Abstract 6222: Exposing the heterogeneity of the lipidome in the TME of cutaneous melanoma following treatment with NUC-7738 in combination with anti-PD-1 therapy
Authors: Dickson Alison L. , Zickuhr Greice M. , Um In Hwa , Zhang Ying , Plummer Ruth , Blagden Sarah P. , Symeonides Stefan N. , Cook Natalie , Evans T.R. Jeffry , Elshani Mustafa , Harrison David J. 
Published: March 2024

Abstract
Background. Malignant melanoma exhibits distinct lipid profiles compared to normal tissue and changes in the lipidome influence multiple aspects of tumor biology. Lipidomic alterations within the tumor microenvironment (TME) may influence the efficacy of anti-PD-1 therapy. In combination with anti-PD-1 agent pembrolizumab, NUC-7738 (3'-deoxyadenosine [3’-dA] which is phosphorylated and protected with a phosphoramidate moiety attached at the 5’-position) has shown promising activity in anti-PD-1 refractory melanoma (Phase 2; NCT03829254). NUC-7738 generates sustained intracellular levels of 3’-dATP, which profoundly alters RNA regulatory processes in tumor cells, resulting in impaired cellular responses and changes in expression of proteins related to lipid biosynthesis. To interrogate components of the TME before and after NUC-7738 + pembrolizumab treatment, we developed a novel workflow incorporating Mass Spectrometry Imaging (MSI) to co-register lipidomic changes with molecular markers. Machine learning accelerated the interpretation of complex data obtained from paired patient biopsies.
Methods. Snap frozen paired biopsies from patients with advanced cutaneous melanoma treated with NUC-7738 ±pembrolizumab were analyzed by desorption electrospray ionization (DESI)-MSI. Specific metabolic (e.g., ASAH1) and immune (e.g., CD8, CD20) markers were investigated by multiplex immunofluorescence (mIF) post DESI-MSI. Target selection was guided by bulk RNA-seq data. Raw MSI data was visualized using Waters HDI® software. Data extracted from selected regions of interest was exported into MetaboAnalyst 5.0 for statistical analysis. LIPID MAPS® Structure Database was used to assign lipid species. mIF/mIHC images were analyzed by HALO® AI.
Results. Single 10 µm tissue sections allowed co-registered DESI-MSI and mIF, suitable for further informatic and AI-enabled image analysis. This facilitated direct comparison of lipids, cells, and protein expression in the TME, before and after treatment with NUC-7738, a compound known to cause profound changes in poly(A) tail regulation. MSI data analyses of the TME uncovered intra-tumoral heterogeneity of the lipidome and demonstrated changes following treatment.
Conclusion. This platform provides a powerful investigative tool to simultaneously explore the myriad of factors in the TME that contribute to tumorigenesis and therapeutic response. Further analyses of the role of the lipidome in the TME and intra-tumoral heterogeneity will be explored in paired biopsies from patients with PD-1 inhibitor refractory melanoma.
Citation Format: Alison L. Dickson, Greice M. Zickuhr, In Hwa Um, Ying Zhang, Ruth Plummer, Sarah P. Blagden, Stefan N. Symeonides, Natalie Cook, T.R. Jeffry Evans, Mustafa Elshani, David J. Harrison. Exposing the heterogeneity of the lipidome in the TME of cutaneous melanoma following treatment with NUC-7738 in combination with anti-PD-1 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6222.