scholarly journals The role of FOXD2-AS1 in cancer: a comprehensive study based on data mining and published articles

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Yongping Zhang ◽  
Chaojie Liang ◽  
Yu Zhang ◽  
Zhinmin Wang ◽  
Ruihuan Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cancer Patients ◽  
Tumor Size ◽  
Meta Analysis ◽  
Disease Free Survival ◽  
Gene Expression Omnibus ◽  
Tnm Stage ◽  
Potential Biomarker ◽  
Tcga Dataset

Abstract Background and aims: Long non-coding RNA (lncRNA) FOXD2 adjacent opposite strand RNA 1 (FOXD2-AS1) is aberrantly expressed in various cancers and associated with cancer progression. A comprehensive meta-analysis was performed based on published literature and data in the Gene Expression Omnibus database, and then the Cancer Genome Atlas (TCGA) dataset was used to assess the clinicopathological and prognostic value of FOXD2-AS1 in cancer patients. Methods: Gene Expression Omnibus databases of microarray data and published articles were used for meta-analysis, and TCGA dataset was also explored using the GEPIA analysis program. Hazard ratios (HRs) and pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the role of FOXD2-AS1 in cancers. Results: This meta-analysis included 21 studies with 2391 patients and 25 GEO datasets with 3311 patients. The pooled HRs suggested that highly expressed FOXD2-AS1 expression was correlated with poor overall survival (OS) and disease-free survival (DFS). Similar results were obtained by analysis of TCGA data for 9502 patients. The pooled results also indicated that FOXD2-AS1 expression was associated with bigger tumor size and advanced TNM stage, but was not related to age, gender, differentiation and lymph node metastasis. Conclusion: The present study demonstrated that FOXD2-AS1 is closely related to tumor size and TNM stage. Additionally, increased FOXD2-AS1 was a risk factor of OS and DFS in cancer patients, suggesting FOXD2-AS1 may be a potential biomarker in human cancers.

scholarly journals HOTAIR as a Prognostic Predictor for Diverse Human Cancers: A Meta- and Bioinformatics Analysis

Cancers ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 778 ◽  
Author(s):  
Halil Ibrahim Toy ◽  
Didem Okmen ◽  
Panagiota I. Kontou ◽  
Alexandros G. Georgakilas ◽  
Athanasia Pavlopoulou
Keyword(s):  
Overall Survival ◽  
Cancer Patients ◽  
Bioinformatics Analysis ◽  
Meta Analysis ◽  
Disease Free Survival ◽  
Progression Free Survival ◽  
Predictive Biomarker ◽  
Free Survival ◽  
Human Cancers ◽  
Potential Biomarker

Several studies suggest that upregulated expression of the long non-coding RNA HOX transcript antisense RNA (HOTAIR) is a negative predictive biomarker for numerous cancers. Herein, we performed a meta-analysis to further investigate the prognostic value of HOTAIR expression in diverse human cancers. To this end, a systematic literature review was conducted in order to select scientific studies relevant to the association between HOTAIR expression and clinical outcomes, including overall survival (OS), recurrence-free survival (RFS)/disease-free survival (DFS), and progression-free survival (PFS)/metastasis-free survival (MFS) of cancer patients. Collectively, 53 eligible studies including a total of 4873 patients were enrolled in the current meta-analysis. Pooled hazard ratios (HRs) with their corresponding 95% confidence intervals (CIs) were calculated to assess the relationship between HOTAIR and cancer patients’ survival. Elevated HOTAIR expression was found to be significantly associated with OS, RFS/DFS and PFS/MFS in diverse types of cancers. These findings were also corroborated by the results of bioinformatics analysis on overall survival. Therefore, based on our findings, HOTAIR could serve as a potential biomarker for the prediction of cancer patient survival in many different types of human cancers.

scholarly journals High Moesin Expression Is a Predictor of Poor Prognosis of Breast Cancer: Evidence From a Systematic Review With Meta-Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiaoli Hu ◽  
Yang Liu ◽  
Zhitong Bing ◽  
Qian Ye ◽  
Chengcheng Li
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Systematic Review ◽  
Cancer Patients ◽  
Poor Prognosis ◽  
Data Extraction ◽  
Meta Analysis ◽  
Gene Expression Omnibus ◽  
Breast Cancer Patients ◽  
Node Metastases

