The Transcriptomic Landscape of Prostate Cancer Development and Progression: An Integrative Analysis

被引:6
|
作者
Marzec, Jacek [1 ]
Ross-Adams, Helen [1 ]
Pirro, Stefano [1 ]
Wang, Jun [1 ]
Zhu, Yanan [2 ]
Mao, Xueying [2 ]
Gadaleta, Emanuela [1 ]
Ahmad, Amar S. [3 ]
North, Bernard V. [3 ]
Kammerer-Jacquet, Solene-Florence [2 ]
Stankiewicz, Elzbieta [2 ]
Kudahetti, Sakunthala C. [2 ]
Beltran, Luis [4 ]
Ren, Guoping [5 ]
Berney, Daniel M. [2 ,4 ]
Lu, Yong-Jie [2 ]
Chelala, Claude [1 ,6 ]
机构
[1] Queen Mary Univ London, Barts Canc Inst, Bioinformat Unit, Ctr Canc Biomarkers & Biotherapeut, London EC1M 6BQ, England
[2] Queen Mary Univ London, Barts Canc Inst, Ctr Canc Biomarkers & Biotherapeut, London EC1M 6BQ, England
[3] Queen Mary Univ London, Wolfson Inst Prevent Med, Barts & London Sch Med, Ctr Canc Prevent, London EC1M 6BQ, England
[4] Barts Hlth NHS, Dept Pathol, London E1 F1R, England
[5] Zhejiang Univ, Med Coll, Dept Pathol, Affiliated Hosp 1, Hangzhou 310058, Peoples R China
[6] Queen Mary Univ London, Life Sci Initiat, Ctr Computat Biol, London EC1M 6BQ, England
基金
英国工程与自然科学研究理事会;
关键词
prostate cancer; tumorigenesis; mRNA; RNAseq; transcriptomic; data integration;
D O I
10.3390/cancers13020345
中图分类号
R73 [肿瘤学];
学科分类号
100214 ;
摘要
Simple Summary There is a tremendous amount of gene expression information available for prostate cancer, but very few tools exist to combine the disparate datasets generated across sample types and technical platforms. We present a method of integrating different types of expression data from different study cohorts to increase analytic power, and improve our understanding of the molecular changes underlying the development and progression of prostate cancer from normal to advanced disease. Using this approach, we identified nine additional disease stage-specific candidate genes with prognostic significance, which were not identified in any one study alone. We have developed a free online tool summarizing our results, and making the complete combined dataset available for further translational research. Next-generation sequencing of primary tumors is now standard for transcriptomic studies, but microarray-based data still constitute the majority of available information on other clinically valuable samples, including archive material. Using prostate cancer (PC) as a model, we developed a robust analytical framework to integrate data across different technical platforms and disease subtypes to connect distinct disease stages and reveal potentially relevant genes not identifiable from single studies alone. We reconstructed the molecular profile of PC to yield the first comprehensive insight into its development, by tracking changes in mRNA levels from normal prostate to high-grade prostatic intraepithelial neoplasia, and metastatic disease. A total of nine previously unreported stage-specific candidate genes with prognostic significance were also found. Here, we integrate gene expression data from disparate sample types, disease stages and technical platforms into one coherent whole, to give a global view of the expression changes associated with the development and progression of PC from normal tissue through to metastatic disease. Summary and individual data are available online at the Prostate Integrative Expression Database (PIXdb), a user-friendly interface designed for clinicians and laboratory researchers to facilitate translational research.
引用
收藏
页码:1 / 24
页数:25
相关论文
共 50 条
  • [21] Integrative analysis of the genomic and transcriptomic landscape identifies ciliary genes as a therapeutic target in bile duct cancer
    Carotenuto, P.
    Piscopo, F.
    Barbato, A.
    Pollastro, C.
    Ferrante, L.
    Evangelista, L.
    Gitano, G.
    Iuliano, A.
    Pisapia, P.
    Salatiello, M.
    Iaccarino, A.
    Malapelle, U.
    Troncone, G.
    Grisendi, G.
    Reggiani-Bonetti, L.
    Salati, M.
    Dominici, M.
    Franco, B.
    ANNALS OF ONCOLOGY, 2024, 35 : S234 - S235
  • [22] Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression
    Li, Yin
    Vongsangnak, Wanwipa
    Chen, Luonan
    Shen, Bairong
    BMC MEDICAL GENOMICS, 2014, 7
  • [23] Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression
    Yin Li
    Wanwipa Vongsangnak
    Luonan Chen
    Bairong Shen
    BMC Medical Genomics, 7
  • [24] Early results of the integrative epigenomic-transcriptomic landscape of colorectal adenoma and cancer
    Lu, You-Wang
    Ding, Zhao-Li
    Mao, Rui
    Zhao, Gui-Gang
    He, Yu-Qi
    Li, Xiao-Lu
    Liu, Jiang
    WORLD JOURNAL OF GASTROINTESTINAL ONCOLOGY, 2024, 16 (02) : 414 - 435
  • [25] Erratum to: The integrative epigenomic-transcriptomic landscape of ER positive breast cancer
    Yang Gao
    Allison Jones
    Peter A. Fasching
    Matthias Ruebner
    Matthias W. Beckmann
    Martin Widschwendter
    Andrew E. Teschendorff
    Clinical Epigenetics, 2016, 8
  • [26] Integrative Metabolomic and Transcriptomic Analysis for the Study of Bladder Cancer
    Loras, Alba
    Suarez-Cabrera, Cristian
    Carmen Martinez-Bisbal, M.
    Quintas, Guillermo
    Paramio, Jesus M.
    Martinez-Manez, Ramon
    Gil, Salvador
    Luis Ruiz-Cerdia, Jose
    CANCERS, 2019, 11 (05)
  • [27] Integrative analysis of prostate cancer aggressiveness
    Feik, Elisabeth
    Schweifer, Norbert
    Baierl, Andreas
    Sommergruber, Wolfgang
    Haslinger, Christian
    Hofer, Philipp
    Maj-Hes, Agnes
    Madersbacher, Stephan
    Gsur, Andrea
    PROSTATE, 2013, 73 (13): : 1413 - 1426
  • [28] Integrative analysis of pharmacologic, genomic, and transcriptomic assays in cancer
    Liu, Manway
    Reddy, Anupama
    Huang, Alan
    Caponigro, Giordano
    Lehar, Joseph
    CANCER RESEARCH, 2011, 71
  • [29] Landscape of chromosome number changes in prostate cancer progression
    Braun, Martin
    Stomper, Julia
    Kirsten, Robert
    Shaikhibrahim, Zaki
    Vogel, Wenzel
    Boehm, Diana
    Wernert, Nicolas
    Kristiansen, Glen
    Perner, Sven
    WORLD JOURNAL OF UROLOGY, 2013, 31 (06) : 1489 - 1495
  • [30] Landscape of chromosome number changes in prostate cancer progression
    Martin Braun
    Julia Stomper
    Robert Kirsten
    David Adler
    Wenzel Vogel
    Diana Böhm
    Nicolas Wernert
    Glen Kristiansen
    Sven Perner
    World Journal of Urology, 2013, 31 : 1489 - 1495