scholarly journals Identification of potential biomarkers associated with pathogenesis of primary prostate cancer based on meta-analysis approaches

2020 ◽  
Author(s):  
Neda Sepahi ◽  
Mehrdad Piran ◽  
Mehran Piran ◽  
Ali Ghanbariasad
Keyword(s):  
Prostate Cancer ◽  
Meta Analysis ◽  
Enrichment Analysis ◽  
Incidence Rates ◽  
P Value ◽  
Diagnosis And Prognosis ◽  
Gene Ontology Database ◽  
Primary Prostate Cancer ◽  
Rising Incidence ◽  
Potential Biomarkers

AbstractWorldwide prostate cancer (PCa) is recognized as the second most common diagnosed cancer and the fifth leading cause of cancer death among men globally. Rising incidence rates of PCa have been observed over the last few decades. It is necessary to improve prostate cancer detection, diagnosis, treatment and survival. However, there are few reliable biomarkers for early prostate cancer diagnosis and prognosis. In the current study, systems biology method was applied for transcriptomic data analysis to identify potential biomarkers for primary PCa. We firstly identified differentially expressed genes (DEGs) between primary PCa and normal samples. Then the DEGs were mapped in Wikipathways and gene ontology database to conduct functional categories enrichment analysis. 1575 unique DEGs with adjusted p-value < 0.05 were achieved from two sets of DEGs. 132 common DEGs between two sets of DEGs were retrieved. The final DEGs were selected from 60 common upregulated and 72 common downregulated genes between datasets. In conclusion, we demonstrated some potential biomarkers (FOXA1, AGR2, EPCAM, CLDN3, ERBB3, GDF15, FHL1, NPY, DPP4, and GADD45A) and HIST2H2BE as a candidate one which are tightly correlated with the pathogenesis of PCa.

scholarly journals Transcriptional landscape of PTEN loss in primary prostate cancer

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Eddie Luidy Imada ◽  
Diego Fernando Sanchez ◽  
Wikum Dinalankara ◽  
Thiago Vidotto ◽  
Ericka M. Ebot ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Meta Analysis ◽  
Pten Loss ◽  
Primary Prostate Cancer ◽  
Expression Atlas ◽  
Transcriptomic Signature ◽  
Transcriptional Changes ◽  
New Biomarkers ◽  
Adaptive Immune Systems ◽  
Transcriptional Landscape

Abstract Background PTEN is the most frequently lost tumor suppressor in primary prostate cancer (PCa) and its loss is associated with aggressive disease. However, the transcriptional changes associated with PTEN loss in PCa have not been described in detail. In this study, we highlight the transcriptional changes associated with PTEN loss in PCa. Methods Using a meta-analysis approach, we leveraged two large PCa cohorts with experimentally validated PTEN and ERG status by Immunohistochemistry (IHC), to derive a transcriptomic signature of PTEN loss, while also accounting for potential confounders due to ERG rearrangements. This signature was expanded to lncRNAs using the TCGA quantifications from the FC-R2 expression atlas. Results The signatures indicate a strong activation of both innate and adaptive immune systems upon PTEN loss, as well as an expected activation of cell-cycle genes. Moreover, we made use of our recently developed FC-R2 expression atlas to expand this signature to include many non-coding RNAs recently annotated by the FANTOM consortium. Highlighting potential novel lncRNAs associated with PTEN loss and PCa progression. Conclusion We created a PCa specific signature of the transcriptional landscape of PTEN loss that comprises both the coding and an extensive non-coding counterpart, highlighting potential new players in PCa progression. We also show that contrary to what is observed in other cancers, PTEN loss in PCa leads to increased activation of the immune system. These findings can help the development of new biomarkers and help guide therapy choices.

scholarly journals Key pathways involved in prostate cancer based on gene set enrichment analysis and meta analysis

2011 ◽  
Vol 10 (4) ◽  
pp. 3856-3887 ◽  
Author(s):  
Q.Y. Ning ◽  
J.Z. Wu ◽  
N. Zang ◽  
J. Liang ◽  
Y.L. Hu ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Meta Analysis ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Key Pathways

Comparison of PET/MRI with multiparametric MRI in diagnosis of primary prostate cancer: A meta-analysis

2019 ◽  
Vol 113 ◽  
pp. 225-231 ◽  
Author(s):  
Mou Li ◽  
Zixing Huang ◽  
Haopeng Yu ◽  
Yi Wang ◽  
Yongchang Zhang ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Meta Analysis ◽  
Multiparametric Mri ◽  
Primary Prostate Cancer

Racial and sex disparities in changing trends of squamous cell cancer of the anus (SSCA).