Owing to metastases and drug resistance, the prognosis of breast cancer is still dismal. Therefore, it is necessary to find new prognostic markers to improve the efficacy of breast cancer treatment. Literature shows a controversy between moesin (MSN) expression and prognosis in breast cancer. Here, we aimed to conduct a systematic review and meta-analysis to evaluate the prognostic relationship between MSN and breast cancer. Literature retrieval was conducted in the following databases: PubMed, Web of Science, Embase, and Cochrane. Two reviewers independently performed the screening of studies and data extraction. The Gene Expression Omnibus (GEO) database including both breast cancer gene expression and follow-up datasets was selected to verify literature results. The R software was employed for the meta-analysis. A total of 9 articles with 3,039 patients and 16 datasets with 2,916 patients were ultimately included. Results indicated that there was a significant relationship between MSN and lymph node metastases (P < 0.05), and high MSN expression was associated with poor outcome of breast cancer patients (HR = 1.99; 95% CI 1.73–2.24). In summary, there is available evidence to support that high MSN expression has valuable importance for the poor prognosis in breast cancer patients.Systematic Review Registrationhttps://inplasy.com/inplasy-2020-8-0039/.

Dissecting novel mechanisms of hepatitis B virus-related hepatocellular carcinoma using meta-analysis of public data.

2021 ◽  
Vol 39 (3_suppl) ◽  
pp. 333-333
Author(s):  
Jihad Aljabban ◽  
Michael Rohr ◽  
Saad A Syed ◽  
Eli Cohen ◽  
Naima Hashi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Hepatitis B ◽  
Meta Analysis ◽  
Causal Analysis ◽  
Gene Expression Omnibus ◽  
Regulatory Proteins ◽  
Public Data ◽  
Viral Regulatory Proteins

333 Background: Hepatitis B is a cause of hepatocellular carcinoma (HCC) globally, irrespective of viral loads. Interestingly, this process is not necessarily mediated through cirrhosis and may in fact involve oncogenic processes. Prior studies have suggested specific oncogenic gene expression pathways affected by viral regulatory proteins. Thus, identifying these genes and associated pathways could highlight predictive factors for HCC transformation, and has implications in early diagnosis and treatment. Methods: We employed our Search, Tag, Analyze, Resource (STARGEO) platform to conduct a meta-analysis of public data from NCBI's Gene Expression Omnibus. We performed meta-analysis consisting of 155 tumor samples compared against 185 adjacent non-tumor samples. We present the results from the meta-analysis in Ingenuity Pathway Analysis. Results:Our analysis revealed LXR/RXR activation, LPS-IL-1 mediation inhibition of RXR, and FXR/RXR activation as top canonical pathways amongst others. Top upstream regulators identified included the Ras family gene RABL6. The role of RABL6 in oncogenesis is beginning to unfold but its specific role in HBV-related HCC remains undefined. Our causal analysis suggests RABL6 mediates pathogenesis of HBV-related HCC through promotion of genes related to cell division, epigenetic regulation, and Akt signaling. Additionally, HOXA10 was a top upstream regulator and was strongly upregulated in our analysis. While described in other cancer, HOXA10 has not been well documented in HBV-related HCC and our causal analysis suggests it mediates pathogenesis through downregulation of tumor suppressors and its protective effect from oxidative stress. Conclusions: This meta-analysis describes possible role of viral regulatory proteins such as RABL6 and HOXA10 in the pathogenesis of HBV -related HCC. Further prospective studies are needed to confirm our findings.

scholarly journals FURIN correlated with immune infiltration serves as a potential biomarker in SARS-CoV-2 infection-related lung adenocarcinoma

2021 ◽  
Author(s):  
Lianxiang Luo ◽  
Manshan Li ◽  
Jiating Su ◽  
Xinyue Yao ◽  
Hui Luo
Keyword(s):  
Gene Expression ◽  
Lung Adenocarcinoma ◽  
Gene Expression Omnibus ◽  
Poor Overall Survival ◽  
Immune Infiltration ◽  
Interactive Analysis ◽  
Kaplan Meier ◽  
Potential Biomarker ◽  
Human Protein Atlas

