Biology subjects

Legg, S.

Publications and source records attributed to Legg, S..

3 recordsLinked to original sources

bioRxiv2026

Integrated Spatial Multi-omic Profiling Identifies HSV-associated Inflammatory Macrophage Niches Linked to Oncolytic Virotherapy Response in Melanoma

BackgroundPrimary and secondary resistance to immune checkpoint blockade (ICB) remains a critical challenge in advanced melanoma. Oncolytic Viruses (OV) selectively lyse tumor cells while generating systemic anti-tumor immune responses with minimal side effects. Yet their clinical use is limited to refractory melanoma patients and are only given in combination with second-line ICB regimens. ICB can both help and hinder OV efficacy depending on the source of checkpoint interactions across the tumor-immune microenvironment (TiME). However, functional checkpoint interactions are typically inferred from gene or protein expression and rarely contextualized within myeloid- and antigen presenting cell-associated immune niches during OV therapy, despite these populations dominating melanoma TiMEs and serving as key regulators of anti-viral immunity. MethodsAn integrated multi-omics framework combining Nanostring GeoMx digital spatial profiling (DSP), COMET sequential immunofluorescence (seqIF) and functional oncology mapping (FuncOmap) was applied to melanoma patient tissues collected pre- and post-neoadjuvant Talimogene Laherparepvec (T-VEC) to characterize immune remodeling and directly quantify checkpoint interaction dynamics associated with pathologic responses to OV therapy. ResultsT-VEC induced broad lymphocyte- and myeloid-associated immune transcriptional activation across melanoma TiMEs; however, pathologic responses could not be defined by bulk transcriptomics or cellular deconvolution alone. COMET seqIF analysis identified that HSV-associated M1/APC-like tumor-associated macrophages (TAMs) were enriched in complete pathologic response (CR) tissues and were a major source of PD-1/PD-L1 interaction niches. While partial (PR) and non-pathologic response (NR) tissues retained melanoma-centered PD-1/PD-L1 interaction niches and were enriched for B cell and M2-like TAM populations. FuncOmap analysis indicated that post-T-VEC PD-1/PD-L1 interaction states were consistently elevated in tumor bed, but not in lymph node tissues, across all pathologic response groups. Suggesting that immune checkpoint interactions may benefit T-VEC therapeutic responses depending on their spatial and immune context relative to OV infection. ConclusionsThese findings highlight the importance of integrated transcriptomic and functional proteomic analyses for resolving the spatial distribution and functional status of immune niches during OV therapy. Resolving PD-1/PD-L1 interaction states to specific M1/APC-like TAM and B cell niches may define mechanisms of responses and resistance to OV therapy.

cancer biology↗

bioRxiv2025

Functional Spatial Mapping of the Tumour Immune Microenvironment In Advanced Melanoma Patients

IntroductionCurrent spatial proteomic approaches quantify immune checkpoint expression but do not directly measure functional receptor/ligand (PD-1/PD-L1) interactions within the tumor immune microenvironment (TiME). Therapeutic antibodies disrupt receptor-ligand interactions and do not target protein abundance. Methods that resolve functional checkpoint interactions provide biologically distinct insight beyond expression-based assays MethodsWe combined computation and quantitative spatial imaging, FuncO:TiME, [Functional Oncology Mapping (FuncOmap)], to map PD-1/PD-L1 interaction states to spatially defined regions of the TiME, in clinically annotated melanoma specimens, collected before and after neoadjuvant immune checkpoint blockade (ICB), ResultsFuncOmap spatially quantified millions of per-pixel PD-1/PD-L1 interactions demonstrated spatial heterogeneity in checkpoint interaction, not reflected by PD-1 expression levels alone. Post-treatment tissues exhibited increased PD-1/PD-L1 interaction states despite no corresponding increase in expression, indicating persistent or augmented functional checkpoint interaction despite therapy. Integration with spatial immune profiling further demonstrated that checkpoint interaction intensity can be contextualized within distinct immune cell populations. ConclusionWe have established the feasibility of spatially resolved functional checkpoint mapping in human melanoma tissues. We demonstrate that receptor-ligand interactions diverge from protein expression patterns. By enabling direct interrogation of functional checkpoint interaction dynamics within intact tissue architecture, FuncO:TiME advances a functional paradigm for studying immune regulation in cancer.

cancer biology↗

bioRxiv2025

AXL-GAS6/PROS1 Interaction: A Critical Switch Between Aberrant- and Healthy Repair Following Alveolar Lung Injury

RationaleIdiopathic pulmonary fibrosis (IPF) is a progressive lung disease characterized by aberrant alveolar repair and excessive fibrosis. The TAM-family receptor tyrosine kinase AXL, activated by GAS6 and PROS1, is implicated in tissue remodeling, but ligand-specific AXL signaling during alveolar repair remains poorly defined. ObjectivesTo investigate ligand specific AXL signaling in IPF and how it impacts epithelial proliferation and repair after alveolar injury in-vivo and in-vitro. MethodsSingle cell RNA sequencing was utilized to understand cell specific expression patterns in IPF patients, followed by functional studies in primary human cell culture and functional spatial digital profiling (FuncOmap) analysis in patient tissue. Longitudinal assessment of repair process after alveolar-specific injury in-vivo was used to complement the in-vitro approach. ResultsAXL expression showed enrichment in basal and aberrant basaloid cells of IPF patients. In-vitro GAS6 increased proliferation of basal cells, while PROS1 counteracted this effect. FuncOmap analysis demonstrates direct in-situ interactions between AXL and both ligands, providing evidence for biological relevance. Investigating longitudinal repair processes in-vivo revealed dynamic regulation of AXL ligands as well as AXL. ConclusionsThese findings highlight the importance of ligand-specific AXL signaling in lung repair and suggest that it dysregulation may contribute to IPF pathogenesis, offering potential therapeutic targets for restoring normal repair processes.

molecular biology↗