Investigating the Influence of the Comprehensive mRNA Expression Levels of Prognostic Genes on Patient Survival in Every Type of Cancer

2020 ◽  
Author(s):  
Minhyeong Lee
Keyword(s):  
Mrna Expression ◽  
Patient Survival ◽  
Scientific Evidence ◽  
Prognostic Indicator ◽  
The Cancer Genome Atlas ◽  
Expression Levels ◽  
Kaplan Meier ◽  
Protective Genes ◽  
Cancer Genome Atlas ◽  
Mrna Expression Levels

This study aimed to rank cancers based on the strength of the relationship between the comprehensive mRNA expression levels of the most harmful or protective genes and patient survival. Using The Cancer Genome Atlas dataset that includes the RNA sequencing and c linical data, we investigated not only gene specific prognostic availability, but also comprehensive prognostic availability of prognostic genes filtered by the Cox coefficient values, and ranked cancers using a specially designed prognostic indicator. Usi ng Kaplan Meier plots, we found that cancers vary in the strength of the influence of their prognostic genes, and can be ranked based on this finding. There is a high probability that the treatment developed by using methods that reduce or increase the exp ression levels of biomarkers, for cancers that ranked at the bottom will not be efficient. The results of this study could be used as scientific evidence for the same.

scholarly journals Investigating Strength that Comprehensive mRNA Expression Level of Prognostic Genes Influences on Patient Survival for Every Cancer Type

2019 ◽  
Author(s):  
Minhyeong Lee
Keyword(s):  
Mrna Expression ◽  
Patient Survival ◽  
Scientific Evidence ◽  
Prognostic Indicator ◽  
Cancer Type ◽  
Rna Seq ◽  
Kaplan Meier ◽  
Specific Cancer ◽  
Protective Genes ◽  
Tcga Dataset

This study aimed to rank cancers by the strength of relationship between comprehensive mRNA expression of the most harmful or protective genes and patient survival. Using TCGA dataset including RNA-SEQ and clinical data, we investigated not only gene specific prognostic availability, but also comprehensive prognostic availability of prognostic genes filtered by cox coefficient, and ranked cancers by specially designed prognostic indicator. Through Kaplan-Meier plots, we checked that cancers vary in the strength of influence of prognostic genes, and they follow as the rank. Developing treatment with method to reduce or increase expression of biomarkers for specific cancer which ranked bottom, it would be not efficient in high probability. The results of this study can be a scientific evidence for that.

scholarly journals TRIM27 interacts with Iκbα to promote the growth of human renal cancer cells through regulating the NF-κB pathway

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chengwu Xiao ◽  
Wei Zhang ◽  
Meimian Hua ◽  
Huan Chen ◽  
Bin Yang ◽  
...  
Keyword(s):  
Cell Lines ◽  
Prognostic Indicator ◽  
The Cancer Genome Atlas ◽  
Mrna Levels ◽  
Loss Of Function ◽  
Protein Levels ◽  
Kaplan Meier ◽  
Cancer Genome Atlas

Abstract Background The tripartite motif (TRIM) family proteins exhibit oncogenic roles in various cancers. The roles of TRIM27, a member of the TRIM super family, in renal cell carcinoma (RCC) remained unexplored. In the current study, we aimed to investigate the clinical impact and roles of TRIM27 in the development of RCC. Methods The mRNA levels of TRIM27 and Kaplan–Meier survival of RCC were analyzed from The Cancer Genome Atlas database. Real-time PCR and Western blotting were used to measure the mRNA and protein levels of TRIM27 both in vivo and in vitro. siRNA and TRIM27 were exogenously overexpressed in RCC cell lines to manipulate TRIM27 expression. Results We discovered that TRIM27 was elevated in RCC patients, and the expression of TRIM27 was closely correlated with poor prognosis. The loss of function and gain of function results illustrated that TRIM27 promotes cell proliferation and inhibits apoptosis in RCC cell lines. Furthermore, TRIM27 expression was positively associated with NF-κB expression in patients with RCC. Blocking the activity of NF-κB attenuated the TRIM27-mediated enhancement of proliferation and inhibition of apoptosis. TRIM27 directly interacted with Iκbα, an inhibitor of NF-κB, to promote its ubiquitination, and the inhibitory effects of TRIM27 on Iκbα led to NF-κB activation. Conclusions Our results suggest that TRIM27 exhibits an oncogenic role in RCC by regulating NF-κB signaling. TRIM27 serves as a specific prognostic indicator for RCC, and strategies targeting the suppression of TRIM27 function may shed light on future therapeutic approaches.