Abstract FURIN, as a proprotein convertase, has been found to be expressed in a variety of cancers and plays an important role in cancer. In addition, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) requires FURIN to enter human cells. However, the role of FURIN in lung adenocarcinoma remains unclear. And the expression of SARS-CoV-2 related gene in lung adenocarcinoma has not been clarified. Therefore, in order to explore the prognostic value and mechanism of FURIN in lung adenocarcinoma, we performed bioinformatics analysis with Oncomine, TIMER (Tumor Immune Estimation Resource), GEPIA (Gene Expression Profiling Interactive Analysis), HPA (human protein atlas), UALCAN, PrognoScan, Kaplan-Meier plotter, cBioPortal, and LinkedOmics databases. And then We used GSE44274 in the GEO (Gene Expression Omnibus) database to analyze the expression of FURIN in LUAD patients who infected with SARS-CoV. FURIN was highly expressed in lung adenocarcinoma and was significantly associated with poor overall survival. FURIN expression was found to be correlated with six major permeable immune cells and with macrophage immune marker in LUAD patients. In addition, SARS-CoV-2 infection might affect the expression of FURIN. FURIN can be used as a promising biomarker for determining prognosis and immune infiltration in LUAD patients.

scholarly journals A Hierarchical Machine Learning Model to Discover Gleason Grade-Specific Biomarkers in Prostate Cancer

Diagnostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 219 ◽  
Author(s):  
Osama Hamzeh ◽  
Abedalrhman Alkhateeb ◽  
Julia Zhuoran Zheng ◽  
Srinath Kandalam ◽  
Crystal Leung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Machine Learning ◽  
Cancer Patients ◽  
Gleason Score ◽  
Class Imbalance ◽  
Gene Expression Omnibus ◽  
Gleason Grade ◽  
Next Generation Sequencing Technology ◽  
Potential Biomarker

(1) Background:One of the most common cancers that affect North American men and men worldwide is prostate cancer. The Gleason score is a pathological grading system to examine the potential aggressiveness of the disease in the prostate tissue. Advancements in computing and next-generation sequencing technology now allow us to study the genomic profiles of patients in association with their different Gleason scores more accurately and effectively. (2) Methods: In this study, we used a novel machine learning method to analyse gene expression of prostate tumours with different Gleason scores, and identify potential genetic biomarkers for each Gleason group. We obtained a publicly-available RNA-Seq dataset of a cohort of 104 prostate cancer patients from the National Center for Biotechnology Information’s (NCBI) Gene Expression Omnibus (GEO) repository, and categorised patients based on their Gleason scores to create a hierarchy of disease progression. A hierarchical model with standard classifiers in different Gleason groups, also known as nodes, was developed to identify and predict nodes based on their mRNA or gene expression. In each node, patient samples were analysed via class imbalance and hybrid feature selection techniques to build the prediction model. The outcome from analysis of each node was a set of genes that could differentiate each Gleason group from the remaining groups. To validate the proposed method, the set of identified genes were used to classify a second dataset of 499 prostate cancer patients collected from cBioportal. (3) Results: The overall accuracy of applying this novel method to the first dataset was 93.3%; the method was further validated to have 87% accuracy using the second dataset. This method also identified genes that were not previously reported as potential biomarkers for specific Gleason groups. In particular, PIAS3 was identified as a potential biomarker for Gleason score 4 + 3 = 7, and UBE2V2 for Gleason score 6. (4) Insight: Previous reports show that the genes predicted by this newly proposed method strongly correlate with prostate cancer development and progression. Furthermore, pathway analysis shows that both PIAS3 and UBE2V2 share similar protein interaction pathways, the JAK/STAT signaling process.

scholarly journals PRINS lncRNA Is a New Biomarker Candidate for HPV Infection and Prognosis of Head and Neck Squamous Cell Carcinomas

Diagnostics ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 762
Author(s):  
Magda Kopczyńska ◽  
Tomasz Kolenda ◽  
Kacper Guglas ◽  
Joanna Sobocińska ◽  
Anna Teresiak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Head And Neck ◽  
Squamous Cell ◽  
Disease Free Survival ◽  
Hpv Infection ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Data Set ◽  
Potential Biomarker

