An Integrated Analysis of The Prognosis And Immune Cell Infiltration of ITGB Superfamily Members In Gastric Cancer

2021 ◽  
Author(s):  
Chuan-hong Li ◽  
Lei Meng ◽  
Zhang-ming Chen ◽  
Wan-nian Sui ◽  
Pei-feng Chen ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
T Cells ◽  
Cell Adhesion ◽  
Mrna Expression ◽  
Cell Lines ◽  
Survival Data ◽  
Expression Patterns ◽  
Expression Level ◽  
Integrated Analysis ◽  
Expression Levels

Abstract Background:Members of the integrin β superfamily(ITGBs) have been shown to be aberrantly expressed in various human cancers and involved in tumorigenesis and progression. However, the diverse expression patterns and prognostic values of the entire ITGB family members in gastric cancer(GC) has not been systematically investigated.Methods:In the current study, Oncomine, GEPIA, Kaplan Meier plotter, TIMER, GeneMANIA, STRING and Metascape database were employed to explore the transcriptional and survival data of ITGB superfamily members in GC. Moreover, we confirmed the mRNA expression levels of ITGB superfamily members in GC cell lines by qRT-PCR.Results:The mRNA expression level of ITGB1/2/4/5/8 was upregulated in GC, while the expression level of ITGB7 was downregulated. Higher expression of ITGB2/7 was significantly associated with the tumor stage of patients with GC. However, we found that the expression level of ITGB1/2/4/5/6/7/8 was remarkably increased in GC cell lines compared to stomach normal cell lines, while ITGB3 expression was decreased in the former than in the latter. Meanwhile,higher expression levels of ITGB2/6/7 were closely correlated with better overall clinical survival (OS) and recurrence-free survival (RFS) in GC patients, while higher ITGB3/4/5 expression were strongly associated with poorer OS and RFS.We also discovered that the functions of ITGBs and their adjacent genes are mainly related to protein complexes involved in cell adhesion. the functions of ITGBs and their adjacent proteins are mainly related to focal adhesion, cell adhesion molecules, proteoglycans in cancer, small cell lung cancer, rap1 signaling pathway, IgA production by intestinal immune network, and microRNAs in cancer.In addition, the expression of ITGBs was significantly correlated with the infiltration of multiple immune cells, including B cells, CD8+ T cells, CD4+ T cells, neutrophils, macrophages, and dendritic cells.Conclusions:Our results suggested that abnormal expression of ITGBs plays a key role in the progression of GC and that ITGBs may be potential prognostic biomarkers and therapeutic targets for GC.

Plasma TS mRNA expression as a potential predictive biomarker for pemetrexed and raltitrexed in gastric cancer.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e21034-e21034
Author(s):  
Baorui Liu ◽  
Jie Shen ◽  
Hao Wang ◽  
Jia Wei ◽  
Lixia Yu ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Mrna Expression ◽  
Predictive Biomarker ◽  
Chemotherapeutic Agents ◽  
Water Soluble ◽  
Expression Level ◽  
Mrna Levels ◽  
Expression Levels ◽  
In Vitro Chemosensitivity

e21034 Background: Plasma mRNA opens up new investigational opportunities and has great potential for use in disease and treatment assessment. Pemetrexed and raltitrexed are novel water-soluble quinazoline folate analogues and act as direct and specific TS inhibitors. Although TS expression levels detected in tumor have shown potential in predicting sensitivity to those two chemotherapeutic agents, current knowledge is limited on the role of plasma TS mRNA as a predictive biomarker. The aim of this study was to investigate the association between plasma TS mRNA expression and in vitro chemosensitivity to pemetrexed and raltitrexed in gastric cancer. Methods: 150 freshly-removed gastric tumor specimens and corresponding blood samples before surgery were collected. Pemetrexed and raltitrexed sensitivity was determined by histoculture drug response assay (HDRA) procedures. Plasma and tumor TS mRNA expression level were determined by quantitative RT-PCR. Results: A significant correlation was observed between plasma and tumor TS mRNA expression levels (rho=0.665, P<0.001). Plasma TS expression level was negatively correlated with in vitro sensitivity to pemetrexed and raltitrexed in gastric cancer (pemetrexed-sensitive sub-group: 0.90, 95% CI: 0.66-1.16; pemetrexed-resistant sub-group: 1.82, 95% CI: 1.38-2.26, P<0.001; raltitrexed-sensitive sub-group: 0.91, 95% CI: 0.64-1.22; raltitrexed-resistant sub-group: 1.62, 95% CI: 1.06-2.17, P=0.013). There was no significant association between clinical characteristics and plasma TS mRNA levels or in vitro chemosensitivity. Conclusions: Our results indicated that plasma TS mRNA expression could be a prominent predictive biomarker for raltitrexed in gastric cancer, enabling the development of ‘‘real-time’’ individualized chemotherapy while tumor progression.

