• Login
• Admin

Tulum, Elizabeth Ann (2024) Using transcriptomics to inform the next generation risk assessment of doxorubicin and niacinamide. MRes thesis, University of Nottingham.

Preview

PDF (USING TRANSCRIPTOMICS TO INFORM THE NEXT GENERATION RISK ASSESSMENT OF DOXORUBICIN AND NIACINAMIDE - final submission) (Thesis - as examined) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader Available under Licence Creative Commons Attribution. Download (5MB) | Preview

Abstract

Human health risk assessments without generating new animal data have resulted in extreme efforts over the past few decades from industry, academia, and regulatory bodies to develop and apply new method approaches. Various non-animal approaches for chemical hazard characterisation has appeared known as new approach methodologies (NAMs) which form the basis of integrated testing and assessment strategies designed to prevent harm to human health.

A bioinformatics workflow was developed to aid the exploration of Next Generation Risk Assessment (NGRA) to determine whether NAMs can be used for safety decisions using various consumer products. The analysis within this thesis continues the analysis conducted in the previous case studies and explores the key concepts relating to HepaRG, HepG2 and MCF-7 cells dosed with doxorubicin and niacinamide. The aim of this thesis has been achieved by addressing a gap of knowledge within Unilever by conducting biological interpretation of exposure to chemicals at different concentrations and the general use of in vitro methods for non-animal risk assessments using high throughput transcriptomics (HTTr) data. By looking at doxorubicin and niacinamide, this has enabled the interpretation of these chemicals using developed methodologies for future analysis of potential chemicals for NGRA. The bioinformatics workflow consisted of using R Studio to align, quantify and conduct differential expression analysis using DESeq2 for all chemical concentrations and cell lines. Furthermore, BMDExpress has been successfully conducted to derive Points of Departure (PoDs) for doxorubicin and niacinamide as well as pathway investigation alongside Ingenuity Pathway Analysis (IPA) to determine mechanisms of action (MoA) for the chemicals of interest.

At least 20 pathways were detected to apply the pathway-level tests. Using these selections, the observed pathway-level PoD ranged from 0.0219μM to 0.4854μM for doxorubicin and 2552.94μM to 24977.10μM for niacinamide across cell lines.

The selected gene or pathway PoDs were derived using BMDExpress2 for HepaRG, HepG2 and MCF-7 cells dosed with doxorubicin were 0.1557μM, 0.0313μM & 0.0219μM respectively. The selected PoDs for HepaRG, HepG2 and MCF-7 cells dosed with niacinamide were 2552.94μM, 5046.89μM & 5444.65μM respectively.

Doxorubicin is a medication that belongs to the anthracycline class of medications. It works by slowing or stopping the growth of cancer cells in your body interfering with the function of DNA. Niacinamide plays a significant role in DNA repair, maintenance of genomic stability and cellular responses to injury including inflammation and apoptosis (cell death). For both chemicals these modes of action have been identified in the BMDExpress and IPA analysis.

Both BMDExpress and IPA are very different software packages with BMDExpress being used for gene and pathway level analysis, deriving PoDs and pathway related analysis while IPA is used solely for pathway interpretation and determining Mechanism of Action (MoA). The combination of using BMDExpress and IPA has demonstrated more robust data can be generated for gene and pathways interpretation. More investigations are required using both software to depict correlations between them as well as considering individual results. This thesis has explained how developing a bioinformatics workflow using BMDExpress and IPA has expanded knowledge in the NGRA space using NAMs for safety decision making as a non-animal alternative approach.

Item Type:	Thesis (University of Nottingham only) (MRes)
Supervisors:	Blanchard, Adam Archer, Nathan
Keywords:	Transcriptomics, Next Generation Risk Assessment
Subjects:	Q Science > QH Natural history. Biology > QH573 Cytology
Faculties/Schools:	UK Campuses > Faculty of Medicine and Health Sciences > School of Veterinary Medicine and Science
Item ID:	77266
Depositing User:	Tulum, Liz
Date Deposited:	19 Jul 2024 10:55
Last Modified:	19 Jul 2024 10:55
URI:	https://eprints.nottingham.ac.uk/id/eprint/77266

Actions (Archive Staff Only)

Edit View