Numerous studies have shown that human papillomavirus (HPV) infection is one of the important risk factors for head and neck squamous cell carcinoma (HNSCC) progression and affects the expression of multiple genes, which might serve as new biomarkers. This study examines the effects of HPV infection on long non-coding RNA (lncRNA) expression and the immune system, particularly PRINS (Psoriasis susceptibility-related RNA Gene Induced by Stress). The Cancer Genome Atlas (TCGA) expression data for lncRNA genes and clinical data were analyzed by GraphPad Prism 5/7. The expressions of PRINS, CDKN2B-AS1, TTTY14, TTTY15, MEG3, and H19 were significantly different in HPV-positive and HPV-negative patients. HPV-positive patients with high PRINS expression demonstrated significantly better overall survival (OS) and disease-free survival (DFS). HPV-positive patients with high PRINS expression showed changes in gene expression associated with immune and antiviral responses. A majority of HPV-positive patients with high PRINS expression demonstrated a high number of immune cells within tumors. PRINS expression was significantly associated with HPV-infection HNSCC tumors. Validation of these results using data set from Gene Expression Omnibus (GEO) indicated that PRINS is upregulated in HPV active infections and in “atypical 1 (IR)” HNSCC clusters, negatively influencing patients’ overall survival. Patients with high PRINS expression display different immunological profiles than those with low expression levels. For instance, they have active HPV infection status or are clustered in the “atypical 1 (IR)” subtype of HNSCC which influences both viral infection and patients’ survival. It is likely that PRINS could be used as a potential biomarker for HNSCC patients, but its role is dual. On the one hand, it stimulates patients’ immune response, while on the other it can be favorable in virus replication.

scholarly journals Prognostic role of SIRT6 in gastrointestinal cancers: a meta-analysis

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 358-365
Author(s):  
Li Shi ◽  
Ying Wang ◽  
Timothy Bonney Oppong ◽  
Xiaoli Fu ◽  
Haiyan Yang ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Gastrointestinal Cancer ◽  
Web Of Science ◽  
Meta Analysis ◽  
Relevant Literature ◽  
Critical Role ◽  
Clinicopathological Parameters ◽  
Gastrointestinal Cancers ◽  
Potential Biomarker

AbstractSirtuin 6 (SIRT6) plays a critical role in the progression and development of gastrointestinal cancers. However, the association between SIRT6 expression and clinicopathological parameters and prognosis in gastrointestinal cancer patients remains inconclusive. Consequently, we conducted this meta-analysis to evaluate the importance of SIRT6 expression in various types of gastrointestinal cancers. PubMed, EMBASE, and Web of Science databases were systematically searched to screen the relevant literature. The reported or estimated hazard ratio (HR) and odds ratio (OR) and their corresponding 95% confidence interval (CI) were pooled to assess the strength of the association. Nine studies involving 867 patients were included in the meta-analysis. Overall analysis showed that high SIRT6 expression was related to better overall survival in gastrointestinal cancers (HR = 0.62, 95% CI = 0.47–0.82). High SIRT6 expression was also related to a favorable tumor node metastasis (TNM) stage (OR = 0.44, 95% CI = 0.28–0.70) among gastrointestinal cancer patients. Our meta-analysis revealed that high SIRT6 expression might be a potential biomarker predicting better prognosis in gastrointestinal cancers, which may offer options for gastrointestinal cancer treatment.

scholarly journals Meta-analysis of the prognostic significance of FOXC2 in various tumors

2019 ◽  
Vol 48 (3) ◽  
pp. 030006051989164
Author(s):  
Bixia Xu ◽  
Yun Tian ◽  
Lin Liu
Keyword(s):  
Cancer Patients ◽  
Meta Analysis ◽  
Prognostic Significance ◽  
Disease Free Survival ◽  
Final Analysis ◽  
Hazard Ratio ◽  
Cancer Specific Survival ◽  
Free Survival ◽  
Forkhead Box

Objective Many studies have focused on correlations between forkhead box protein C2 (FOXC2) and various tumors but discrepant results have been reported. Thus, we conducted this meta-analysis to assess the prognostic role of FOXC2 in tumors. Methods Four electronic databases (PubMed, Embase, Web of Science, and SinoMed) were screened through September 2019. Results The final analysis included 15 reports and 2115 patients; results suggested that cancer patients with FOXC2 had worse overall survival (hazard ratio 2.14, 95% confidence interval (CI) 1.74–2.64), cancer-specific survival (hazard ratio 2.65, 95% CI 1.44–4.89), and disease-free survival (hazard ratio 1.93, 95% CI 1.49–2.50) than patients lacking FOXC2. Conclusions The presence of FOXC2 was associated with poor survival in cancer patients. FOXC2 could be a promising prognostic marker in the future.

