Immunotherapy has emerged as a major breakthrough that has the ability to improve survival outcomes for multiple solid tumor types, however effective response requires the combination of blocking inhibitory signals on the tumor surface and antigen presentation to the tumor surface for proper immune recognition. Several commercially available and robust methods exist for identification of tumors displaying immune-inhibitory surface receptors, including PD-L1 and CTLA-4, however it is currently difficult to predict effectiveness of antigen presentation on the cell surface. To address this, we utilized clinical and next-generation sequencing data generated by The Cancer Genome Atlas (TCGA) to identify gene signatures that are correlated to tumor mutational burden (TMB) within cancers of epithelial origins as a surrogate for neoantigen signatures. We identifiedLINC00261as a top gene correlated to mutational burden (TMB), whose expression activates DNA damage response pathwaysin vitroalong with resistance to cisplatin.LINC00261expression was also significantly correlated to MHC Class II genes involved in endogenous neoantigen presentation expression within the TCGA-LUAD cohort. This relationship was confirmedin vitrothrough ectopic reintroduction ofLINC00261for key MHC Class II presentation genes. Interferon gamma-induced MHC gene activationin vitrowas also able to induce endogenous expression ofLINC00261. Our results suggest there is a mechanistic relationship betweenLINC00261expression and functional MHC Class II neoantigen presentation in LUAD. The silencing ofLINC00261in LUAD results in compromised DNA repair, accumulation of mutations, and reduced antitumor immune response.

Bone metastasis remains one of the biggest challenges in the treatment of prostate cancer, and other solid tumors such as breast, lung, and colon. Modeling a complex microenvironment in-vitro, such as the bone niche, requires interrogation of cell-cell interactions, specific extracellular matrix proteins and a high calcium environment. Here, we present a fast and cost-effective system in which commercially available, non-adhesive, cell culture vessels are coated with amorphous calcium phosphate (ACP) as a surrogate for bone matrix. We further present modified protocols for subculturing cells, as well as nucleic acid and protein collection in high calcium samples. We find that prostate epithelial cell lines show increased adhesion and proliferation when cultured in these surfaces, as well as independence from androgen starvation. We observe gene expression changes on ACP surfaces in early adenocarcinoma cell lines which may reflect alterations relevant to prostate cancer progression.

Defects in DNA repair allow for the age-dependent accumulation of mutations, which is significantly linked to the age-dependent increase in the development of neoplasia. Our lab has identified the long non-coding RNA LINC00261 as a critical activator of DNA damage signaling whose expression increases with age in normal lung tissue but is lost in the majority of Lung Adenocarcinomas (LUAD). We therefore undertook a mechanistic investigation on the relationship between LINC00261 function in lung and the accumulation of mutations by utilizing expression and mutational load data from The Cancer Genome Atlas, as well as in vitro mechanistic investigation into the functional relationship between LINC00261 and tumor mutational burden (TMB). Here we report (1) the observation of an age-dependent increase in LINC00261 expression in normal lung tissue within the TCGA adjacent non-tumor lung dataset; (2) a significant correlation between TMB and LINC00261 expression, where elevated LINC00261 levels are associated with decreased TMB; (3) LINC00261 effects on TMB were driven primarily by transition mutations, characteristic of defects in nucleotide excision repair. Standard of care treatment for disseminated LUAD often includes systemic platinum-based chemotherapies, including cisplatin, that act by inducing lethal levels of DNA damage. We observed that the presence of LINC00261 in LUAD causes cellular resistance to cisplatin-mediated DNA-damage in vitro. Our results suggest that patients with tumors expressing LINC00261 should be considered for non-platinum based therapeutic strategies. High mutational loads are also associated with the creation of neoantigens, allowing for immune recognition and when combined with PD-L1 expression levels can serve as an indicator for successful immunotherapy. Testing for PD-L1 expression is now standard of care, however exome sequencing to determine TMB is not often pursued outside academic medical centers due to expense, extensive bioinformatic involvement, and difficulty interpreting results. In addition, high levels of TMB does not always confer active neoantigen presentation as MHC Class II genes are often dysregulated in cancer. We therefore sought to determine if LINC00261 can function as a surrogate biomarker for TMB and provide complimentary indications to PD-L1 testing for successful immunotherapeutic response. Reintroduction of ectopic LINC00261 was able to activate expression of MHC Class II genes involved in neoantigen presentation. Conversely, Interferon gamma addition was able to induce endogenous expression of LINC00261 in vitro. Our results suggest there is a mechanistic relationship between LINC00261 expression and functional MHC Class II neoantigen presentation in LUAD. This was supported by observations that LINC00261 expression is significantly correlated to MHC Class II expression within TCGA LUAD cohort. Taken together, our results suggest LINC00261 shows promise as a biomarker of mutational burden and MHC Class II expression. Citation Format: Jonathan Castillo, Tianchun Xue, Mayela Norwood, Samantha Joseph, Crystal N. Marconett. LINC00261 acts as a surrogate biomarker for tumor DNA mutational burden and immunotherapeutic response in lung adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr A006.