scholarly journals FXYD2 mRNA Expression Represents a New Independent Factor That Affects Survival of Glioma Patients and Predicts Chemosensitivity of Patients to Temozolomide

2021 ◽  
Author(s):  
Fang Wang ◽  
Kaijia Zhou ◽  
Tao Jiang ◽  
Hui Liang ◽  
Ming Zhang
Keyword(s):  
Mrna Expression ◽  
Survival Data ◽  
Expression Patterns ◽  
Prognostic Indicator ◽  
World Health ◽  
Independent Factor ◽  
Survival Times ◽  
Who Grade ◽  
Expression Levels ◽  
Mrna Expression Levels

Abstract Glioma is the most common primary intracranial tumor. Owing to the poor prognosis associated with high-grade gliomas, there is an urgent need to identify biomarkers related to prognosis and treatment sensitivity. Clinical features, FXYD2 mRNA expression levels, and survival data were analyzed for 1265 glioma samples from the Chinese Glioma Genome Map Project and two independent databases. The expression patterns for FXYD2 mRNA were compared using the chi-square test, and overall survival (OS) of glioma patients was evaluated according to FXYD2 mRNA expression levels. The factors affecting glioma survival were evaluated by Cox univariate and multivariate regression analysis. We found patients with primary oligodendroglioma, low World Health Organization (WHO) grade, low WHO molecular grade, isocitrate dehydrogenase (IDH) mutation, and combined deletion of 1p19q showed higher FXYD2 mRNA expression and longer survival times. Moreover, temozolomide (TMZ) chemotherapy was found to be an independent factor affecting survival in patients with high FXYD2 mRNA expression, but not in patients with low expression. So FXYD2 mRNA expression represents a new independent factor affecting the survival of glioma patients and may serve as an independent prognostic indicator to predict the sensitivity of gliomas to TMZ.

scholarly journals Immunohistochemical Basigin Expression Level in Thyroid Cancer Tissues

2020 ◽  
Author(s):  
Wan-Ping Guo ◽  
Deng Tang ◽  
Yu-Yan Pang ◽  
Xiao-Jiao Li ◽  
Gang Chen ◽  
...  
Keyword(s):  
Thyroid Cancer ◽  
Cell Adhesion ◽  
Diagnostic Odds Ratio ◽  
Cell Interactions ◽  
Expression Level ◽  
Integrated Analysis ◽  
Expression Levels ◽  
Using Data ◽  
Cancer Tissues ◽  
Cell Cell

Abstract Background: Thyroid cancer (TC) is the most common endocrine malignancy, Basigin (also known as BSG) plays a crucial role in tumor cell invasion, metastasis, and angiogenesis. This study was designed to identify the change of BSG expression in TC and its possible potential mechanism. Methods: The BSG expression levels in TC were demonstrated using data collected from in-house immunohistochemical (IHC), RNA-sequencing (RNA-seq), microarrays and literatures. Integrated analysis was performed to determined BSG expression levels in TC comprehensively. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed with the integration of BSG co-expressed genes and differentially expressed genes (DEGs) in TC tissues to explore the potential mechanisms of BSG in TC. Results: The protein expression level of BSG was significantly higher in TC cases based on the IHC experiments. In addition, the combined SMD for BSG expression was 0.39 (p<0.0001), the diagnostic odds ratio was 3.69, and the AUC of the sROC curve was 0.6986 using 1182 TC cases and 437 non-cancerous cases from 17 independent datasets. Furthermore, BSG co-expressed genes tended to be enriched in gene terms of the extracellular matrix (ECM), cell adhesion, and cell-cell interactions. The expression levels of nine hub BSG co-expressed genes were markedly up-regulated in TC cases. Conclusion: BSG expression levels were closely correlated with the progression of TC and may affect the signals of the ECM, cell adhesion, and cell-cell interactions.

scholarly journals Identification of Potential Indicators for Survival in Patients With Thyroid Cancer Based on Mrna Expression Levels of Family With Sequence Similarity 3 Members

