title: Proteogenomic studies on cancer drug resistance: towards biomarker discovery and target identification.
abstract: Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment. Areas covered: In this review, we will present recent advances in proteogenomic investigations of cancer drug resistance with an emphasis on integrative proteogenomic pipelines and the biomarker discovery which contributes to achieving the goal of using precision/personalized medicine for cancer treatment. Expert commentary: The discovery and comprehensive understanding of potential biomarkers help identify the cohort of patients who may benefit from particular treatments, and will assist real-time clinical decision-making to maximize therapeutic efficacy and minimize adverse effects. With the development of MS-based proteomics and NGS-based sequencing, a growing number of proteogenomic tools are being developed specifically to investigate cancer drug resistance.
authors.affiliation: a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.
authors.forename: Shuyue
authors.initials: S
authors.lastname: Fu
authors.affiliation: b Department of Pathology , Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital , Chengdu , P.R. China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Liu
authors.affiliation: c West China School of Public Health, Sichuan University , Chengdu , P.R.China.
authors.forename: Maochao
authors.initials: M
authors.lastname: Luo
authors.affiliation: d Department of Oncology , Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital , Chengdu , P.R. China.
authors.forename: Ke
authors.initials: K
authors.lastname: Xie
authors.affiliation: e Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia.
authors.forename: Edouard C
authors.initials: EC
authors.lastname: Nice
authors.affiliation: f School of Medicine , Yangtze University , P. R. China.
authors.forename: Haiyuan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.
authors.forename: Canhua
authors.initials: C
authors.lastname: Huang
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D000071696:Proteogenomics; D020543:Proteome / Q000235:genetics; D040901:Proteomics
chemical_list: D014408:Biomarkers, Tumor; D020543:Proteome
keywords: Biomarker Discovery; Cancer drug resistance; Precision/personalized Medicine; Proteogenomics