Gene expression based inference of cancer drug sensitivity.

Antineoplastic Agents / pharmacology Gene Expression Humans Machine Learning Male Melanoma / drug therapy Sequence Analysis, RNA

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
27 09 2022
Historique:
received: 18 11 2021
accepted: 12 09 2022
entrez: 27 9 2022
pubmed: 28 9 2022
medline: 30 9 2022
Statut: epublish

Résumé

Inter and intra-tumoral heterogeneity are major stumbling blocks in the treatment of cancer and are responsible for imparting differential drug responses in cancer patients. Recently, the availability of high-throughput screening datasets has paved the way for machine learning based personalized therapy recommendations using the molecular profiles of cancer specimens. In this study, we introduce Precily, a predictive modeling approach to infer treatment response in cancers using gene expression data. In this context, we demonstrate the benefits of considering pathway activity estimates in tandem with drug descriptors as features. We apply Precily on single-cell and bulk RNA sequencing data associated with hundreds of cancer cell lines. We then assess the predictability of treatment outcomes using our in-house prostate cancer cell line and xenografts datasets exposed to differential treatment conditions. Further, we demonstrate the applicability of our approach on patient drug response data from The Cancer Genome Atlas and an independent clinical study describing the treatment journey of three melanoma patients. Our findings highlight the importance of chemo-transcriptomics approaches in cancer treatment selection.

Identifiants

DOI: 10.1038/s41467-022-33291-z PMID: 36167836 PMC: PMC9515171
pubmed: 36167836
doi: 10.1038/s41467-022-33291-z
pii: 10.1038/s41467-022-33291-z
pmc: PMC9515171
doi:

Substances chimiques

Antineoplastic Agents 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

5680

Informations de copyright

© 2022. The Author(s).

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Auteurs

Smriti Chawla (S)

Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.

Anja Rockstroh (A)

Australian Prostate Cancer Research Centre-Queensland, Faculty of Health, School of Biomedical Sciences, Centre for Genomics and Personalised Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia.
ORCID: 0000-0002-2700-375X

Melanie Lehman (M)

Australian Prostate Cancer Research Centre-Queensland, Faculty of Health, School of Biomedical Sciences, Centre for Genomics and Personalised Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia.
Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.

Ellca Ratther (E)

Australian Prostate Cancer Research Centre-Queensland, Faculty of Health, School of Biomedical Sciences, Centre for Genomics and Personalised Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia.

Atishay Jain (A)

Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.

Anuneet Anand (A)

Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.

Apoorva Gupta (A)

Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, Delhi, 110042, India.

Namrata Bhattacharya (N)

Australian Prostate Cancer Research Centre-Queensland, Faculty of Health, School of Biomedical Sciences, Centre for Genomics and Personalised Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia.
Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.

Sarita Poonia (S)

Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.

Priyadarshini Rai (P)

Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.

Nirjhar Das (N)

Department of Electrical Engineering, Indian Institute of Technology Delhi, Hauz Khas, Delhi, 110016, India.
ORCID: 0000-0001-7753-4391

Angshul Majumdar (A)

Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.
Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.
Department of Electronics & Communications Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.
Department of Electrical Engineering, Indian Institute of Technology Delhi, Hauz Khas, Delhi, 110016, India.

Gaurav Ahuja (G)

Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.
ORCID: 0000-0002-2837-9361

Brett G Hollier (BG)

Australian Prostate Cancer Research Centre-Queensland, Faculty of Health, School of Biomedical Sciences, Centre for Genomics and Personalised Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia.
ORCID: 0000-0002-1204-6001

Colleen C Nelson (CC)

Australian Prostate Cancer Research Centre-Queensland, Faculty of Health, School of Biomedical Sciences, Centre for Genomics and Personalised Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia. colleen.nelson@qut.edu.au.
ORCID: 0000-0001-6410-4843

Debarka Sengupta (D)

Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India. debarka@iiitd.ac.in.
Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India. debarka@iiitd.ac.in.
Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India. debarka@iiitd.ac.in.
ORCID: 0000-0002-6353-5411

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Classifications MeSH

questionsmedicales.fr › Actions chimiques et utilisations › Actions pharmacologiques › Utilisations thérapeutiques › Antinéoplasiques › Gene expression based inference of cancer drug...
questionsmedicales.fr › Phénomènes génétiques › Expression des gènes › Gene expression based inference of cancer drug...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Gene expression based inference of cancer drug...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › Intelligence artificielle › Apprentissage machine › Gene expression based inference of cancer drug...
questionsmedicales.fr › Tumeurs › Tumeurs par type histologique › Naevus et mélanomes › Mélanome › Gene expression based inference of cancer drug...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Gene expression based inference of cancer drug...