Project ID CM-HD2024_34


Co Supervisor 1A Faculty of Dentistry, Oral & Craniofacial Sciences, Centre for Host-Microbiome InteractionsWebsite

Co Supervisor 1B Faculty of Dentistry, Oral & Craniofacial Sciences, Centre for Host-Microbiome InteractionsWebsite

Additional Supervisor Prof Martin Ulmschneider

Gum repair or regeneration? Multiomic analysis of periodontal granulation tissue to elucidate roles in wound healing

(i) Gum disease (periodontitis) is the leading cause of tooth loss in adults and is associated with numerous systemic diseases. Following surgical treatment, healing usually occurs by repair, but tissue regeneration is also possible. Current treatment protocols advocate removal of granulation tissue from the affected areas to facilitate healing but there is limited evidence justifying this approach. The composition and role of periodontal granulation tissue in wound healing is poorly understood. Greater understanding will lead to improved clinical outcomes in promoting tissue regeneration rather than fibrotic repair.

(ii) Aim – To gain novel insights into the molecular pathways governing periodontal wound healing by using granulation tissue biopsies and gingival crevicular fluid to determine the transcriptome, proteome, microbiome and metabolome of periodontal tissue.

(iii) Techniques/Skills – Sample collection in accordance with Good Clinical Practice and processing according to protocols benchmarked for oral samples. Transcriptomic analysis of granulation tissue biopsies with next-generation sequencing. Training in standard library preparation workflows for transcriptomics. Multiplex microbead immunoassays of gingival crevicular fluid to determine levels of biomarkers. Metabolome analysis from whole mouth saliva samples using GC-MS on-target analysis or NMR off-target analysis. Bioinformatic analysis of acquired data with to interrogation using a systems analysis approach.

(iv) Yr1 – Training in acquiring and processing of samples. Training in generation and acquisition of raw data. Bioinformatic skills including programming,
Yr2 – Continue sample and raw data acquisition for multiomics analysis.
Yr3 – Primarily bioinformatic interrogation of data using systems analysis approach.
Yr4 – Development of in silico model based upon system analysis and write-up thesis

Representative Publications

Regulation of gingival fibroblast phenotype by periodontal ligament cells in vitro. Garna, D. F., Hughes, F. J. & Ghuman, M. S., Apr 2022, In: Journal of Periodontal Research. 57, 2, p. 402-411
Simplified intestinal microbiota to study microbe-diet-host interactions in a mouse model P Kovatcheva-Datchary, S Shoaie, S Lee, A Wahlström… – Cell reports, 2019