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 Preserved miR-361-3p Expression Is an Independent Prognostic Indicator of Favorable Survival in Cervical Cancer

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Shikai Liu ◽  
Lili Song ◽  
Hairong Yao ◽  
Liang Zhang ◽  
Dongkui Xu ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Prognostic Indicator ◽  
Bioinformatic Analysis ◽  
The Cancer Genome Atlas ◽  
Primary Therapy ◽  
Free Survival ◽  
Kaplan Meier ◽  
Cancer Genome Atlas ◽  
Using Data ◽  
Independent Indicator

In this study, we aimed to assess the independent prognostic value of miR-361-3p in terms of overall survival (OS) and recurrence-free survival (RFS) in cervical cancer, as well as its possible regulative network. A retrospective analysis was performed by using data from the Cancer Genome Atlas-Cervical Cancer (TCGA-CESC). Results showed that decreased miR-361-3p expression was associated with lymphovascular invasion and poor responses to primary therapy. The patients with recurrence and the deceased cases had substantially lower miR-361-3p expression compared to their respective controls. By generating Kaplan-Meier curves of OS and RFS, we found that high miR-361-3p expression was associated with better survival outcome. More importantly, univariate and multivariate analysis confirmed that high miR-361-3p expression was an independent indicator of favorable OS (HR: 0.377, 95% CI: 0.233–0.608, p<0.001) and RFS (HR: 0.398, 95% CI: 0.192–0.825, p=0.013). By performing bioinformatic analysis, we identified 24 genes that were negatively correlated with miR-361-3p expression. Among the potential targeting genes, SOST, MTA1, TFRC, and YAP1 are involved in some important signaling pathways modulating cervical cancer cell invasion, migration, and drug sensitivity. Therefore, it is meaningful to verify the potential regulative effect of miR-361-3p on the expression of these genes in the future.

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 Racial Differences in Expression Levels of miRNA Machinery-Related Genes, Dicer, Drosha, DGCR8, and AGO2, in Asian Korean Papillary Thyroid Carcinoma and Comparative Validation Using the Cancer Genome Atlas

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Jaegil Kim ◽  
Woo-Jae Park ◽  
Kwang-Joon Jeong ◽  
Sun Hee Kang ◽  
Sun Young Kwon ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Mrna Expression ◽  
Racial Differences ◽  
Clinicopathological Characteristics ◽  
The Cancer Genome Atlas ◽  
Papillary Thyroid ◽  
Expression Levels ◽  
White American ◽  
Mrna Expression Levels

Aberrant regulation of microRNA (miRNA) machinery components is associated with various human cancers, including papillary thyroid carcinoma (PTC), which is the most common type of thyroid cancer, and a higher prevalent female malignancy. The purpose of this study is to investigate racial differences in mRNA expression levels of four miRNA machinery components, Dicer, Drosha, DGCR8, and AGO2, and their correlations with clinicopathological characteristics. Forty PTC samples from female Asian Korean PTC patients were enrolled. Using qPCR, we examined mRNA expression levels of the components and next validated our results by comparison with results of female white American in the TCGA PTC project. Interestingly, mRNA expression levels of the selected factors were altered in the TCGA PTC samples. However, only Drosha showed a significantly lower expression level in Asian Korean PTC samples. Furthermore, the mRNA expression levels of the four components showed no association with clinicopathological characteristics in both groups. On the other hand, positive correlations were observed between altered mRNA expression levels of Dicer and Drosha and DGCR8 and Drosha in TCGA PTC samples. These findings collectively revealed that altered mRNA expression levels of miRNA machinery components might be responsible for racial differences in the carcinogenesis of PTC.

