Computational Molecular Pathology Research for Cancer Diagnostics and Biomarkers

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

Research is conducted to characterize and develop new animal models of human disease and to develop the means to better characterize disease relevance produced in the model, addressing critical barriers to research progress. Additional aims include the development of new research technologies and means to interrogate cancer tissues for the evaluation and application of disease biomarkers. The research is also aimed to translate approaches to cancer treatment intended for clinical application. Progress was made in developing research resources useful in developing and characterizing new models of human cancer and in cancer diagnostics. The research resulted in methods and computational capabilities utilized to detect and quantify a metastasis promoting protein in the nuclear membrane that contributed to mechanistic insight in cell sensing and metastasis. Work in modeling breast cancer focused on elevated CLIC4 expression in human breast cancers and its alignment with early invasion and poor outcome in women. CLIC4 in the host microenvironment is required for lung metastasis, while the absence of host CLIC4, results in a microenvironment in the primary tumor and the pre-metastatic lungs that is unfavorable for tumor viability and lung colonization in the model. In particular the primary tumor microenvironment within mice deficient in CLIC4 develops necrosis and vascular abnormalities, detected through computational molecular tissue analyses. Research also focused on a highly topical and outstanding issue in tumor immunology. In pulmonary adenocarcinoma, we collaboratively posed whether the driver oncogene influences the kinds of immune cells that infiltrate the lung or their activation status. this frame of reference was undertaken for its potential clinical relevance. We profiled several lung adenocarcinomas for their immune cell infiltrations, evaluating primarily macrophages and T cell subsets, in addition to reactive tumor-associated fibroplasia in these tumors. In a small, highly curated set of samples, all specimens had some degree of immune response infiltration amid cancer cells. We did not observe a clear difference among the tumors using a limited set of parameters (CD8, CD68, CD4, FOXP3, PDL1), where mutant EGFR was the driving oncogene, versus mutant KRAS. However, the degree of fibrosis did appear to correlate with lymphocyte infiltration. This set of analyses provides a strong demonstration of the immune cell infiltration complexity in the context of tumor heterogeneity. Finally, the investigation provided correlates between presence of T regulatory lymphyocytes, high CCL5 expression and CD8+ effector function in human pulmonary adenocarcinomas. Work also continued on drug development for combined targeted therapy for mucosal melanomas. Clinical and pathological correlates between human and canine mucosal melanomas are substantial, and the relatively greater incidence of spontaneous naturally occurring mucosal melanoma in dogs represents a promising opportunity for predictive modeling. Both canine and human mucosal melanomas appear to harbor BRAF, NRAS and c-kit mutations uncommonly, compared to human cutaneous melanomas, although both species share AKT and MAPK signaling activation. The genomic landscapes of human and canine mucosal melanoma appear highly diverse and generally lack recurring hotspot mutations associated with cutaneous melanomas. Although much remains to be determined, evidence indicates that Ras/MAPK and/or PI3K/AKT/mTOR signaling pathway activations are common in both species and may represent targets for therapeutic intervention. Through this research sapanisertib, an mTORC1/2 inhibitor, was selected from a PI3K/mTOR inhibitor library to collaborate with MEK inhibition; the latter preclinical efficacy was demonstrated previously for canine mucosal melanoma. Combined inhibition of MEK and mTORC1/2, using trametinib and sapanisertib, produced apoptosis and cell-cycle alteration, synergistically reducing cell survival in canine mucosal melanoma cell lines with varying basal signaling activation levels. Compared with individual inhibitors, a staggered sapanisertib dose, coupled with daily trametinib, was optimal for limiting primary mucosal melanoma xenograft growth in mice, and tumor dissemination in a metastasis model, while minimizing hematologic and renal side effects. Inhibitors downmodulated respective signaling targets and the combination additionally suppressed pathway reciprocal crosstalk. Further studies in the pharmacokinetics of the two-drug combination are ongoing.