGs. Secondly, Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3A (APOBEC3A) was recognized as a protective factor for OC, which was also verified through basic experiments such as quantitative reverse transcription PCR (RT-qPCR), immunohistochemistry (IHC), Cell Counting Kit-8 (CCK-8), and transwell assays. Thirdly, the correlation analyses of APOBEC3A expression with tumor-infiltrating immune cells (TICs), inhibitory checkpoint molecules (ICPs), Immunophenoscores (IPS), and response to anti-PD-L1 immunotherapy were further applied along with single-sample GSEA (ssGSEA), demonstrating APOBEC3A as a promising biomarker to forecast the immunotherapy response of OC patients. Last, the relationship between APOBEC3A expression with tumor mutation burden (TMB), DNA damage response (DDR) genes, and m6A-related regulators was also analyzed along with the experimental verification of immunofluorescence (IF) and RT-qPCR, comprehensively confirming the intimate association of APOBEC3A with genomic instability in OC. In conclusion, APOBEC3A was identified as a protective signature and a promising prognostic biomarker for forecasting the survival and immunotherapy effect of OC patients, which might accelerate the clinical application and improve immunotherapy effect.

Low GNG12 Expression Predicts Adverse Outcomes: A Potential Therapeutic Target for Osteosarcoma.

BackgroundG protein subunit gamma 12 (GNG12) is observed in some types of cancer, but its role in osteosarcoma is unknown. This study hypothesized that GNG12 may be a potential biomarker and therapeutic target. We aimed to identify an association between GNG12 and osteosarcoma based on the Gene Expression Omnibus and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) databases.MethodsOsteosarcoma samples in GSE42352 and TARGET database were selected as the test cohorts. As the external validation cohort, 78 osteosarcoma specimens from The Second Affiliated Hospital of Nanchang University were collected. Patients with osteosarcoma were divided into high and low GNG12 mRNA-expression groups; differentially expressed genes were identified as GNG12-related genes. The biological function of GNG12 was annotated using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis, and immune infiltration analysis. Gene expression correlation analysis and competing endogenous RNA regulatory network construction were used to determine potential biological regulatory relationships of GNG12. Overall survival, Kaplan–Meier analysis, and log-rank tests were calculated to determine GNG12 reliability in predicting survival prognosis.ResultsGNG12 expression decreased in osteosarcoma samples. GNG12 was a highly effective biomarker for osteosarcoma [area under the receiver operating characteristic (ROC) curve (AUC) = 0.920], and the results of our Kaplan–Meier analysis indicated that overall survival and progression-free survival differed significantly between low and high GNG-expression group (p < 0.05). Functional analyses indicated that GNG12 may promote osteosarcoma through regulating the endoplasmic reticulum. Expression correlation analysis and competing endogenous RNA network construction showed that HOTTIP/miR-27a-3p may regulate GNG12 expression. Furthermore, the subunit suppresses adaptive immunity via inhibiting M1 and M2 macrophage infiltration. GNG12 was inhibited in metastatic osteosarcoma compared with non-metastatic osteosarcoma, and its expression predicted survival of patients (1, 3, and 5-year AUCs were 0.961, 0.826, and 0.808, respectively).ConclusionThis study identified GNG12 as a potential biomarker for osteosarcoma prognosis, highlighting its potential as an immunotherapy target.

Protein Kinase D3 Promotes the Reconstruction of OSCC Immune Escape Niche Via Regulating MHC-I and Immune Inhibit Molecules Expression.

Protein kinase D3 (PKD3) has been involved in various aspects of tumorigenesis and progression in many kinds of cancer types. However, whether PKD3 regulates immune escape in tumor microenvironment is rarely reported. Here, we explored the function and mechanism of PKD3 in reconstructing the immune escape niche of oral squamous cell carcinoma (OSCC). Both the Western blotting analysis in OSCC cells and the gene expression correlation analysis from The Cancer Genome Atlas shows that the expression of Fas and programmed cell death-ligand 1 (PD-L1) was positively correlated with PKD3, while major histocompatibility complex-I (MHC-I) was negatively correlated with PKD3. Knockdown of PKD3 significantly decreased the expression of Fas and PD-L1 and increased the expression of MHC-I. Furthermore, when PKD3 was overexpressed in oral precancerous cells, Fas, PD-L1, and MHC-I showed an opposite trend to that observed when PKD3 was knocked down. In addition, PKD3 knockdown decreased the secretion of transforming growth factor β, CC-chemokine ligand 21, interleukin-10 by OSCC cells. Finally, the tumor cell antigen, which was extracted from PKD3 knockdown OSCC cells, significantly induced the growth and activation of T lymphocytes. These results demonstrate that PKD3 promotes the immune escape of OSCC cells by regulating the expression of Fas, PD-L1, MHC-I, transforming growth factor β, CC-chemokine ligand 21, interleukin-10, and plays a key role in reconstructing the tumor immune escape niche.

