Identification of a Key Glioblastoma Candidate Gene, FUBP3, Based on Weighted Gene Co-expression Network Analysis

Background: Glioblastoma multiforme (GBM) is the most common aggressive malignant brain tumor. However, the molecular mechanism of glioblastoma formation is still poorly understood. To identify candidate genes that may be connected to glioma growth and development, weighted gene co-expression network analysis (WGCNA) was performed to construct a gene co-expression network between gene sets and clinical characteristics. We also explored the function of the key candidate gene.Methods: Two GBM datasets were selected from GEO Datasets. The R language was used to identify differentially expressed genes. WGCNA was used to construct a gene co-expression network in the GEO glioblastoma samples. A custom Venn diagram website was used to find the intersecting genes. The GEPIA website was used for survival analysis to determine the significant gene, FUBP3. OS,DSS, and PFI analyses, based on the UCSC Cancer Genomics Browser, were performed to verify the significance of FUBP3. Immunohistochemistry was performed to evaluate the expression of FUBP3 in glioblastoma and adjacent normal tissue. KEGG and GO enrichment analyses were used to reveal possible functions of FUBP3. Microenvironment analysis was used to explore the relationship between FUBP3 and immune infiltration. Immunohistochemistry was performed to verify the results of the microenvironment analysis.Results: GSE70231 and GSE108474 were selected from GEO Datasets, then 715 and 694 differentially expressed genes (DEGs) from GSE70231 and GSE108474, respectively, were identified. We then performed weighted gene co-expression network analysis (WGCNA) and identified the most downregulated gene modules of GSE70231 and GSE108474, and 659 and 3915 module genes from GSE70231 and GSE108474, respectively, were selected. Five intersection genes (FUBP3, DAD1, CLIC1, ABR, and DNM1) were calculated by Venn diagram. FUBP3 was then identified as the only significant gene by survival analysis using the GEPIA website. OS, DSS, and PFI analyses verified the significance of FUBP3. Immunohistochemical analysis revealed FUBP3 expression in GBM and adjacent normal tissue. KEGG and GO analyses uncovered the possible function of FUBP3 in GBM. Tumor microenvironment analysis showed that FUBP3 may be connected to immune infiltration, and immunohistochemistry identified a positive correlation between immune cells (CD4+ T cells, CD8+ T cells, and macrophages) and FUBP3.Conclusion: FUBP3 is associated with immune surveillance in GBM, indicating that it has a great impact on GBM development and progression. Therefore, interventions involving FUBP3 and its regulatory pathway may be a new approach for GBM treatment.

P02.04 Tissue-infiltrating Th9 cells in human endometrial cancer

BackgroundEndometrial cancer (EC) is a hormone-related carcinoma with increased morbidity among female patients of all backgrounds. The immune microenvironment of EC is uncertain.Materials and Methods102 patients were recruited in the present study. 90 postoperative specimens from the patients were analyzed by immunohistochemistry. The leukocyte landscape of endometrial cancer was mapped using high-dimensional single-cell profiling (CyTOF) for 12 patients.ResultsNK cells, MDMs, and neutrophils were enriched in adjacent normal tissue. CCR5+CD38+ PD1+Th9 cells were enriched in the invasive margin. Additionally, PD1+ESRneg T cells and Siglec1+CCR5+CD40+ESRhi macrophage were infiltrated in the tumors.Abstract P02.04 Figure 1ConclusionsImmunological landscape of EC might shed light on new immunotherapuetic approach.Disclosure InformationH. Tong: None. H. Feng: None. X. Wan: None.

