Cargando…

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

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 knowl...

Descripción completa

Detalles Bibliográficos
Autores principales: Karimi, Mohammad Reza, Karimi, Amir Hossein, Abolmaali, Shamsozoha, Sadeghi, Mehdi, Schmitz, Ulf
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8769701/
https://www.ncbi.nlm.nih.gov/pubmed/34471925
http://dx.doi.org/10.1093/bib/bbab343
_version_ 1784635208081866752
author Karimi, Mohammad Reza
Karimi, Amir Hossein
Abolmaali, Shamsozoha
Sadeghi, Mehdi
Schmitz, Ulf
author_facet Karimi, Mohammad Reza
Karimi, Amir Hossein
Abolmaali, Shamsozoha
Sadeghi, Mehdi
Schmitz, Ulf
author_sort Karimi, Mohammad Reza
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8769701
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-87697012022-01-20 Prospects and challenges of cancer systems medicine: from genes to disease networks Karimi, Mohammad Reza Karimi, Amir Hossein Abolmaali, Shamsozoha Sadeghi, Mehdi Schmitz, Ulf Brief Bioinform Review 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. Oxford University Press 2021-09-01 /pmc/articles/PMC8769701/ /pubmed/34471925 http://dx.doi.org/10.1093/bib/bbab343 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
Karimi, Mohammad Reza
Karimi, Amir Hossein
Abolmaali, Shamsozoha
Sadeghi, Mehdi
Schmitz, Ulf
Prospects and challenges of cancer systems medicine: from genes to disease networks
title Prospects and challenges of cancer systems medicine: from genes to disease networks
title_full Prospects and challenges of cancer systems medicine: from genes to disease networks
title_fullStr Prospects and challenges of cancer systems medicine: from genes to disease networks
title_full_unstemmed Prospects and challenges of cancer systems medicine: from genes to disease networks
title_short Prospects and challenges of cancer systems medicine: from genes to disease networks
title_sort prospects and challenges of cancer systems medicine: from genes to disease networks
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8769701/
https://www.ncbi.nlm.nih.gov/pubmed/34471925
http://dx.doi.org/10.1093/bib/bbab343
work_keys_str_mv AT karimimohammadreza prospectsandchallengesofcancersystemsmedicinefromgenestodiseasenetworks
AT karimiamirhossein prospectsandchallengesofcancersystemsmedicinefromgenestodiseasenetworks
AT abolmaalishamsozoha prospectsandchallengesofcancersystemsmedicinefromgenestodiseasenetworks
AT sadeghimehdi prospectsandchallengesofcancersystemsmedicinefromgenestodiseasenetworks
AT schmitzulf prospectsandchallengesofcancersystemsmedicinefromgenestodiseasenetworks