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Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.
Cao, Shaolong; Wang, Jennifer R; Ji, Shuangxi; Yang, Peng; Dai, Yaoyi; Guo, Shuai; Montierth, Matthew D; Shen, John Paul; Zhao, Xiao; Chen, Jingxiao; Lee, Jaewon James; Guerrero, Paola A; Spetsieris, Nicholas; Engedal, Nikolai; Taavitsainen, Sinja; Yu, Kaixian; Livingstone, Julie; Bhandari, Vinayak; Hubert, Shawna M; Daw, Najat C; Futreal, P Andrew; Efstathiou, Eleni; Lim, Bora; Viale, Andrea; Zhang, Jianjun; Nykter, Matti; Czerniak, Bogdan A; Brown, Powel H; Swanton, Charles; Msaouel, Pavlos; Maitra, Anirban; Kopetz, Scott; Campbell, Peter; Speed, Terence P; Boutros, Paul C; Zhu, Hongtu; Urbanucci, Alfonso; Demeulemeester, Jonas; Van Loo, Peter; Wang, Wenyi.
Afiliación
  • Cao S; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Wang JR; Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Ji S; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Yang P; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Dai Y; Department of Statistics, Rice University, Houston, TX, USA.
  • Guo S; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Montierth MD; Baylor College of Medicine, Houston, TX, USA.
  • Shen JP; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Zhao X; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Chen J; Baylor College of Medicine, Houston, TX, USA.
  • Lee JJ; Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Guerrero PA; Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Spetsieris N; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Engedal N; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Taavitsainen S; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Yu K; Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Livingstone J; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Bhandari V; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Hubert SM; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Daw NC; Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
  • Futreal PA; Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.
  • Efstathiou E; Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Lim B; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
  • Viale A; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.
  • Zhang J; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
  • Nykter M; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
  • Czerniak BA; Department of Medical Biophysics, University of Toronto, Toronto ON, Canada.
  • Brown PH; Department of Thoracic Head Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Swanton C; Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Msaouel P; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Maitra A; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Kopetz S; Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Campbell P; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Speed TP; Department of Thoracic Head Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Boutros PC; Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.
  • Zhu H; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Urbanucci A; Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Demeulemeester J; The Francis Crick Institute, London, UK.
  • Van Loo P; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Wang W; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Nat Biotechnol ; 40(11): 1624-1633, 2022 11.
Article en En | MEDLINE | ID: mdl-35697807
ABSTRACT
Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of total mRNA content. Here we present a method to quantify tumor-specific total mRNA expression (TmS) from bulk sequencing data, taking into account tumor transcript proportion, purity and ploidy, which are estimated through transcriptomic/genomic deconvolution. We estimate and validate TmS in 6,590 patient tumors across 15 cancer types, identifying significant inter-tumor variability. Across cancers, high TmS is associated with increased risk of disease progression and death. TmS is influenced by cancer-specific patterns of gene alteration and intra-tumor genetic heterogeneity as well as by pan-cancer trends in metabolic dysregulation. Taken together, our results indicate that measuring cell-type-specific total mRNA expression in tumor cells predicts tumor phenotypes and clinical outcomes.
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Texto completo: 1 Colección: 01-internacional Asunto principal: Neoplasias Tipo de estudio: Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: Nat Biotechnol Asunto de la revista: BIOTECNOLOGIA Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Asunto principal: Neoplasias Tipo de estudio: Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: Nat Biotechnol Asunto de la revista: BIOTECNOLOGIA Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos