Spatially-resolved single cell atlas of liposarcoma reveals lineage hierarchies, immune niches, and regulatory circuits

ABSTRACT Well-differentiated and dedifferentiated liposarcoma (WDLPS and DDLPS) exhibit markedly different clinical behaviors, with DDLPS showing greater aggressiveness, higher recurrence and metastasis rates, and worse outcomes. Using single-nucleus multiome sequencing, epigenomic profiling, and spatial transcriptomics, we characterized cellular and epigenetic heterogeneity between these subtypes at single-cell and spatial resolution. We found distinct phenotypic states reflecting altered lineage differentiation and plasticity: DDLPS is dominated by early-differentiated progenitor-like cells, sclerotic WDLPS displays broader mesenchymal lineage plasticity, and adipocytic WDLPS contains abundant committed adipocytes. The DDLPS immune microenvironment was dominated by immunosuppressive macrophages, whereas WDLPS harbored more T cells and inflammatory macrophages. Notably, sclerotic WDLPS displayed intermediate cellular and molecular features, suggesting it may represent a distinct WDLPS subtype. Importantly, we identified novel gene regulatory circuits underlying each state, including FABP4/PPARG programs in adipocytic WDLPS, GLI2/TCF7L2/RBPJ/KLF7 programs in sclerotic WDLPS, and KLF7/FOSL2/SP3/GLI2/RBPJ programs in DDLPS. H3K27ac-marked enhancers were enriched near adipocytic marker genes in WDLPS and mesenchymal markers in DDLPS. Together, these findings reveal the cellular heterogeneity of tumor and immune compartments across liposarcoma subtypes and identify regulatory programs driving their differentiation states. Competing Interest Statement EpiCypher is a commercial developer and supplier of the CUTANA platform used in this study and holds a patent (#WO2020132388A1) for related technologies. J.L.M., A.S., L.M.A.-S., D.N.M., C.C.S., B.J.V., C.L.W., and M.C.K., are or were employed by (and own shares in) EpiCypher, with M.-C.K. also a board member of same. EFNH reports consulting fees from Sonata therapeutics. AJL reports consulting and/or advisory board relationships with the following entities: AbbVie, Adaptimmune, AJCC, Astra-Zeneca, Bain Capital, Bayer, Bio-AI Health, BMS, CAP, Caris, Deciphera, Elsevier, Foghorn Therapeutics, Gothams, GSK, Illumina, Invitae / Archer DX, Iterion Therapeutics, Merck, Novartis, Nucleai, OncoKB (MSKCC), Paige, Pfizer, Regeneron, Roche / Genentech, SpringerNature, SpringWorks, Tempus, ThermoFisher, USCAP. NS reports current clinical trial research funding/grant support through the institution from AstraZeneca, Ascentage, Deciphera, Cogent, Boehringer Ingelheim, IDRX, Ningo Newbay, and Bayer. Advisory Board consultant (last 2 yrs) for Aadi Biosciences, Adatimmune, Bayer, Deciphera, Ipsen, and Boehringer Ingelheim. KR reports research funding support through the institution from Cyclacel Inc, consulting and/or advisory agreements from Daiichi Sankyo and Jivanu Therapeutics, and equity in Jivanu Therapeutics and Koshika Therapeutics.