Author ORCID Identifier

https://orcid.org/0000-0003-1038-5218

Date of Graduation

8-2020

Document Type

Dissertation (PhD)

Program Affiliation

Genes and Development

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Giulio Draetta, M.D., Ph.D.

Committee Member

Andrea Viale, M.D.

Committee Member

Nicholas Navin, Ph.D.

Committee Member

Anirban Maitra, M.B.B.S.

Committee Member

Haoqiang Ying, M.D., Ph.D.

Committee Member

Richard Behringer, Ph.D.

Abstract

In recent years, technological advancements, such as next-generation sequencing and single-cell interrogation techniques, have enriched our understanding in tumor heterogeneity. By dissecting tumors and characterizing clonal lineages, we are better understanding the intricacies of tumor evolution. Tumors are represented by the presence of and dynamic interactions amongst clonal lineages. Each lineage and each cell contributes to tumor dynamics through intrinsic and extrinsic mechanisms, and the variable responses of clones to perturbations in the environment, especially therapeutics, underlie disease progression and relapse. Thus, there exists a pressing need to understand the molecular mechanisms that determine the functional heterogeneity of tumor sub-clones to improve clinical outcomes.

Clonal replica tumors (CRTs) is an in vivo platform created specifically to enable robust tracing and functional study of clones within a tumor. The establishment of CRTs is built upon our current concept of tumor heterogeneity, intrinsic cancer cell hierarchy and clonal self-renewal properties. The model allows researchers to create large cohorts of tumors in different animals that are identical in their clonal lineage composition (clonal correlation amongst tumors >0.99). CRTs allow simultaneously tracking of tens of thousands of clonal lineages in different animals to provide a high level of resolution and biological reproducibility. CRTs are comprised of barcoded cells that can be identified and quantified. A critical feature is that we have developed a systematic method to isolate and expand essentially any of the clonal lineages present within a CRT in their naïve state; that is, we can characterize each sub-clonal lineage at the molecular and functional levels and correlate these findings with the behavior of the same lineage in vivo and in response to drugs.

Here, based on the CRT model and its concept, we studied differential chemo-resistance among clones, where we identified pre-existing upregulation in DNA repair as a mechanism for chemo-resistance. Furthermore, through stringent statistical testing, we demonstrated orthotopic CRTs to be a powerful and robust model to quantitatively track clonal evolution. Specifically, we longitudinally tracked clones in models of pancreatic ductal adenocarcinoma (PDAC) from primary tumor expansion through metastasization, where we captured unexpected clonal dynamics and “alternating clonal dominance” naturally occurring in unperturbed tumors. Moreover, by characterizing pro- and none-metastasizing clones, we were able to identified key clonal intrinsic factors that determined the nature of tumor metastases. Finally, I will discuss distinct clonal evolution patterns that emerged under different environmental pressures, leading to the hypothesis of “tumor clonal fingerprint”, where the characteristic of a tumor could be defined by actively maintained ratio of different tumor lineages, which could provide measurable insights to how we approach treatments.

Keywords

Tumor heterogeneity, functional heterogeneity, longitudinal lineage tracing model, clonal dynamics, pancreatic cancer, long-term self-renewal lineages, dissemination and metastasis, cancer stem cell, sub-clonal gene signature, prognostic stratification

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