Differentially Regulated miRNAs and Their Related Molecular Pathways in Lichen Sclerosus

Lichen sclerosus (LS) is a chronic inflammatory skin disorder with unknown pathogenesis. The aberrant expression of microRNAs (miRNAs) is considered to exert a crucial role in LS. We used the next-generation sequencing technology (RNASeq) for miRNA profiling and Ingenuity Pathway Analysis (IPA) for molecular network analysis. We performed qRT-PCR, miRNA transfection and Matrigel assays for functional studies. We identified a total of 170 differentially expressed miRNAs between female LS and matched adjacent normal tissue using RNASeq, with 119 upregulated and 51 downregulated. Bioinformatics analysis revealed molecular networks that may shed light on the pathogenesis of LS. We verified the expression of a set of miRNAs that are related to autoimmunity, such as upregulated miR-326, miR-142-5p, miR-155 and downregulated miR-664a-3p and miR-181a-3p in LS tissue compared to the matched adjacent normal tissue. The differentially expressed miRNAs were also verified in blood samples from LS patients compared to healthy female volunteers. Functional studies demonstrated that a forced expression of miR-142-5p in human dermal fibroblast PCS-201-010 cells resulted in decreased cell proliferation and migration. These findings suggest that differentially expressed miRNAs may play an important role in LS pathogenesis; therefore, they could serve as biomarkers for LS management.

CXCR3 Expression and Genome-Wide 3′ Splice Site Selection in the TCGA Breast Cancer Cohort

CXCR3 is a chemokine receptor with two well-characterized isoforms that have unique, context-dependent roles: CXCR3-A and CXCR3-B, which are produced through alternative 3′ splice site selection (A3SS). RNA-seq data from The Cancer Genome Atlas (TCGA) were used to correlate CXCR3 expression with breast cancer progression. This analysis revealed significant CXCR3 expression patterns associated with survival and differential expression between the tumor and adjacent normal tissue. TCGA data were used to estimate abundance of immune cells in breast cancer, which demonstrated the association of CXCR3 with immune infiltration, particularly in the triple-negative subtype. Given the importance of A3SS in CXCR3, genome-wide analysis of A3SS events was performed to identify events that were differentially spliced between breast cancer tissue and adjacent normal tissue. A total of 481 splicing events in 424 genes were found to be differentially spliced. The parent genes of differentially spliced events were enriched in RNA processing and splicing functions, indicating an underappreciated role of A3SS in the integrated splicing network of breast cancer. These results further validated the role of CXCR3 in immune infiltration of tumors, while raising questions about the role of A3SS splicing.

CD147 promotes melanoma cell growth via SOX4-mediated glycolytic metabolism

Purpose: To determine the functional roles of cluster of differentiation 147 (CD147) in glycolysis in melanoma cells.Methods: CD147 expression in melanoma tissue and adjacent normal tissue was determined using quantitative real time polymrase chain reaction (qRT-PCR) and immunohistochemistry. Cell Counting Kit-8 (CCK-8) and colony formation assays were used to evaluate cell viability and colony formation, respectively. The role of CD147 in glycolysis in melanoma cells was investigated by determining glucose uptake, production of lactate, and cellular level of ATP.Results: CD147 was enhanced more in melanoma tissue than that in the adjacent normal tissue (p < 0.001). CD147 overexpression promoted the viability and colony formation of melanoma cells. On the other hand, CD147 silencing decreased the viability and colony formation of melanoma cells. Glucose uptake, production of lactate, and cellular level of ATP were upregulated in melanoma cells by CD147 overexpression and downregulated by shRNA-mediated depletion of CD147. CD147 increased expression of C-X-C motif chemokine ligand 1 (CXCL1) to activate the sex-determining region Y-related high-mobility group box 4 (SOX4) pathway. Knockdown of CXCL1 attenuated the positive regulatory effect of CD147 on SOX4. Besides, overexpression of SOX4 reversed the suppressive effects of CD147 silencing on melanoma cell viability, colony formation, and glycolysis.Conclusion: CD147 contributes to melanoma cell growth via upregulation of SOX-mediated glycolysis, thus providing a therapeutic avenue for the management of melanoma. Keywords: Cluster of differentiation 147, CD147, Sex-determining region Y-related high-mobility group box 4, Melanoma, Cell growth, Glycolysis

High expression of tissue O-linked glycans is associated with a malignant phenotype of cholangiocarcinoma

