Janice Leung

Assistant Professor

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Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.

Multi 'omics integration of the HIV airway epithelium: integration of the microbiome, transcriptome and methylome (2022)

RATIONALE: People living with HIV (PLWH) appear to have increased proneness to chronic obstructive pulmonary disease (COPD) independent of their cigarette smoke exposure. Previous studies have shown that HIV infection is associated with changes in the airway microbiome and host response, however, the exact mechanism of disease progression is still unknown. We hypothesize that airway epithelial dysbiosis in PLWH increases the susceptibility to COPD in this group.METHODS: Airway epithelial cell brushings were obtained from 18 COPD+HIV+,16 COPD-HIV+, 22 COPD+HIV- and 20 COPD-HIV- subjects. Microbiome, methylation, and transcriptome profiles were measured using 16s amplicon sequencing (Illumina Miseq®), Illumina Infinium Methylation EPIC chip®, and RNA sequencing (NovaSeq6000®), respectively. Microbiome analysis was performed using QIIME 2™, and transcriptome and methylation analyses were performed using R language. The three datasets were integrated using Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO) implemented in the mixOmics R package. Fifty repeats of 10-fold cross-validations and a correlation threshold of 0.7 were set to determine key interactions between bacterial ASVs, CpG methylation sites, and gene transcripts amongst the subjects based on their COPD, HIV, and combined COPD and HIV statuses. RESULTS: The microbiome analysis identified that the groups most associated with disease (COPD+, HIV+, and COPD+HIV+ groups) had reduced alpha diversity (Shannon Diversity Index p=0.0013, p=0023, and p=0.0002, respectively), and significantly disrupted microbial communities (Bray Curtis PERMANOVA p=0.001, p=0.007 and p=0.001, respectively) compared to their relatively ”healthy” counterparts. This was accompanied by changes in the host transcriptome and epigenome, our analysis of which identified top genes and CpG sites that were differentially regulated in patients with COPD and/or HIV. Integration of the three -omes identified features that were correlated with one another at a threshold>0.70. On combining the COPD and HIV statuses of subjects, the multiomic integration identified correlations between the bacterial ASV Bacteroidetes Prevotella and transcriptomic features FUZ, FASTKD3, and ACVR1B, and epigenetic features CpG-FUZ and CpG-PHLDB3. It may be that these features together influence host pathways regulating mucociliary clearance, respiration and energy, cell cycle, and immunity.

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The airway epithelial response to human immunodeficiency virus: implications for HIV-associated chronic obstructive pulmonary disease (2022)

RATIONALE: Despite the reduction in HIV-related mortality since the introduction of antiretroviral therapy, people living with HIV (PLWH) face a higher risk of developing age-associated comorbidities such as chronic obstructive pulmonary disease (COPD). Studies have found that HIV and COPD are independently associated with increased susceptibility and worse manifestations from respiratory viral infections. We hypothesize that COPD in PLWH is marked by increased inflammation in the airway epithelium which may potentiate injury during respiratory viral infections. METHODS: Primary human bronchial epithelial cells obtained from control, COPD, HIV, and HIV/COPD donors were cultured as monolayers and air-liquid interfaces (ALIs). RNA and protein lysates from these cultures were used to quantify HIV receptor mRNA and protein expression via qRT-PCR and western blot, respectively. ALI cultures were infected with respiratory syncytial virus (RSV) for 90 minutes and transepithelial electrical resistance (TEER) values were taken at time points: 0h, 24h, 48h and 72h. ALI cultures underwent immunohistochemistry staining for E-Cadherin quantification and mucus production quantification through Periodic Acid Schiff and MUC5AC staining. RESULTS: Western blot analysis of monolayer lysates demonstrated increased expression of CXCR4 in PLWH with and without COPD and increased expression of CCR5 in PLWH with COPD compared to control individuals. There was a trend towards higher CD4 expression in PLWH with and without COPD compared to control individuals. However, these differences were not found in either protein or mRNA HIV receptor expression in ALIs. TEER data demonstrated a decrease in epithelial resistance in RSV-infected ALIs derived from COPD and PLWH with COPD compared to PLWH without COPD and control individuals. There were no significant differences seen in E-cadherin expression and mucus production in RSV-infected ALIs. CONCLUSION: With an increased expression of HIV canonical receptors in the basal epithelial layer, particularly CCR5 and CXCR4, in PLWH with COPD, a greater interaction between virus and the airway epithelium may be possible, potentially causing damage to the airway epithelium. Furthermore, RSV infection induces greater epithelial permeability in patients with COPD regardless of HIV status. This could indicate that post-viral small airway injury may be driven more by COPD status rather than HIV infection alone.

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