Projects
From wet to dry, traditional biochemistry to high-throughout, research to development, you can always scrub in.
Bioinformatics
We have been focusing on the data analysis of proteomic and metaproteomic data. Along with the publication, we would like to organize and share the codes with community. iMetalab a whole suite of tools with that purpose. We are working on machine learning on large datasets.
We are developing, in collaboration with Dr. Alain Stintzi and Dr. Mathieu Lavallée-Adam, bioinformatics tools for the identification and quantitation of metaproteomes. We adopted an iterative database search strategy, termed MetaPro-IQ, which constructs a shrunken, sample-specific, non-redundant database 5. The resulting sample-specific database was used to obtain high-efficiency protein identifications in the analysis of gut microbiome samples. We also developed a fully automated, data processing software platform termed MetaLabnorth_eastexternal link, that includes new data processing approaches to speed up searches, and covers the major components of the bioinformatics and statistical pipelines for metaproteomics (imetalab.ca;north_eastexternal link online version of MetaLab).
Technology Development
NorthOmics has a long history for proteomic technology development, from sample extraction, digestion, chip/reactor-based MS pre-MS handling, which have been used in glycosylation, acetylation as well as phosphorylation analysis. These technologies effectively increased the density and throughput of the analysis.
We are interested in the development of new technologies to address protein bioanalytical challenges. Currently, we are developing approaches for the study of post-translation modifications including: protein glycosylation. methylation and acetylation. These technologies are then used with our ongoing applied projects and in collaborations.
Metaproteomics
Though not long since joining in, we have been leading the metaproteomic identification and quantification, thanks to the optimization of sample preparation and development of bioinformatics tools, like Metalab. Now, quite a few projects have branched related to drug screenning, echology, immunology etc.
Microbiome assay: We are developing, in collaboration with Dr. Alain Stintzi, a new assay called RapidAIM (rapid assay of an individual’s microbiome) to study compound-microbiome interactions using individual microbiomes . Briefly, the RapidAIM approach consists of ex vivo growth and maintenance of microbiotas from individual participants in multi-well plates in the presence of select compounds, followed by characterization of their response over time.
Human Disease & Medicine
Microbiome-host studies: In collaboration with Dr. Alain Stintzi and Dr. David Mack (CHEO), we are studying the interaction between the host and gut microbiome in inflammatory bowel disease (IBD) in a pediatric cohort. We use proteomics to discover the changes in the host , metaproteomics to study the functional changes occurring in the microbiome, and cross-kingdom analysis to reveal potential relationships between the host and microbiome.
Circadian cycle: Many behavioral and physiological processes have daily fluctuations or circadian rhythms, which are controlled by an intrinsic timekeeping mechanism. The circadian system ensures that the timing of these processes is optimal with respect to other ongoing internal events, as well as to the external environment. In mammals, a central pacemaker that is situated in the suprachiasmatic nucleus (SCN) of the brain coordinates rhythms in peripheral tissues. We are studying, in collaboration with Dr. Mary Cheng (UofT), the circadian proteome in different tissues, as well as the changes in the circadian proteome in normal aging and aging related diseases such as Alzheimer’s Disease.
Proprotein convertases: The importance of this nine-member family of serine proteases for health is underscored by pathologies associated with dysregulated proprotein convertase subtilisin/kexin like (PCSK) activity including cancer, diabetes, obesity, arthritis, atherosclerosis and cardiovascular disease (CVD). We use in vitro and ex vivo models to study cellular biology of PCSKs, the relationships between post-translational modifications, interacting proteins and PCSK function, as well as their transcriptional regulation . In collaboration with Dr. Paul Wiseman (McGill) we are defining PCSK and protein partner trafficking. We use PCSK knockout mice models to study PCSK roles in energy and lipid homeostasis. These studies are complemented by our genetic screening of Canadian cohorts for PCSK9 and LDLR variants, correlating these, with risk of- or protection from high cholesterol levels and CVD, and carried out with collaborators Dr. Michel Chrétien (IRCM/OHRI) and Dr. Teik Chye Ooi (TOH).