Objective This study aimed to investigate the expression of O-linked glycoprotein glycans in tissue of patients with cholangiocarcinoma compared with adjacent normal tissue. Methods Sixty patients with cholangiocarcinoma were included in the study. Permethylated O-linked glycans from intrahepatic cholangiocarcinoma tissue and adjacent normal tissue were analyzed using nano-spray ionization-linear ion trap mass spectrometry. Histochemistry of peanut agglutinin lectin was used for detection and localization of galactose (Gal) 1, N-acetyl-galactosamine (GalNAc) 1. Results O-linked glycans from patients with cholangiocarcinoma were composed of di- to hexa-saccharides with a terminal galactose and sialic acids (N-acetylneuraminic acid [NeuAc]). A total of eight O-linked glycan structures were detected. Gal1GalNAc1 and Gal2 N-acetyl-glucosamine 1 GalNAc1 expression was significantly higher in tissue from patients with cholangiocarcinoma compared with adjacent normal tissue, while NeuAc1Gal1GalNAc1 expression was significantly lower. High Gal1GalNAc1 expression was significantly associated with the late stage of cholangiocarcinoma (stages II–IV), lymphatic invasion, and vascular invasion. Conclusion Our study shows expression of O-linked glycans in progression of cholangiocarcinoma and highlights the association of Gal1GalNAc1 with lymphatic and vascular invasion of cholangiocarcinoma.

Knockdown of Microtubule Associated Serine/threonine Kinase Like Expression Inhibits Gastric Cancer Cell Growth and Induces Apoptosis by Activation of ERK1/2 and Inactivation of NF-κB Signaling

SummaryMicrotubule-associated serine/threonine kinase (MASTL) functions to regulate chromosome condensation and mitotic progression. Therefore, aberrant MASTL expression is commonly implicated in various human cancers. This study analyzed MASTL expression in gastric cancer vs. adjacent normal tissue for elucidating the association with clinicopathological data from patients. This work was then extended to investigate the effects of MASTL knockdown on tumor cells in vitro. The level of MASTL expression in gastric cancer tissue was assessed from the UALCAN, GEPIA, and Oncomine online databases. Lentivirus carrying MASTL or negative control shRNA was infected into gastric cancer cells. RT-qPCR, Western blotting, cell viability, cell counting, flow cytometric apoptosis and cell cycle, and colony formation assays were performed. MASTL was upregulated in gastric cancer tissue compared to the adjacent normal tissue, and the MASTL expression was associated with advanced tumor stage, Helicobacter pylori infection and histological subtypes. On the other hand, knockdown of MASTL expression significantly reduced tumor cell viability and proliferation, and arrested cell cycle at G2/M stage but promoted tumor cells to undergo apoptosis. At protein level, knockdown of MASTL expression enhanced levels of cleaved PARP1, cleaved caspase-3, Bax and p-ERK1/2 expression, but downregulated expression levels of BCL-2 and p-NF-κB-p65 protein in AGS and MGC-803 cells. MASTL overexpression in gastric cancer tissue may be associated with gastric cancer development and progression, whereas knockdown of MASTL expression reduces tumor cell proliferation and induces apoptosis. Further study will evaluate MASTL as a potential target of gastric cancer therapeutic strategy.

Combination the Gene Expression of Adjacent Normal and Tumor Makes more Robust Gene Signature as Cancer Prognosis Biomarker

Purpose: We tried to explore new gene signature via the combination of tumor-derived expression profile and the adjacent normal-derived expression profile to find more robust cancer biomarker. Methods: Log2 transformed ratio of tumor tissue and the adjacent normal tissue (Log2TN) expression, tumor-derived expression, and normal-derived expression were used to do univariate Cox regression in The Cancer Genome Atlas (TCGA) lung squamous cell carcinoma (LUSC) respectively. Then, we used factor analysis and least absolute shrinkage and selection operator Cox (LASSO-Cox) to select gene signature in TCGA LUSC for Log2TN, tumor, and adjacent normal respectively.Results: By comparing Log2TN with tumor and adjacent normal in LUSC, we found that genes derived from Log2TN show more robust (p = 0.006 and p = 0.001) and have lower p-values (p < 0.001). Gene signature selected from Log2TN shows the best generalization in the three GEO datasets even though only tumor-derived expression profiles were available in the three datasets. Enrichment analysis showed that the tumor cells mainly focus on proliferation with losing functional of metabolism.Conclusions: These results indicate that (1) Log2TN could get more robust genes and gene signature than tumor-derived expression profiles used traditionally; (2) the adjacent-normal tissue may also play an important role in the progress and outcome of the tumor.Implications for Cancer Survivors: By combined of tumor-derived expression profile and the adjacent normal-derived expression profile, we could find more robust gene signature than traditionally method. Using these robust gene signatures, robust cancer biomarkers could be constructed and will do great help to improve cancer prognosis.