2020 ◽  
Author(s):  
Yuting Ma ◽  
Junfeng Shi ◽  
Yongping Liu ◽  
Ruiyan Pan ◽  
Hongyan Qiu ◽  
...  
Keyword(s):  
Thyroid Cancer ◽  
Mrna Expression ◽  
Survival Data ◽  
Immune Cell ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Expression Levels ◽  
Online Databases ◽  
Neck Malignancy ◽  
Mrna Expression Levels

Abstract Background: Thyroid cancer (THCA) is a common head and neck malignancy. The family with sequence similarity 3 (FAM3) is a cytokine-like gene family with four members, which is presumed to participate in the development of many cancer types. However, the expression patterns of FAM3s in THCA and their prognostic values, have not yet been established. Methods: We investigated differential expressions of FAM3 mRNA and protein in THCA, then validated the findings for FAM3B by immunohistochemistry. We also investigated survival data with respect to FAM3 expression patterns in patients with THCA. FAM3s information regarding their relationships with clinical pathological parameters were obtained and FAM3 mutations were assessed. KEGG and GO pathway regarding FAM3C were obtained using online databases. To investigate potential correlations between FAM3s and immune cell infiltration, we investigated the roles of FAM3s in immune cells of patients with THCA. Results: The mRNA expression of FAM3C were significantly elevated in THCA tissues; high expression levels of FAM3C protein were also observed in THCA tissues. A significant association between the pathological stage and the expression of FAM3C was found in patients with THCA. Patients with THCA who had high mRNA expression levels of FAM3C exhibited significantly more favourable prognosis, compared with patients who had low mRNA expression levels of FAM3C. Conclusions: Overall, FAM3C may play vital roles in the pathogenesis and development of THCA, and these findings constitute novel insights for biomarkers of immunotherapeutic targeted agents and may aid in the identification of prognostic biomarkers for THCA.

scholarly journals FXYD2 mRNA expression represents a new independent factor that affects survival of glioma patients and predicts chemosensitivity of patients to temozolomide

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kaijia Zhou ◽  
Tao Jiang ◽  
Yanwei Liu ◽  
Zheng Zhao ◽  
Lijie Huang ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Survival Data ◽  
Expression Patterns ◽  
Prognostic Indicator ◽  
Multivariate Regression Analysis ◽  
Independent Factor ◽  
Chi Square ◽  
Expression Levels ◽  
Genome Map ◽  
Mrna Expression Levels

Abstract Purpose Glioma is the most common primary intracranial tumor. Owing to the poor prognosis associated with high-grade gliomas, there is an urgent need to identify biomarkers related to prognosis and treatment sensitivity. Here, we analyze the expression of FXYD2 mRNA in gliomas, and explore its clinical prognostic value and significance in this disease. Methods Clinical features, FXYD2 mRNA expression levels, and survival data were analyzed for 516 glioma patients from the Chinese Glioma Genome Map Project, 481 from the cancer genome map datbase and 268 from the molecular braintumor database. The expression patterns for FXYD2 mRNA were compared using the chi-square test, and overall survival (OS) of glioma patients was evaluated according to FXYD2 mRNA expression levels. The factors affecting glioma survival were evaluated by Cox univariate and multivariate regression analysis. Results FXYD2 mRNA expression was related to the grade of gliomas. The higher the level, the lower the expression. Meanwhile related to the pathological classification of gliomas. Oligodendroglioma, IDH-mutant and 1p/19q-codeleted was higher than Astrocytoma, IDH-mutant, higher than Glioblastoma, IDH-wildtype. Moreover, temozolomide (TMZ) chemotherapy was found to be an independent factor affecting survival in patients with high FXYD2 mRNA expression, but not in patients with low expression. Conclusion FXYD2 mRNA expression represents a new independent factor affecting the survival of glioma patients and may serve as an independent prognostic indicator to predict the sensitivity of gliomas to TMZ.

scholarly journals Immunohistochemical Basigin Expression Level in Thyroid Cancer Tissues

2020 ◽  
Author(s):  
Wan-Ping Guo ◽  
Deng Tang ◽  
Yu-Yan Pang ◽  
Xiao-Jiao Li ◽  
Gang Chen ◽  
...  
Keyword(s):  
Thyroid Cancer ◽  
Cell Adhesion ◽  
Diagnostic Odds Ratio ◽  
Cell Interactions ◽  
Expression Level ◽  
Integrated Analysis ◽  
Expression Levels ◽  
Using Data ◽  
Cancer Tissues ◽  
Cell Cell

