Graduation Date

Spring 5-4-2024

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Programs

Biomedical Informatics

First Advisor

Dr. Javeed Iqbal

Abstract

Mantle Cell Lymphoma (MCL) is a B-cell lymphoma characterized by t(11;14) leading to CyclinD1 (CCND1) overexpression with highly variable clinical response. Although the tumor intrinsic mechanisms have been fairly studied, the role of the tumor microenvironment (TME) in survival and therapeutic responses is marginally examined. Herein, we integrated high-throughput genomics and characterized TME using a highly multiplexed, spatially resolved, single-cell digital pathology approach termed imaging mass cytometry (IMC) to delineate the tumor-immune landscape. We identified eight MCL genomic subtypes with distinct signatures and prognoses. Subsets C2, C5, and C6 had poorer outcomes with a 5-year overall survival (OS) of 33-50% and a median OS of 3.2-4.5 years. In contrast, subtypes C1, C3, C4, C7, and C8 showed better survival, with a 5-year OS of 62-88% and a median OS of 8.2-11.8 years. Subtypes with complex genomic alterations, like deletions and mutations involving TP53 and regions on chromosomes 13, 17, and 11, correlated with shorter survival. Conversely, subtypes with gains in MYC, mutation/deletion of ATM, mutations in SP140, and deletions on chromosome 6 associated with longer survival, broadly categorizing the subtypes into two groups based on survival outcomes. Extrinsic factors such as TME reveal nine major cellular compartments, with neoplastic cells constituting 58% and various immune cell types forming the tumor milieu. Notably, TP53-altered genetic subtypes were characterized by an increase in T-regulatory, CD8+ T-cells, and endothelial cells, alongside heightened exhaustion markers on immune and neoplastic cells. Poor prognostic indicators included elevated PDL-2 or low HLADR on CD8+ T cells and high CD45RA on SOX11+/- malignant cells. Spatial analysis identified distinct cellular neighborhoods correlated with TP53 alterations. Thus, to further explore the underlying pathobiology of this most lethal TP53 subtype in MCL, we generated modified cell lines to study the functional significance of p53 deficiency in MCL. We v performed RNA-seq on these p53-modified cells to determine their transcriptomic features. Notably, we found that BCR signaling was remarkably repressed upon WT p53 expression, suggesting that p53 deficiency may contribute to resistance against BTK inhibitor treatment. Using the CUT&RUN assay to determine the TP53 targets, besides canonical targets, we observed changes in an expansive list of genes and pathways upon p53 modification, including the BCR signaling. Interestingly, PTPN6, targeted by TP53 and a negative regulator of BCR, modulated BCR pathway activity which may potentially alter ibrutinib responsiveness. Thus, this study suggests a more granular risk stratification recovering previously known subtypes and identifying novel subgroups. TME analysis of the TP53 altered subgroup demonstrates that, far from being histopathologically monotonous, MCL has a complex tumor-immune architecture, and that changes in tumor topology can be correlated with clinically relevant features. This analysis identified candidate biomarkers and therapeutic targets such as TIM-3, PD-L2, HLA-DR that are relevant for combination treatment strategies in immuno-oncology and cellular therapies. Loss of PTPN6 could act as an alternative biomarker in patients with p53 functional loss likely to respond to ibrutinib treatment indicating pharmacological inhibition of PTPN6 might be a novel approach to enhance the efficacy of BCR-targeted therapies.

Comments

2024 Copyright, the authors

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