scholarly journals OncoRank: A pan-cancer method of combining survival correlations and its application to mRNAs, miRNAs, and lncRNAs

2016 ◽  
Author(s):  
Jordan Anaya
Keyword(s):  
Mirna Target ◽  
Patient Survival ◽  
The Cancer Genome Atlas ◽  
P Values ◽  
Cancer Pathways ◽  
Large Numbers ◽  
Protective Genes ◽  
Cancer Genome Atlas ◽  
Pan Cancer ◽  
Genome Atlas

OncoRank adopts a method for finding recurrent miRNA-target interactions to find genes with consistent relationships to patient survival across cancers. Genes are first ranked in each cancer by their Cox coefficients, and these ranks are then combined by applying Fisher's method. Using ranks instead of the raw coefficients or p-values allows each cancer to be weighted equally and prevents bias from cancers with large numbers of patients. OncoLnc (http://www.oncolnc.org) is a newly available resource for Cox coefficients and utilizes data from 21 cancers in The Cancer Genome Atlas. Using this resource I applied OncoRank to mRNAs, miRNAs, and lncRNAs and in each case found consistently harmful or protective genes. These genes may be members of central cancer pathways and should be of interest to cancer researchers.

scholarly journals Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer

Cancers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 4902
Author(s):  
Hoang Dang Khoa Ta ◽  
Wei-Jan Wang ◽  
Nam Nhut Phan ◽  
Nu Thuy An Ton ◽  
Gangga Anuraga ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Cycle ◽  
Signaling Pathways ◽  
Family Members ◽  
The Cancer Genome Atlas ◽  
Protein Coding ◽  
Expression Levels ◽  
Kaplan Meier ◽  
Cancer Genome Atlas ◽  
Cycle Regulation

In recent decades, breast cancer (BRCA) has become one of the most common diseases worldwide. Understanding crucial genes and their signaling pathways remain an enormous challenge in evaluating the prognosis and possible therapeutics. The “Like-Smith” (LSM) family is known as protein-coding genes, and its member play pivotal roles in the progression of several malignancies, although their roles in BRCA are less clear. To discover biological processes associated with LSM family genes in BRCA development, high-throughput techniques were applied to clarify expression levels of LSMs in The Cancer Genome Atlas (TCGA)-BRCA dataset, which was integrated with the cBioPortal database. Furthermore, we investigated prognostic values of LSM family genes in BCRA patients using the Kaplan–Meier database. Among genes of this family, LSM4 expression levels were highly associated with poor prognostic outcomes with a hazard ratio of 1.35 (95% confidence interval 1.21–1.51, p for trend = 3.4 × 10−7). MetaCore and GlueGo analyses were also conducted to examine transcript expression signatures of LSM family members and their coexpressed genes, together with their associated signaling pathways, such as “Cell cycle role of APC in cell cycle regulation” and “Immune response IL-15 signaling via MAPK and PI3K cascade” in BRCA. Results showed that LSM family members, specifically LSM4, were significantly correlated with oncogenesis in BRCA patients. In summary, our results suggested that LSM4 could be a prospective prognosticator of BRCA.

scholarly journals TCGA mRNA Expression Analysis of the Heme Biosynthesis Pathway in Diffusely Infiltrating Gliomas: A Comparison of Typically 5-ALA Fluorescent and Non-Fluorescent Gliomas

Cancers ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2043
Author(s):  
Mario Mischkulnig ◽  
Barbara Kiesel ◽  
Daniela Lötsch ◽  
Thomas Roetzer ◽  
Martin Borkovec ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Aminolevulinic Acid ◽  
Heme Biosynthesis ◽  
The Cancer Genome Atlas ◽  
Biosynthesis Pathway ◽  
Who Grade ◽  
Expression Levels ◽  
Coproporphyrinogen Oxidase ◽  
Grade Ii ◽  
Mrna Expression Levels