SKIL facilitates tumorigenesis and immune escape of NSCLC via upregulating TAZ/autophagy axis

Immune escape is an important mechanism in tumorigenesis. The aim of this study was to investigate roles of SKIL in tumorigenesis and immune escape of non-small-cell lung cancer (NSCLC). SKIL expression levels in NSCLC cell line, clinical sample, and adjacent normal tissue were measured by quantitative PCR, western blot, or immunohistochemistry. Lentivirus was used to overexpress/silence SKIL or TAZ expression. Malignant phenotypes of NSCLC cells were evaluated by colony formation, transwell, and MTT assays, and in xenograft mice model. Syngeneic mice model and flow cytometry were used to evaluate T cell infiltration. Quantitative PCR and western blot were applied to evaluate relevant mRNA and protein levels, respectively. Co-immunoprecipitation was applied to unveil the interaction between SKIL and TAZ. SKIL expression was higher in NSCLC tissue compared to adjacent normal tissue. Silencing of SKIL inhibited malignant phenotypes of NSCLC cells and promoted T cell infiltration. SKIL-knockdown inhibited autophagy and activated the STING pathway in NSCLC cells through down-regulation of TAZ. Silencing of TAZ cancelled the effects of SKIL overexpression on malignant phenotypes and autophagy of NSCLC cells. Inhibition of autophagy reversed the effects of SKIL/TAZ overexpression on the STING pathway. In conclusion, SKIL promoted tumorigenesis and immune escape of NSCLC cells through upregulation of TAZ/autophagy axis and inhibition on downstream STING pathway.

miR-21 Overexpression Promotes Esophageal Squamous Cell Carcinoma Invasion and Migration by Repressing Tropomyosin 1

The migration and invasion of esophageal squamous cell carcinoma are associated with clinical outcomes, however, the mechanisms remain poorly understood. Here, we found that miR-21 is significantly overexpressed in ESCC, lung cancer, and bladder cancer compared with the adjacent normal tissue. MiR-21 and TPM1 expressions were analyzed by RT-qPCR and WB in 30 ESCC, 10 lung cancer, and 10 bladder cancer clinical specimens, each with matched adjacent normal tissue. Knockdown and overexpression of miR-21 as well as knockdown of TPM1 in ESCC cell lines were performed using synthetic oligonucleotides. TPM1 3 ′ UTR luciferase reporter constructs were used to investigate targeting of TPM1 by miR-21. ESCC migration and invasion were assessed using transwell migration and invasion assays. Inhibition of miR-21 reduced migration and invasion in two ESCC cell lines, and overexpression of miR-21 promoted migration and invasion in vitro. Interestingly, TPM1 exhibited inverse patterns of expression compared with miR-21 in tissues and cell lines. Luciferase reporter assays demonstrated that TPM1 was directly regulated by miR-21. Moreover, the forced overexpression of miR-21 repressed the TPM1 expression, while silencing of miR-21 restored the TPM1 expression in ESCC cell lines. What is more, simultaneous silencing of miR-21 and TPM1 expressions did not alter the migratory and invasive characteristics demonstrating that the effects of miR-21 were mediated through TPM1. In conclusion, the aberrant overexpression of miR-21 is common in cancer and promotes the migration and invasion of ESCC through inhibiting the TPM1 expression. These results suggest that miR-21 may be a novel predictive marker and therapeutic target for treatment of ESCC.