LMP student seminars: 13 November

Each week during term time, MSc and PhD candidates in the Department of Laboratory Medicine and Pathobiology present their research.

Anyone is welcome. No need to register.

Location: Medical Sciences Building, rooms 4171 or 4279, see below.

As part of the core research curriculum, students taking LMP1001/2/3: Graduate Seminars in Laboratory Medicine and Pathobiology will present their projects. Please see abstracts below.

1. Brain and Neuroscience

Location: MSB 4279

Bryan Kartono

• Title: Elucidating the role of C9orf72 in the synapse
• Supervisor: Dr. Janice Robertson

4. Infectious Diseases, Inflammation and Immunology

Location: MSB 4279

Noor Alsmadi

• Title: Utilizing Genome-Scale Metabolic Modelling to Study the Metabolism of a Defined Human Gut Bacterial Community HDC1
• Supervisor: Dr. Dana Philpott and Dr. Radhakrishnan Mahadevan

3. Cardiovascular, Physiology and Metabolism/ Molecular and Cell Biology and Regenerative Medicine

Location: MSB 4171

Sarah Aloi

• Title: Evaluating the Effect of a Novel Storage Protocol for Fresh Osteochondral Allograft Preservation
• Supervisor: Dr. Adele Changoor

Wei Shen Liang

• Title: Characterizing the human balance organ with single-nucleus multiomics
• Supervisor: Dr. Alain Dabdoub

Abstracts

Bryan Kartono: Elucidating the role of C9orf72 in the synapse

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that causes the progressive degeneration of upper and lower motor neurons, resulting in the loss of muscle control and death within 2-5 years. ALS shares features with frontotemporal dementia (FTD), with up to 15% of ALS patients displaying FTD symptoms. The G4C2 hexanucleotide repeat expansions in C9orf72 (C9) are the common genetic cause, although the precise mechanisms remain unclear. ALS and FTD are characterized by persistent synaptic dysfunction, including disruptions in neuronal structure, neurotransmitter systems, and ion channel regulation, driven by glutamatergic signaling abnormalities and neuronal hyperexcitability. While our understanding of the pathological consequences of C9 loss is limited by our lack of knowledge about the function of C9, there is a growing understanding that genes associated with ALS/FTD, such as C9, may contribute to maintaining normal synaptic function, as mutations in these genes often lead to synaptic dysfunction. Hence, it is my hypothesis that C9 is involved in maintaining the normal physiology of the synapse. In this study, my aim is to assess neuronal morphology and investigate alterations in protein pathways associated with synaptic function in the context of C9 deficiency in primary cortical neuron cultures. I have detected significant differences in the neuron morphology among C9-WT, C9-hetKO, and C9-homoKO, particularly in neuronal branching. Additionally, I have identified impaired protein pathways associated with synaptic function in the context of C9 deficiency, including the Arf6-Rac1-LIMK-Cofilin, PI3K/AKT/mTOR, and RAF/MEK/ERK pathways.

Noor Alsmadi: Utilizing Genome-Scale Metabolic Modelling to Study the Metabolism of a Defined Human Gut Bacterial Community HDC1

The gut microbiome is a complex ecosystem that is associated with numerous chronic diseases, including inflammatory bowel disease, obesity, and irritable bowel syndrome, among others. This is attributed to its important role in immune system development and homeostasis, host metabolism, as well as maintenance of gut epithelial barrier integrity, primarily through microbial antigens and metabolite production. As such, this makes the gut microbiome an attractive target for therapeutic interventions that aim to modulate levels of microbial-derived antigens and/or metabolites in the gut to promote health. Studying the metabolism of interacting bacteria in gut microbial communities is difficult to perform using purely experimental means given the complexity and diversity of the gut microbiome. Genome-scale metabolic models are mathematical representations of the reaction networks of an organism that enable the study of cross-feeding interactions and metabolic pathways in microbial communities. My work utilizes genome-scale metabolic modelling to study the metabolism of a minimal defined human gut bacterial community called Human Defined Community 1 (HDC1). Whole genome sequencing and assembly was performed using DNA samples from bacterial isolates from HDC1. Taxonomic characterization using genome assemblies showed that the community represents the major phyla in the human gut microbiome, making it a suitable model for further metabolic characterization. Functional genome annotation was performed using Bakta followed by genome-scale metabolic model reconstruction using CarveMe. To study the metabolism of the community, CarveMe models were then integrated into a community model and used to simulate and study the metabolism of HDC1 under different dietary conditions. All in all, my work highlights the utility of using in silico metabolic modelling tools to mechanistically study the metabolism of a defined gut microbial community.

Sarah Aloi: Evaluating the Effect of a Novel Storage Protocol for Fresh Osteochondral Allograft Preservation 

Articular cartilage is the thin, connective tissue that lines the ends of bones in articular joints, such as the knee. Acute joint injury from sports and other traumas may lead to the development of cartilage lesions, which become symptomatic as cartilage degrades and exposes underlying bone. An effective surgical technique to treat these lesions is osteochondral allograft transplantation, which involves resecting and replacing the damaged tissue with a size-matched graft consisting of viable hyaline cartilage and subchondral bone obtained from a cadaveric donor. Success rates of this transplantation procedure increase when chondrocyte viability in the donor tissue is maintained at a minimum of 70% in storage, however, certain tissue bank storage protocols maintain these levels only up to 14 to 28 days, significantly limiting the availability of grafts for transplantation. A pilot study testing a novel storage media formulation recently developed in our lab revealed that absolute chondrocyte viability was maintained at 97.0% and 93.1% after 28 and 42 days of storage, exceeding the performance of standard Lactated Ringer’s solution-based storage, which revealed 74.1% and 59.7% viability after 28 and 42 days of storage, respectively. These findings merit further development of the novel media formulation with specific aims to evaluate the effect that supplements of hyaluronic acid and doxycycline have on chondrocyte viability, cellular metabolic and apoptotic activity and biochemical composition of cartilage up to and beyond 56 days of storage.

Wei Shen Liang: Characterizing the human balance organ with single-nucleus multiomics

Background: The utricle is a vestibular organ responsible for detecting horizontal linear acceleration. Its sensory epithelium is composed of mechanosensory hair cells interdigitated by supporting cells, and the periphery is surrounded by nonsensory transitional epithelial cells. There is currently no data available on the developing human utricle at single-cell resolution. Therefore, we used single-nucleus multiomic sequencing to unveil the transcriptomic and epigenomic profiles of the fetal human utricle.

Methods: We dissected the utricle from the inner ear at gestational week 19 and separated the sensory epithelium and surrounding transitional epithelium from the underlying mesenchyme using thermolysin. After tissue lysis, the single nuclei suspension was used to perform the 10x Chromium Single Cell Multiome ATAC + Gene Expression protocol followed by sequencing. The multiomic dataset underwent quality control and batch correction, followed by dimension reduction and clustering using various bioinformatic tools,

Results: Integration of snRNA- and snATAC-seq data revealed distinct populations of hair cells, supporting cells, and transitional epithelial cells in the utricle. By performing motif enrichment analysis in accessible peaks and calculating their correlation with gene expression, we inferred gene regulatory networks detected active transcription factors in each cell type.

Conclusion: Our study generated the first human fetal utricle single-nucleus multiomic dataset, revealing the cellular heterogeneity and gene regulatory networks within the organ. By establishing a better understanding of the human utricle, we anticipate that our data will contribute to preclinical studies to design therapies to treat vestibular dysfunction.

Contact

No need to register.

Contact lmp.grad@utoronto.ca with any questions