Wednesday, April 2, 2025
4/2/2025
Genomic Instability in Lung Cancer: Unraveling the Impact of the APOBEC3 Family - PROJECT SUMMARY Genomic instability creates heterogeneity in cancer cells, fueling evolution and treatment resistance. However, the costs of genomic damage can lead to cell death or immune detection. In lung cancer, somatic mutagenesis driven by the APOBEC3 (A3) family of cytosine deaminases is enriched in 75% of nonsmoking patients. A3 mutagenesis is associated with driver mutations, resistance to targeted therapies, and poor prognosis. Yet, the precise A3 family members (A3A/B/C/D/F/G/H) responsible for lung cancer mutagenesis are still unknown. Thus, the etiology of many somatic mutations in lung cancer remains poorly understood, a critical barrier to improved therapeutics and prognostics. To dissect the mechanisms of A3 mutagenesis in cancer, my lab developed a novel pipeline that measures endogenous A3 mutagenesis in human cancer cell lines using whole genome sequencing (WGS) and in vitro propagation. I aim to study A3 mutagenesis in lung cancer. Based on preliminary data, I hypothesize that multiple A3s are critical in lung cancer mutagenesis (Aim 1). To identify the A3 mutators in LUAD, I established A3 KO cell lines in multiple LUAD cell lines. I will use them in our de novo A3 mutagenesis detection protocol to determine the major mutators (Aim 1.1). Additionally, I will test proposed surrogate measures of active A3 mutagenesis using my WGS data set as a “gold standard” to evaluate A3 mutagenesis (Aim 1.2). With this toolkit, I will test the prevalence of A3 mutagenesis in a broad range of LUAD cell lines (Aim 1.3). A3 enzymes play a key protective role in healthy tissues by regulating genotoxic retroelements, but this role has been unexplored in cancer biology. Endogenous retroelements can activate during cancer and drive genome instability. They are active in lung cancers, including LUAD, and particularly in Squamous cell lung carcinoma (LUSC). Exogenous expression of A3s can inhibit genome-destabilizing retroelements, including LINE-1 and Alu. However, a link between A3 activity and retroelement regulation in cancer has been completely overlooked. I hypothesize that A3s limit genome instability and protect cancer cells by inhibiting retrotransposition (Aim 2) . To explore retroelement regulation by A3 in lung cancer, I will use LINE-1 and Alu Retrotransposition Assays to determine if endogenous A3s can repress retroelements (aim 2.1); Next, I will compare the levels of retrotransposition breakpoints in the A3 KO and wildtype LUAD WGS datasets I have, to directly test endogenous A3s as regulators of retroelements (aim 2.2). Finally, I will investigate the impact of A3-dependent regulation of retrotransposition by exploring immune signaling and DNA damage driven by LINE-1 and Alu in the absence of A3s in the NSLC cell lines (aim 2.3). This aim will expand the repertoire of A3s beyond somatic mutagenesis to include protecting genomic integrity. The data collected will dissect paralogs driving A3 mutagenesis, evaluate accurate surrogate methods for assessing A3 mutagenesis, and explore A3 activity outside of cancer mutagenesis. This will pave the way for research on specific targets and tools for treatment and prognosis.
HHS’ Tracking Accountability in Government Grants System (TAGGS) website provides access to detailed descriptions of grants, loans, aggregated direct payments and other types of financial assistance awarded by the HHS Operating Divisions (OPDIVs) and the Office of the Secretary Staff Divisions (STAFFDIVs).