2016 ◽  
Vol 34 (4_suppl) ◽  
pp. 520-520
Author(s):  
Arjun Gupta ◽  
Hong Zhu ◽  
Alana Christie ◽  
Jeffrey John Meyer ◽  
Saad A. Khan ◽  
...  
Keyword(s):  
Squamous Cell ◽  
Cell Cancer ◽  
The United States ◽  
Incidence Rates ◽  
P Value ◽  
Black Females ◽  
White Males ◽  
Rate Of Increase ◽  
Rising Incidence ◽  
Sex Disparities

520 Background: Squamous cell carcinoma of the anus (SSCA) is one of only few cancers with rising incidence in the United States (US). This is believed to represent changing epidemiology of human papillomavirus (HPV) and Human Immunodeficiency Virus (HIV). We explored the racial and sex disparities in the rising incidence of SSC. Methods: The Surveillance, Epidemiology, and End Results (SEER) database was used to identify subjects with SCCA from 2000-2012. Age-standardized incidence rates (IR) per 100,000 for 2000-2012 time period were generated in Rate Session in SEER for white males (WM), white females (WF), black males (BM) and black females (BF). The 2000 US standard population was used for age standardization. The trend of change of IR between groups was compared by testing the interaction between time and group in the linear regression model. SAS 9.4 was used for analysis Results: Among 11,739 new cases of SSCA racial and sex distribution of cases was WM:32%, WF:54%, BM:5.4%, BF:5.4%. Median overall survival (OS) was WM:101 months (m), WF:139 m, BM: 71 m, BF 103 m (p < 0.005). The IR had the highest rate of increase for WF and BM (0.06/100,000 cases annually) while rates for BF and WM increased by 0.04 and 0.02/100,000 cases annually respectively. The overall test for difference in trend among WF, WM, BF and BM groups had a p-value of 0.0099. Conclusions: The rate of increase of SSCA IR is highest for WF and BM. Additionally WF have the highest age standardized incidence of SCCA as well as the highest OS compared to other groups. These data support disparities in epidemiology and survival of anal cancer.

scholarly journals Meta-analysis of Transcriptomic Data Reveals Pathophysiological Modules Involved with Atrial Fibrillation

2020 ◽  
Author(s):  
Rodrigo Haas Bueno ◽  
Mariana Recamonde-Mendoza
Keyword(s):  
Atrial Fibrillation ◽  
Differentially Expressed Genes ◽  
Complex Disease ◽  
Meta Analysis ◽  
Differential Expression Analysis ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
P Value

Atrial fibrillation (AF) is a complex disease and affects millions of people around the world. The biological mechanisms that are involved with AF are complex and still need to be fully elucidated. Therefore, we performed a meta-analysis of transcriptome data related to AF to explore these mechanisms aiming at more sensitive and reliable results. Public transcriptomic datasets were downloaded, analyzed for quality control, and individually pre-processed. Differential expression analysis was carried out for each individual dataset, and the results were meta-analytically aggregated using the r-th ordered p-value method. We analyzed the final list of differentially expressed genes through network analysis, namely topological and modularity analysis, and functional enrichment analysis. The meta-analysis of transcriptomes resulted in 589 differentially expressed genes, whose protein-protein interaction network presented 11 hubs-bottlenecks and four main identified functional modules. These modules were enriched for, respectively, 23, 54, 33, and 53 biological pathways involved with the pathophysiology of AF, especially with the disease's structural and electrical remodeling processes. Stress of the endoplasmic reticulum, protein catabolism, oxidative stress, and inflammation are some of the enriched processes. Among hubs-bottlenecks genes, which are highly connected and probably have a key role in regulating these processes, we found HSPA5, ANK2, CTNNB1, and VWF. Further experimental investigation of our findings may shed light on the pathophysiology of the disease and contribute to the identification of new therapeutic targets and treatments.

scholarly journals Farming, Reported Pesticide Use, and Prostate Cancer

2012 ◽  
Vol 7 (2) ◽  
pp. 102-109 ◽  
Author(s):  
Camille Ragin ◽  
Brionna Davis-Reyes ◽  
Helina Tadesse ◽  
Dennis Daniels ◽  
Clareann H. Bunker ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Pesticide Exposure ◽  
Meta Analysis ◽  
P Value ◽  
Cancer Type ◽  
Case Control Studies ◽  
Prostate Hyperplasia ◽  
Unpublished Studies ◽  
Pubmed Database ◽  
Increased Risk

Prostate cancer is the leading cancer type diagnosed in American men and is the second leading cancer diagnosed in men worldwide. Although studies have been conducted to investigate the association between prostate cancer and exposure to pesticides and/or farming, the results have been inconsistent. We performed a meta-analysis to summarize the association of farming and prostate cancer. The PubMed database was searched to identify all published case–control studies that evaluated farming as an occupational exposure by questionnaire or interview and prostate cancer. Ten published and two unpublished studies were included in this analysis, yielding 3,978 cases and 7,393 controls. Prostate cancer cases were almost four times more likely to be farmers compared with controls with benign prostate hyperplasia (BPH; meta odds ratio [OR], crude = 3.83, 95% confidence interval [CI] = 1.96-7.48, Q-test p value = .352; two studies); similar results were obtained when non-BPH controls were considered, but with moderate heterogeneity between studies (meta OR crude = 1.38, 95% CI = 1.16-1.64, Q-test p value = .216, I2 = 31% [95% CI = 0-73]; five studies). Reported pesticide exposure was inversely associated with prostate cancer (meta OR crude = 0.68, 95% CI = 0.49-0.96, Q-test p value = .331; four studies), whereas no association with exposure to fertilizers was observed. Our findings confirm that farming is a risk factor for prostate cancer, but this increased risk may not be due to exposure to pesticides.