CD3D, GZMK, and KLRB1 Are Potential Markers for Early Diagnosis of Rheumatoid Arthritis, Especially in Anti-Citrullinated Protein Antibody-Negative Patients.

Early diagnosis and monitoring of rheumatoid arthritis (RA) progress are critical for effective treatment. In clinic, the detection of rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPA) are usually combined to diagnose early RA. However, the poor specificity of RF and high heterogeneity of ACPA make the early diagnosis of RA still challenging. Bioinformatics analysis based on high-throughput omics is an emerging method to identify novel and effective biomarkers, which has been widely used in many diseases. Herein, utilizing an integrated strategy based on expression correlation analysis and weighted gene coexpression network analysis (WGCNA), we identified 76 RA-trait different expression genes (DEGs). Combined with protein-protein interaction (PPI) network construction and clustering, new hub genes associated in RA synovia, CD3D, GZMK, and KLRB1, were identified. We verified the specificity of these genes in the synovium of RA patients through three external datasets. We also observed high sensitivity and specificity of them for ACPA-negative patients. CD3D, GZMK, and KLRB1 are potentially key mediators of RA pathogenesis and markers for RA diagnosis.

Correlation analysis of TGF-β1 gene polymorphism and expression with incidence and severity of lumbar disc herniation.

Correlation analysis of TGF-β1 gene polymorphism and expression with incidence and severity of lumbar disc herniation.

Correlation analysis of Ki67 and CK7 expression with clinical characteristics and prognosis of postoperative cervical adenocarcinoma patients.

The purpose of this study is to investigate the correlation between cytokeratin 7 (CK7) and marker of proliferation Ki67 protein expression and clinical characteristics and prognosis of patients with cervical adenocarcinoma after surgery. A total of 126 patients with cervical adenocarcinoma treated by surgery in our hospital from June 2011 to September 2015 were enrolled in this study. Immunohistochemistry (IHC) was used to detect the expression of CK7 and Ki67 in 126 cases of cervical adenocarcinoma tissues. The chi-square (χ2) test was used to compare the relationship between the positive expression rate of CK7 or Ki67 and clinicopathological features. Kaplan-Meier method was used to analyze the survival of different protein expression groups and Cox proportional hazards regression model was used to analyze the risk factors affecting the prognosis. The positive rate of CK7 was correlated with muscle invasion, vascular invasion, differentiation, and lymph node metastasis (all P<0.05). The positive expression rate of Ki67 was related to the degree of myometrial invasion and International Federation of Gynecology and Obstetrics (FIGO) stage (both P<0.05). Both CK7 and Ki67 may be independent risk factors for the prognosis of patients with cervical adenocarcinoma after surgery (both P<0.05), and their high expression heralds worse prognosis. The CK7 and Ki67 proteins may be key regulatory factors in the development of cervical adenocarcinoma after surgery, and their overexpression may lead to worse prognosis. Both CK7 and Ki67 may provide new markers for prognosis evaluation of cervical adenocarcinoma.

A novel lncRNA-miRNA-mRNA competing endogenous RNA regulatory network in lung adenocarcinoma and kidney renal papillary cell carcinoma.

BackgroundGPRIN1 may be a novel tumor regulator, but its role and mechanism in tumors are still unclear.MethodsFirst, a pan‐cancer correlation analysis was conducted on the expression and prognosis of GPRIN1 based on the data downloaded from The Cancer Genome Atlas (TCGA) database. Second, the Starbase database was used to predict the upstream miRNAs and lncRNAs of GPRIN1, and the expression analysis, survival analysis, and correlation analysis were performed to screen the microRNA (miRNAs)/long non‐coding RNAs (lncRNAs) that had a correlation with kidney renal papillary cell carcinoma (KIRP) or lung adenocarcinoma (LUAD). Third, the CIBERSORT algorithm was employed to calculate the proportion of various types of immune cells, and then the R packages were used for evaluating the relation between GPRIN1 expression and tumor immune cell infiltration as well as between GPRIN1 and the immune cell biomarker. Finally, the correlation analysis was made on GPRIN1 and immune checkpoints (CD274, CTLA4, and PDCD1).ResultsThe pan‐cancer analysis suggested that GPRIN1 was up‐expressed in KIRP and LUAD, and it correlated with poor prognosis. LINC00894/MMP25‐AS1/SNHG1/LINC02298/MIR193BHG‐miR‐140‐3p was likely to be the most promising upstream regulation pathway of GPRIN1. Upexpression of LINC00894/MMP25‐AS1/SNHG1/LINC02298/MIR193BHG and downexpression of miR‐140‐3p were found relevant with poor outcomes of KIRP and LUAD. GPRIN1 expression was significantly correlated with tumor immune cell infiltration, immune cell biomarkers, and immune checkpoints.ConclusionsThe competitive endogenous (ceRNA) of miR‐140‐3p‐GPRIN1 axis and its upstream lncRNAs are closely related to KIRP and LUAD, and might affect the prognosis and therapeutic effect of KIRP and LUAD.