Author ORCID Identifier

0000-0001-6759-9829

Date of Graduation

8-2023

Document Type

Dissertation (PhD)

Program Affiliation

Genetics and Epigenetics

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Swathi Arur, Ph.D.

Committee Member

Guillermina Lozano, Ph.D.

Committee Member

Don Gibbons, MD/Ph.D.

Committee Member

Jichao Chen, Ph.D.

Committee Member

Nicholas Navin, Ph.D.

Committee Member

George Calin, MD/Ph.D.

Abstract

DICER1 is a multidomain enzyme discovered and widely recognized for its function in small non-coding microRNA (miRNA) synthesis. In cancer development, DICER1 functions as a haploinsufficient tumor suppressor which regulates miRNAs and Epithelial-to-Mesenchymal Transition (EMT). The Arur laboratory discovered that DICER1 is phosphorylated by active ERK and that ERK-mediated phosphorylation triggers DICER1 to translocate from the cytoplasm to the nucleus of cells in worms, mice and humans. Further, a heterozygous allele of a genetically engineered mouse model of phosphomimetic Dicer1 when combined with heterozygous Kras oncogenic background contributes to lung tumor progression in vivo. Mechanisms through which phosphomimetic Dicer1 regulates tumor progression remain undefined.

In this thesis, I discovered that phosphorylation of DICER1 regulates lung tumor progression through a mechanism that is distinct from its function as a haploinsufficient tumor suppressor. I find that the presence of phosphorylated nuclear DICER1 is unique to transformed Alveolar Type 2 (AT2) cells and is not observed in wild-type lung alveolar cells. Furthermore, I find that the expression of phosphorylated DICER1 is much higher in the nucleus of AT2 tumor cells that harbor oncogenic Kras and phosphomimetic Dicer1 compared to murine tumors lacking phosphomimetic Dicer1. I demonstrate that distinct from DICER1 canonical function in regulating miRNAs and EMT, presence of phosphorylated nuclear DICER1 in the transformed AT2 cells with oncogenic Kras mutation promotes late-stage tumor progression independent of miRNAs and EMT. To determine the mechanism through which phosphorylated nuclear DICER1 regulates late-stage tumor progression, I used single-cell RNA sequencing, immunofluorescence staining and ATAC- sequencing. I discovered that the murine AT2 tumor cells exhibit altered chromatin compaction. Specifically, I find that the presence of phosphorylated nuclear DICER1 in the AT2 tumor cells leads to “open” chromatin at loci of gastrointestinal genes and enhancer regulatory elements which are normally “closed” in wild-type AT2 cells and AT2 tumor cells from oncogenic Kras mutant tumors without phosphomimetic Dicer1. As a consequence of the altered chromatin compaction, AT2 tumor cells from disorganized advanced lung tumors express gastrointestinal genes while losing expression of alveolar genes. Collectively, these findings indicate that sub-populations of tumor cells are transitioning from a restricted alveolar state to a broader endodermal lineage state in the presence of phosphomimetic nuclear DICER1.

In human lung adenocarcinomas (LUADs), I find that the expression of phosphorylated nuclear DICER1 in an advanced tumor coincides with the expression of gastric genes. In addition, using immunohistochemistry, I show that moderate to high rate of phosphorylated DICER1 positivity correlates with oncogenic mutations in KRAS. Finally, using LUAD cell lines, I define a novel multimeric chromatin-DICER1 nuclear complex comprised of the Mediator complex subunit-12, CBX1, MACROH2A.1 and transcriptional regulators. Altogether, these findings support the model that phosphorylated nuclear DICER1 functions downstream of the KRAS/ERK axis to alter chromatin compaction, causing AT2 tumor cells to undergo lineage reprogramming as a mechanism for lung adenocarcinoma progression. These data have direct implications for patient management, including the potential use of phosphorylated DICER1 as a biomarker and as a new therapeutic target for patients with aggressive lung adenocarcinomas.

Keywords

DICER1, Lung Cancer, Lung adenocarcinoma, tumor progression, invasion, transdifferentiation, miRNAs, chromatin remodeling

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