title: The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes.
abstract: Although individual pseudogenes have been implicated in tumour biology, the biomedical significance and clinical relevance of pseudogene expression have not been assessed in a systematic way. Here we generate pseudogene expression profiles in 2,808 patient samples of seven cancer types from The Cancer Genome Atlas RNA-seq data using a newly developed computational pipeline. Supervised analysis reveals a significant number of pseudogenes differentially expressed among established tumour subtypes and pseudogene expression alone can accurately classify the major histological subtypes of endometrial cancer. Across cancer types, the tumour subtypes revealed by pseudogene expression show extensive and strong concordance with the subtypes defined by other molecular data. Strikingly, in kidney cancer, the pseudogene expression subtypes not only significantly correlate with patient survival, but also help stratify patients in combination with clinical variables. Our study highlights the potential of pseudogene expression analysis as a new paradigm for investigating cancer mechanisms and discovering prognostic biomarkers.
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.
authors.forename: Leng
authors.initials: L
authors.lastname: Han
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.|Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.
authors.forename: Siyuan
authors.initials: S
authors.lastname: Zheng
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.|Division of Biostatistics, The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX 77030, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.
authors.forename: Mary E
authors.initials: ME
authors.lastname: Edgerton
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.
authors.forename: Lixia
authors.initials: L
authors.lastname: Diao
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.
authors.forename: Yanxun
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.
authors.forename: Roeland G W
authors.initials: RGW
authors.lastname: Verhaak
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, USA.|Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Han
authors.initials: H
authors.lastname: Liang
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism*; D015870:Gene Expression; D052138:Genes, Neoplasm; D006801:Humans; D009369:Neoplasms / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D011544:Pseudogenes
chemical_list: D014408:Biomarkers, Tumor