Omics approaches for the assessment of biological responses to nanoparticles

Yasmin Abdelkader; Luis Perez-Davalos; Richard LeDuc; Rene P Zahedi; Hagar I Labouta

doi:10.1016/j.addr.2023.114992

Omics approaches for the assessment of biological responses to nanoparticles

Adv Drug Deliv Rev. 2023 Sep:200:114992. doi: 10.1016/j.addr.2023.114992. Epub 2023 Jul 5.

Authors

Yasmin Abdelkader¹, Luis Perez-Davalos², Richard LeDuc³, Rene P Zahedi⁴, Hagar I Labouta⁵

Affiliations

¹ Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St., Cairo 12622, Egypt.
² Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada.
³ Children's Hospital Research Institute of Manitoba, 513 - 715 McDermot Av. W, Winnipeg, Manitoba R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada.
⁴ Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada; Department of Internal Medicine, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; CancerCare Manitoba Research Institute, 675 McDermot Av., Manitoba R3E 0V9, Canada.
⁵ Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario M5S 3M2, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada; Faculty of Pharmacy, Alexandria University, 1 Khartoum Square, Azarita, Alexandria, Egypt, 21521. Electronic address: hagar.labouta@unityhealth.to.

PMID: 37414362
DOI: 10.1016/j.addr.2023.114992

Abstract

Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein synthesis, cell cycle, metabolism, and other subcellular processes. While conventional methods have limitations in characterizing responses to NPs, omics approaches can analyze complete sets of molecular entities that change upon exposure to NPs. This review discusses key omics approaches, namely transcriptomics, proteomics, metabolomics, lipidomics and multi-omics, applied to the assessment of biological responses to NPs. Fundamental concepts and analytical methods used for each approach are presented, as well as good practices for omics experiments. Bioinformatics tools are essential to analyze, interpret and visualize large omics data, and to correlate observations in different molecular layers. The authors envision that conducting interdisciplinary multi-omics analyses in future nanomedicine studies will reveal integrated cell responses to NPs at different omics levels, and the incorporation of omics into the evaluation of targeted delivery, efficacy, and safety will improve the development of nanomedicine therapies.

Keywords: Bioinformatics; Lipidomics; Metabolomics; Multi-omics; Nanomedicine; Nanoparticles; Nanotoxicity; Proteomics; Secretomics; Transcriptomics.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Genomics* / methods
Humans
Metabolomics / methods
Nanoparticles*
Proteomics / methods