scholarly journals The relationship between the expression of Ki-67 and the prognosis of osteosarcoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ming Zeng ◽  
Jian Zhou ◽  
Lifang Wen ◽  
Yanshan Zhu ◽  
Yingquan Luo ◽  
...  
Keyword(s):  
Overall Survival ◽  
Distant Metastasis ◽  
Meta Analysis ◽  
Disease Free Survival ◽  
Cochrane Library ◽  
Significant Heterogeneity ◽  
Ki 67 ◽  
Potential Biomarker ◽  
Tcga Dataset ◽  
Enneking Stage

Abstract Background A number of studies have linked positive Ki-67 expression with the prognosis of osteosarcoma (OS) patients. However, the results have been conflicting. To address this controversy, we conducted an analysis using a meta-analysis and a TCGA dataset to estimate the value of Ki-67 expression in the prognosis of OS. Methods A comprehensive search for relevant papers was conducted using NCBI PubMed, Embase, Springer, ISI Web of Knowledge, the Cochrane Library, and CNKI regardless of the publication year. The associations between Ki-67 expression and the clinical features and main prognostic outcomes of OS were measured. The TCGA dataset was also analyzed. The pooled odds ratio (OR) and its 95% confidential intervals (CIs) were utilized for statistical analysis. Results Overall, a total of 12 studies with 500 cases were included, and the results indicated that the expression of Ki-67 was significantly associated with Enneking stage (OR = 6.88, 95% CI: 2.92–16.22, p < 0.05), distant metastasis (OR = 3.04, 95% CI: 1.51–6.12, p < 0.05) and overall survival (OR = 8.82, 95% CI: 4.68–16.65, p < 0.05) in OS patients. Additionally, we observed no significant heterogeneity among all retrieved studies. Associations between Ki-67 expression and overall survival and disease-free survival of sarcoma were confirmed using the TCGA and Kaplan-Meier plotter datasets. Conclusion The present study strongly suggests that positive Ki-67 expression was associated with Enneking stage, distant metastasis, and overall survival of OS, and it may be used as a potential biomarker to predict prognosis and guide clinical therapy for OS.

Expression analysis of the human kallikrein 7 (KLK7) in breast tumors: a new potential biomarker for prognosis of breast carcinoma

2004 ◽  
Vol 91 (01) ◽  
pp. 180-186 ◽  
Author(s):  
Maroulio Talieri ◽  
Eleftherios Diamandis ◽  
Dimitrios Gourgiotis ◽  
Kostandina Mathioudaki ◽  
Andreas Scorilas
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Patients ◽  
Serine Proteases ◽  
Direct Sequencing ◽  
Progesterone Receptors ◽  
Disease Free Survival ◽  
Normal Breast ◽  
Breast Cancer Patients ◽  
Potential Biomarker

SummaryKallikreins are a subgroup of serine proteases that are involved in the post-translational processing of polypeptide precursors. Growing evidence suggests that many kallikreins are implicated in carcinogenesis. Human kallikrein gene 7 (KLK7; HSCCE) is a new member of the human kallikrein gene family. KLK7 is expressed in normal breast tissue and is up-regulated in breast cancer cells by estrogens and glucocorticoids. In the present study, expression of the KLK7 gene in 92 breast cancer tissues was analyzed by reverse transcription-PCR (RT-PCR) and direct sequencing of several samples. The results were correlated with other clinicopathological variables and patient outcome. KLK7 gene expression was significantly lower in breast cancer patients of low stage (I/II) (p = 0.011) and patients with positive progesterone receptors (p = 0.022). Survival analysis showed that breast cancer patients with KLK7 positive tumors have relatively shorter disease-free survival (DFS) and overall survival (OS) than patients with KLK7 negative tumors. These data suggest that KLK7 gene expression may be used as a marker of unfavorable prognosis for breast cancer patients.

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