A DNA hypermethylation profile reveals new potential biomarkers for prostate cancer diagnosis and prognosis

The Prostate ◽  
2014 ◽  
Vol 74 (12) ◽  
pp. 1171-1182 ◽  
Author(s):  
Nadia Ashour ◽  
Javier C. Angulo ◽  
Guillermo Andrés ◽  
Raúl Alelú ◽  
Ana González-Corpas ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Diagnosis ◽  
Dna Hypermethylation ◽  
Prostate Cancer Diagnosis ◽  
Diagnosis And Prognosis ◽  
Cancer Diagnosis And Prognosis ◽  
Potential Biomarkers

scholarly journals Prostate Cancer in Lebanon: Incidence, Temporal Trends, and Comparison to Countries From Different Regions in the World

2021 ◽  
Vol 28 ◽  
pp. 107327482110552
Author(s):  
Najla A. Lakkis ◽  
Mona H. Osman
Keyword(s):  
Prostate Cancer ◽  
Incidence Rate ◽  
Task Force ◽  
Public Awareness ◽  
Temporal Trends ◽  
The United States ◽  
Incidence Rates ◽  
P Value ◽  
The World ◽  
Slow Growing

Background Prostate cancer is the most common malignancy in men globally. This study aims at investigating the incidence rates and trends of prostate cancer in Lebanon, and to compare them to those of countries from different regions in the world. Methods Data on prostate cancer were obtained from the Lebanese national cancer registry for the years 2005 to 2016. The calculated age-standardized incidence and age-specific rates were expressed as per 100 000 population. Results In Lebanon, prostate cancer is ranked as the most common cancer in men. The age-standardized incidence rate of prostate cancer has increased from 29.1 per 100 000 in 2005 to 37.3 per 100 000 in 2016; the highest rate was in 2012, surpassing the global average incidence rate for that year. The age-specific incidence rate of prostate cancer has increased exponentially starting at the age of 50 years to reach its peak in men aged 75 years or more. Two trends were identified in the age-standardized incidence rate of prostate cancer; an average significant increase of 7.28% per year for the period 2005–2009 ( P-value < .05), followed by a non-significant decrease of around .99% for the period between 2009 and 2016 ( P-value > .05). The age-standardized incidence rate in Lebanon was higher than most countries in the Middle East and North Africa region and Asia, but lower than the rates reported in Australia, America, and different European countries. Conclusion Prostate cancer is the leading cancer among men in Lebanon. Screening practices, changes in population age structure, and prevalence of genetic and risky lifestyle factors may explain the increased incidence rates of prostate cancer. Given the controversy of screening recommendations and the slow growing nature of prostate cancer, increasing public awareness on ways of prevention, and implementing the latest screening recommendation of the United States Preventive Services Task Force are the suggested way forward.

scholarly journals Transcriptional landscape of PTEN loss in primary prostate cancer

2020 ◽  
Author(s):  
Eddie Luidy Imada ◽  
Diego Fernando Sanchez ◽  
Wikum Dinalankara ◽  
Thiago Vidotto ◽  
Ericka M Ebot ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Meta Analysis ◽  
Pten Loss ◽  
Adaptive Immune ◽  
Primary Prostate Cancer ◽  
Expression Atlas ◽  
Transcriptomic Signature ◽  
Transcriptional Changes ◽  
Adaptive Immune Systems ◽  
Transcriptional Landscape

ABSTRACTPTEN is the most frequently lost tumor suppressor in primary prostate cancer (PCa) and its loss is associated with aggressive disease. However, the transcriptional changes associated with PTEN loss in PCa have not been described in detail. Here, we applied a meta-analysis approach, leveraging two large PCa cohorts with experimentally validated PTEN and ERG status, to derive a transcriptomic signature of PTEN loss, while also accounting for potential confounders due to ERG rearrangements. Strikingly, the signature indicates a strong activation of both innate and adaptive immune systems upon PTEN loss, as well as an expected activation of cell-cycle genes. Moreover, we made use of our recently developed FC-R2 expression atlas to expand this signature to include many non-coding RNAs recently annotated by the FANTOM consortium. With this resource, we analyzed the TCGA-PRAD cohort, creating a comprehensive transcriptomic landscape of PTEN loss in PCa that comprises both the coding and an extensive non-coding counterpart.

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