Abstract Background Thyroid cancer (TC) is the most common endocrine malignancy, Basigin (also known as BSG) plays a crucial role in tumor cell invasion, metastasis, and angiogenesis. This study was designed to identify the change of BSG expression in TC and its possible potential mechanism. Methods The BSG expression levels in TC were demonstrated using data collected from in-house immunohistochemical (IHC), RNA-sequencing (RNA-seq), microarrays and literatures. Integrated analysis was performed to determined BSG expression levels in TC comprehensively. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed with the integration of BSG co-expressed genes and differentially expressed genes (DEGs) in TC tissues to explore the potential mechanisms of BSG in TC. Results The protein expression level of BSG was significantly higher in TC cases based on the IHC experiments. In addition, the combined SMD for BSG expression was 0.39 (p < 0.0001), the diagnostic odds ratio was 3.69, and the AUC of the sROC curve was 0.6986 using 1182 TC cases and 437 non-cancerous cases from 17 independent datasets. Furthermore, BSG co-expressed genes tended to be enriched in gene terms of the extracellular matrix (ECM), cell adhesion, and cell-cell interactions. The expression levels of nine hub BSG co-expressed genes were markedly up-regulated in TC cases. Conclusion BSG expression levels were closely correlated with the progression of TC and may affect the signals of the ECM, cell adhesion, and cell-cell interactions.

scholarly journals Unique Gene Expression Patterns in Human T-cell Lines Generated from Multiple Sclerosis Patients by Stimulation with a Synthetic MOG Peptide

2005 ◽  
Vol 12 (3) ◽  
pp. 203-209 ◽  
Author(s):  
Mathilda Mandel ◽  
Michael Gurevich ◽  
Gad Lavie ◽  
Irun R. Cohen ◽  
Anat Achiron
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Cell Lines ◽  
Healthy Subjects ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Gene Expression Patterns ◽  
T Cell Lines ◽  
Myelin Antigens

Multiple sclerosis (MS) is an autoimmune disease where T-cells activated against myelin antigens are involved in myelin destruction. Yet, healthy subjects also harbor T-cells responsive to myelin antigens, suggesting that MS patient-derived autoimmune T-cells might bear functional differences from T-cells derived from healthy individuals. We addressed this issue by analyzing gene expression patterns of myelin oligodendrocytic glycoprotein (MOG) responsive T-cell lines generated from MS patients and healthy subjects. We identified 150 transcripts that were differentially expressed between MS patients and healthy controls. The most informative 43 genes exhibited >1.5-fold change in expression level. Eighteen genes were up-regulated including BCL2, lifeguard, IGFBP3 and VEGF. Twenty five genes were down-regulated, including apoptotic activators like TNF and heat shock protein genes. This gene expression pattern was unique to MOG specific T-cell lines and was not expressed in T-cell lines reactive to tetanus toxin (TTX). Our results indicate that activation in MS that promotes T-cell survival and expansion, has its own state and that the unique gene expression pattern that characterize autoreactive T-cells in MS represent a constellation of factors in which the chronicity, timing and accumulation of damage make the difference between health and disease.

scholarly journals Synaptotagmin 13 Is Highly Expressed in Estrogen Receptor-Positive Breast Cancer

2021 ◽  
Vol 28 (5) ◽  
pp. 4080-4092
Author(s):  
Takahiro Ichikawa ◽  
Masahiro Shibata ◽  
Takahiro Inaishi ◽  
Ikumi Soeda ◽  
Mitsuro Kanda ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Estrogen Receptor ◽  
Mrna Expression ◽  
Cell Lines ◽  
Mrna Levels ◽  
Pcr Array ◽  
Array Analysis ◽  
Expression Levels ◽  
Er Positive ◽  
Mrna Expression Levels

Background: Accumulating evidence indicates tumor-promoting roles of synaptotagmin 13 (SYT13) in several cancers; however, no studies have investigated its expression in breast cancer (BC). This study aimed to clarify the significance of SYT13 in BC. Methods: SYT13 mRNA expression levels were evaluated in BC cell lines. Polymerase chain reaction (PCR) array analysis was conducted to determine the correlation between expression levels of SYT13 and other tumor-associated genes. Then, the association of SYT13 expression levels in the clinical BC specimens with patients’ clinicopathological factors was evaluated. These findings were subsequently validated using The Cancer Genome Atlas (TCGA) database. Results: Among 13 BC cell lines, estrogen receptor (ER)-positive cells showed higher SYT13 mRNA levels than ER-negative cells. PCR array analysis revealed positive correlations between SYT13 and several oncogenes predominantly expressed in ER-positive BC, such as estrogen receptor 1, AKT serine/threonine kinase 1, and cyclin-dependent kinases 4. In 165 patients, ER-positive specimens exhibited higher SYT13 mRNA expression levels than ER-negative specimens. The TCGA database analysis confirmed that patients with ER-positive BC expressed higher SYT13 levels than ER-negative patients. Conclusion: This study suggests that SYT13 is highly expressed in ER-positive BC cells and clinical specimens, and there is a positive association of SYT13 with the ER signaling pathways.

