Holden, S. B. | bioRxiv Science

bioRxiv2025

Transposable Elements and Homotypic Niches Drive Immune Dynamics and Resistance in Melanoma Epigenetic-based immunotherapy

Melanoma plasticity drives immune evasion and therapy resistance through dynamic cell-state transitions beyond genetic alterations. Epigenetic remodeling critically influences such processes, yet its role in reshaping the tumor ecosystem under therapeutic pressure remains unresolved. Here, we profiled longitudinal biopsies from melanoma patients treated in the phase Ib NIBIT-M4 epi-immunotherapy clinical trial (NCT02608437), testing the combination of a DNMT1 inhibitor with anti-CTLA4 using single-cell multiome and high-resolution spatial transcriptomics. Integrated analyses resolved seven malignant meta-programs, including a rare Wnt/{beta}-catenin-driven melanocytic state and a de-differentiated neural crest-like state enriched in non-responders. Spatial modeling revealed that homotypic clustering stabilizes resistant programs, with neural crest-like cells forming compact, centrally localized niches, whereas Wnt/{beta}-catenin subpopulations displayed a bimodal architecture, either cohesive clusters sustained by adhesion or dispersed, transcriptionally plastic cells. Responders exhibited progressive enrichment of an antigen presentation/interferon program and coordinated remodeling of the tumor microenvironment with T and B cell expansion, whereas tumors from non-responder patients maintained stable composition of neural crest-like clusters. Epigenetic therapy reactivated transposable elements, providing both regulatory signals that prime innate immunity within microenvironment and generating antigens that drive immunoediting and immunogenicity of Antigen presentation/interferon cell states in responders. Finally, NFATC2 emerged as a master regulator of neural crests-like transcriptional phenotypes and promoter of resistance to therapeutic interventions in melanoma patients. NFATC2 perturbation was able to shift tumor cells towards more differentiated and immunogenic states. These findings reveal how epigenetic-based immunotherapy reshapes melanoma ecosystems, provide mechanistic insights into how multiple transcriptional programs promote tumor plasticity and resistance to both combinatorial therapies and immune checkpoint blockade, identify spatial clustering as a principle stabilizing resistant niches, and highlight {beta}-catenin and NFATC2 as actionable vulnerabilities to overcome resistance.

genomics↗

bioRxiv2025

Topography Aware Optimal Transport for Alignment of Spatial Omics Data

Understanding the spatial organization of tissues is essential for uncovering cellular communication, developmental processes, and disease mechanisms. Recent advances in spatial omics technologies have provided unprecedented insight into tissue spatial organization, but challenges remain in aligning spatial slices and integrating complementary single-cell and spatial data. Here, we propose TOAST (Topography-aware Optimal Alignment of Spatially-resolved Tissues), a novel OT-based framework that extends the classical Fused Gromov-Wasserstein (FGW) objective to more comprehensively model the heterogeneity of local molecular interactions. By introducing spatial coherence, quantified through the entropy of local neighborhoods, and neighborhood consistency, which preserves the expression profiles of neighboring spots, TOASTs objective function significantly improves the alignment of spatially resolved tissue slices and the mapping between single-cell and spatial data. Through comprehensive evaluations on both simulated and real-world datasets, including human brain cortex Visium data, Axolotl brain Stereo-seq data, mouse embryo seqFISH data, and Imaging Mass Cytometry from multiple cancer types, we demonstrate that our method consistently outperforms traditional FGW and other OT-based alignment methods. Specifically, TOAST improves the accuracy of spatial slice alignment, better preserves cell type compositions, recovers lineage trajectories in developmental brain data, and reconstructs spatial relationships in spatial transcriptomics mouse embryo data. By integrating spatial constraints into OT, our framework provides a principled approach to enhance the biological interpretability of spatially resolved omics data and facilitate multimodal data integration.

bioinformatics↗