Mohammed Muzamil Khan Successfully Defends

Congratulations to Mohammed Muzamil Khan on the successful defense of their thesis.

"From Lesions to Treatment: A Multi-Species Multi-Transcriptomics Study of Oral (Pre-) Cancer Conditions" Great job Muzamil!

To learn more about Muzamil's thesis, read their abstract below: 

ABSTRACT

Cancer incidence rates in 2024 are estimated to grow, according to the latest statistics from the American Cancer Society, with cancer-related death rates declining overall due to improved intervention strategies. However, these strategies remain only partially effective for some cancers due to their rapid expansion, sub-clonal evolution, and molecular heterogeneity with added complexities related to socioeconomic status. One such type is classified as head and neck squamous cell carcinoma (HNSCC), with most cases affecting the upper aerodigestive tract or, more commonly, the oral cavity with oral squamous cell carcinoma (OSCC) pathology. HNSCC/OSCC’s five-year survival rate is ~50% for localized stages and reduces to ~35% when metastasized. OSCC etiology is associated with tobacco usage, alcohol consumption, or sexually transmitted human papillomavirus (HPV) infections. The HPV-negative subtype is highly heterogeneous in its molecular composition and is understudied compared to other solid tumor types; hence, there is a need for early detection strategies in addition to effective therapeutics for improving outcomes. With the advances in computational methodologies to study human diseases, multi-omic data modalities are becoming a crucial tool to improve patient care and have already led to remarkable discoveries. In my thesis, bioinformatics, statistical, and machine learning methodologies were leveraged to study the transcriptome-wide changes across different modalities (bulk and single-cell) of pre-cancer conditions in humans and of post-treatment conditions of tumors in mice.

In my first aim, the transcriptional changes of early lesions of OSCC progression were studied. OSCC arises through a multi-step process characterized by an aberrant increase in normal epithelia with preneoplastic tendencies, and comprises premalignant lesions (PML) of varying histologies that include hyperplasia, metaplasia, and dysplasia with moderate to severe pathology. Clinicians have characterized the various lesions according to their pathology. However, a rigorous molecular characterization of these lesions and of the concomitant microbiota are lacking. In this project, we leverage bulk RNA sequencing to study the molecular profiles of oral lesions at different stages of transformation, and to characterize their defining pathways and host/microbiome interactions. To this end, we generated a unique dataset from a cohort of 66 patients harboring distinct histopathologies with healthy oral mucosa, PMLs (HkNR and dysplasia), and OSCC. Using Total RNA-sequencing technology, we studied the global transcriptome (host + microbiome) of the oral mucosa from these groups. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome to the evolution of PML to OSCC. Collectively, this study revealed molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage. 

My second aim is focused on elucidating the mechanisms of action of candidate therapeutics. As the efficacy rate of FDA-approved drugs for HNSCC tumors remains relatively low, due to a combination of factors, including tumor heterogeneity, late diagnosis, and drug resistance, the need to develop targeted therapies focusing on selected cancer pathways represent a promising avenue. In previous studies, our labs have shown that pharmacological blockade of Wnt/β-catenin/CBP activity with small molecule inhibitors effectively abolished oncogenic cell phenotypes in OSCC. However, the underlying mechanisms promoting changes in OSCC cell identities remain poorly understood. To address this knowledge gap, we induced oral tumors in immunocompetent mice using a tobacco-associated carcinogen, 4-NQO, that mimics human OSCC. We then treated them with E7386, an orally active small molecule inhibitor of β-catenin/CBP activity, at two concentrations – 25 mg/kg and 50 mg/kg. We generated a single-cell RNA sequencing dataset with ~50K cells to explore the post-treatment effects and to better understand the inhibitor’s mechanisms of action.  Our analyses indicated shifts in cellular diversity between treatment groups, with the proportion of epithelial cells decreasing upon treatment – consistent with greatly diminished tumor volumes – while endothelial and fibroblast populations increased compared to the 4NQO control group, providing further evidence for the inhibitor’s antitumor activity. In the immune compartment, we found enrichment of effector T-cell (Cd8+ and Cd4+) activity and decrease in disease-associated neutrophil activity in the inhibitor-treated profiles.  Additionally, epithelial sub-typing using known markers revealed a decrease in basal cancer stem-like cells (Krt5+, Krt14+) concomitant with an increase in cycling cells (Top2a+, Cdc20+). Finally, we identified a decrease in a stress cell phenotype associated with the AP-1 complex (Jun+, Fos+), and decreased cell plasticity in response to E7386, confirmed by functional validations through staining experiments. Overall, this study provides cellular characterizations of murine oral tumors and presents further evidence of Wnt/β-catenin/CBP inhibition as a promising therapeutic strategy in OSCC.

In summary, my studies have contributed to advancing early detection and treatment strategies and to unveil molecular mechanisms of treatment response in OSCC.

Major Professor: Stefano Monti