Prospects and challenges of cancer systems medicine: from genes to disease networks

Karimi, Mohammad Reza, Karimi, Amir Hossein, Abolmaali, Shamsozoha, Mehdi, Sadeghi, and Schmitz, Ulf (2022) Prospects and challenges of cancer systems medicine: from genes to disease networks. Briefings in Bioinformatics, 23 (1). bbab343.

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It is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.

Item ID: 69341
Item Type: Article (Research - C1)
ISSN: 1477-4054
Keywords: systems biology, transcriptomics, proteomics, metabolomics, proteogenomics, biological networks
Funders: Cancer Institute New South Wales (CI NSW), National Health and Medical Research Council (NHMRC), Cancer Council NSW (CC)
Projects and Grants: NHMRC Fellowship #1196405, CC project grant RG20–12
Date Deposited: 14 Sep 2021 03:50
FoR Codes: 31 BIOLOGICAL SCIENCES > 3101 Biochemistry and cell biology > 310114 Systems biology @ 34%
31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310204 Genomics and transcriptomics @ 33%
31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310205 Proteomics and metabolomics @ 33%
SEO Codes: 28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280102 Expanding knowledge in the biological sciences @ 60%
28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280103 Expanding knowledge in the biomedical and clinical sciences @ 40%
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