scholarly journals Early Response of CD8+ T Cells in COVID-19 Patients

2021 ◽  
Vol 11 (12) ◽  
pp. 1291
Author(s):  
Deni Ramljak ◽  
Martina Vukoja ◽  
Marina Curlin ◽  
Katarina Vukojevic ◽  
Maja Barbaric ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
T Cells ◽  
Mrna Expression ◽  
Cd8 T Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Effector Memory ◽  
Healthy Controls ◽  
Ifn Γ

Healthy and controlled immune response in COVID-19 is crucial for mild forms of the disease. Although CD8+ T cells play important role in this response, there is still a lack of studies showing the gene expression profiles in those cells at the beginning of the disease as potential predictors of more severe forms after the first week. We investigated a proportion of different subpopulations of CD8+ T cells and their gene expression patterns for cytotoxic proteins (perforin-1 (PRF1), granulysin (GNLY), granzyme B (GZMB), granzyme A (GZMA), granzyme K (GZMK)), cytokine interferon-γ (IFN-γ), and apoptotic protein Fas ligand (FASL) in CD8+ T cells from peripheral blood in first weeks of SARS-CoV-2 infection. Sixteen COVID-19 patients and nine healthy controls were included. The absolute counts of total lymphocytes (p = 0.007), CD3+ (p = 0.05), and CD8+ T cells (p = 0.01) in COVID-19 patients were significantly decreased compared to healthy controls. In COVID-19 patients in CD8+ T cell compartment, we observed lower frequency effector memory 1 (EM1) (p = 0.06) and effector memory 4 (EM4) (p < 0.001) CD8+ T cells. Higher mRNA expression of PRF1 (p = 0.05) and lower mRNA expression of FASL (p = 0.05) at the fifth day of the disease were found in COVID-19 patients compared to healthy controls. mRNA expression of PRF1 (p < 0.001) and IFN-γ (p < 0.001) was significantly downregulated in the first week of disease in COVID-19 patients who progressed to moderate and severe forms after the first week, compared to patients with mild symptoms during the entire disease course. GZMK (p < 0.01) and FASL (p < 0.01) mRNA expression was downregulated in all COVID-19 patients compared to healthy controls. Our results can lead to a better understanding of the inappropriate immune response of CD8+ T cells in SARS-CoV2 with the faster progression of the disease.

scholarly journals N-Glycomic and Transcriptomic Changes Associated with CDX1 mRNA Expression in Colorectal Cancer Cell Lines

Cells ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 273 ◽  
Author(s):  
Stephanie Holst ◽  
Jennifer Wilding ◽  
Kamila Koprowska ◽  
Yoann Rombouts ◽  
Manfred Wuhrer
Keyword(s):  
Colorectal Cancer ◽  
Mrna Expression ◽  
Cell Lines ◽  
Cancer Cell ◽  
Tumor Development ◽  
Cancer Cell Lines ◽  
Expression Levels ◽  
Nuclear Factors ◽  
Homeobox Protein ◽  
Regulated Gene Expression

The caudal-related homeobox protein 1 (CDX1) is a transcription factor, which is important in the development, differentiation, and homeostasis of the gut. Although the involvement of CDX genes in the regulation of the expression levels of a few glycosyltransferases has been shown, associations between glycosylation phenotypes and CDX1 mRNA expression have hitherto not been well studied. Triggered by our previous study, we here characterized the N-glycomic phenotype of 16 colon cancer cell lines, selected for their differential CDX1 mRNA expression levels. We found that high CDX1 mRNA expression associated with a higher degree of multi-fucosylation on N-glycans, which is in line with our previous results and was supported by up-regulated gene expression of fucosyltransferases involved in antenna fucosylation. Interestingly, hepatocyte nuclear factors (HNF)4A and HNF1A were, among others, positively associated with high CDX1 mRNA expression and have been previously proven to regulate antenna fucosylation. Besides fucosylation, we found that high CDX1 mRNA expression in cancer cell lines also associated with low levels of sialylation and galactosylation and high levels of bisection on N-glycans. Altogether, our data highlight a possible role of CDX1 in altering the N-glycosylation of colorectal cancer cells, which is a hallmark of tumor development.

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