5-Aminolevulinic acid (5-ALA) is a fluorescent dye that after metabolization to Protoporphyrin IX (PpIX) by the heme biosynthesis pathway typically leads to visible fluorescence in WHO grade IV but not grade II gliomas. The exact mechanism for high PpIX levels in WHO grade IV gliomas and low PpIX levels in WHO grade II gliomas is not fully clarified. To detect relevant changes in mRNA expression, we performed an in-silico analysis of WHO grade II and IV glioma sequencing datasets provided by The Cancer Genome Atlas (TCGA) to investigate mRNA expression levels of relevant heme biosynthesis genes: Solute Carrier Family 15 Member 1 and 2 (SLC15A1 and SLC15A2), Aminolevulinate-Dehydratase (ALAD), Hydroxymethylbilane-Synthase (HMBS), Uroporphyrinogen-III-Synthase (UROS), Uroporphyrinogen-Decarboxylase (UROD), Coproporphyrinogen-Oxidase (CPOX), Protoporphyrinogen-Oxidase (PPOX), ATP-binding Cassette Subfamily B Member 6 (ABCB6)/G Member 2 (ABCG2) and Ferrochelatase (FECH). Altogether, 258 WHO grade II and 166 WHO grade IV samples were investigated. The mRNA expression levels showed significant differences in 8 of 11 examined genes between WHO grade II and IV gliomas. Significant differences in mRNA expression included increases of HMBS, UROD, FECH and PPOX as well as decreases of SLC15A2, ALAD, UROS and ABCB6 in WHO IV gliomas. Since the majority of changes was found in directions that might actually impair PpIX accumulation in WHO grade IV gliomas, additional studies are needed to analyze the corresponding factors of the heme biosynthesis also on protein level.

scholarly journals The Expression Profiles of ADME Genes in Human Cancers and Their Associations with Clinical Outcomes

Cancers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3369
Author(s):  
Dong Gui Hu ◽  
Peter I. Mackenzie ◽  
Pramod C. Nair ◽  
Ross A. McKinnon ◽  
Robyn Meech
Keyword(s):  
Cancer Patient ◽  
Anticancer Drugs ◽  
Patient Survival ◽  
Expression Profiles ◽  
The Cancer Genome Atlas ◽  
Specific Patient ◽  
Kaplan Meier ◽  
High Interindividual Variability ◽  
Cancer Genome Atlas ◽  
Cancer Types

ADME genes are a group of genes that are involved in drug absorption, distribution, metabolism, and excretion (ADME). The expression profiles of ADME genes within tumours is proposed to impact on cancer patient survival; however, this has not been systematically examined. In this study, our comprehensive analyses of pan-cancer datasets from the Cancer Genome Atlas (TCGA) revealed differential intratumoral expression profiles for ADME genes in 21 different cancer types. Most genes also showed high interindividual variability within cancer-specific patient cohorts. Using Kaplan-Meier plots and logrank tests, we showed that intratumoral expression levels of twenty of the thirty-two core ADME genes were associated with overall survival (OS) in these cancers. Of these genes, five showed significant association with unfavourable OS in three cancers, including SKCM (ABCC2, GSTP1), KIRC (CYP2D6, CYP2E1), PAAD (UGT2B7); sixteen showed significant associations with favourable OS in twelve cancers, including BLCA (UGT2B15), BRCA (CYP2D6), COAD (NAT1), HNSC (ABCB1), KIRC (ABCG2, CYP3A4, SLC22A2, SLC22A6), KIRP (SLC22A2), LIHC (CYP2C19, CYP2C8, CYP2C9, CYP3A5, SLC22A1), LUAD (SLC15A2), LUSC (UGT1A1), PAAD (ABCB1), SARC (ABCB1), and SKCM (ABCB1, DYPD). Overall, these data provide compelling evidence supporting ADME genes as prognostic biomarkers and potential therapeutic targets. We propose that intratumoral expression of ADME genes may impact cancer patient survival by multiple mechanisms that can include metabolizing/transporting anticancer drugs, activating anticancer drugs, and metabolizing/transporting a variety of endogenous molecules involved in metabolically fuelling cancer cells and/or controlling pro-growth signalling pathways.

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