Tertiary lymphoid structures (TLSs) are critical regulators of antitumor immunity, yet their spatial organization, maturation, and clinical relevance remain incompletely defined across cancers. We analyzed spatial transcriptomics spanning 12 cancer types to construct a pan-cancer TLS atlas and characterized TLS spatial architecture and maturation states. TLS maturation was accompanied by coordinated remodeling of distinct niche cell populations and distance-dependent gradients in tumor programs, orthogonally supported by ultrahigh-plex single-cell spatial profiling. To enable scalable TLS profiling, we trained an artificial intelligence framework that predicts TLS maturation states directly from hematoxylin and eosin–stained images and evaluated it across TCGA and independent therapy cohorts. We further derived a maturation-aware composite score capturing intratumoral TLS state composition, which robustly stratifies patients across cancer and treatment contexts, outperforming conventional TLS metrics.

Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive sarcoma characterized by the pathognomonic EWS::WT1 fusion protein (FP), an oncogenic chimeric transcription factor (OCTF) resulting from the t(11;22)(p13;q12) translocation. Recent studies have identified “neogenes” (NGs), genes normally silent in normal tissues but transcriptionally activated by OCTFs, as potential tumor-specific markers in fusion-driven cancers. In this study, we investigated the expression and regulation of DSRCT-specific NGs (DSRCT_NGs) using multimodal data across different cohorts of patients, PDX, and cell line data. We evaluated bulk and single-nucleus RNA sequencing of patient specimens from MD Anderson Cancer Center, revealing the robust ability for DSRCT_NGs to distinguish FP-positive DSRCT from samples failing detection of the EWS::WT1 FP. To elucidate the regulatory role of the EWS::WT1 FP in driving NG expression, we performed knockdown experiments in four DSRCT cell lines. This consistently resulted in a reduction of DSRCT_NG expression. Isoform-specific expression of EWS::WT1 in LP9 and MeT-5A mesothelial cells revealed that the E–KTS isoform of EWS::WT1 predominantly drives DSRCT_NG expression. Mechanistically, ATAC-seq and ChIP-seq analyses demonstrated that EWS::WT1 directly binds to accessible chromatin regions near NG transcription start sites, enriched for WT1 motifs and active histone marks. Integration of Hi-ChIP data further revealed that EWS::WT1 facilitates long-range enhancer-promoter looping at DSRCT_NG loci, promoting the expression of nearby genes. Collectively, these findings establish DSRCT_NGs as direct transcriptional outputs of the EWS::WT1 FP and implicate their loci as regulatory regions of the DSRCT transcriptome. Their fusion-dependent expression, chromatin accessibility, and promoter-enhancer connectivity underscore their potential utility as highly specific biomarkers and therapeutic targets in DSRCT.

Muscle-invasive bladder cancer (MIBC) is clinically heterogeneous, and current molecular subtyping does not capture the spatial organization of tumor states and microenvironmental context. Here, we construct a spatial atlas of MIBC by integrating spatial transcriptomics from 22 tumors with matched bulk RNA and whole-exome sequencing data. We identify a continuous, spatially organized luminal-to-basal axis within individual tumors that is associated with greater chromosomal instability and transcriptional plasticity. Luminal tumor cores are enriched for FGFR3 and NECTIN4, whereas basal-like states localize toward invasive margins and are associated with elevated EGFR signaling, epithelial–mesenchymal transition, genomic instability, immune infiltration, and greater chemotherapy sensitivity. Spatial analyses further reveal lineage- and location-associated differences in tertiary lymphoid structure states. Pan-cohort analyses across over 3,000 tumors confirm conserved FGFR3–EGFR lineage exclusivity and associated immune programs. Together, these findings define a spatial framework for understanding lineage states, immune architecture, and therapeutic vulnerabilities in MIBC.

Purpose: SMARCB1-deficient renal medullary carcinoma (RMC) is an ultrarare, lethal malignancy refractory to therapies approved for other renal cell carcinomas, and its rarity makes randomized trials logistically unfeasible. We investigated whether wild-type (WT) epidermal growth factor receptor (EGFR) is a therapeutically actionable dependency in RMC and translated this insight into a deployable clinical regimen. Experimental Design: EGFR expression was assessed by Clinical Laboratory Improvement Amendments–certified immunohistochemistry in RMC tumors and by integrated RNA and chromatin immunoprecipitation sequencing of primary tumors and adjacent kidney. Panitumumab was compared with erlotinib in patient- and cell line–derived xenografts, and its mechanism defined by immunoblotting, confocal co-localization, cell-cycle and apoptosis assays, and natural killer (NK) cell coculture. Panitumumab-based therapy was then evaluated prospectively in 26 patients with RMC across 10 centers on two continents. Results: RMC showed uniformly high membranous EGFR (median H-score 300), with enhancer and promoter reprogramming at the EGFR locus and a ligand switch from EGF to epiregulin and amphiregulin. EGFR expression was uncoupled from SMARCB1 status in vitro. Panitumumab outperformed erlotinib in RMC xenografts, suppressed AKT and ERK1/2 signaling, and routed EGFR to LAMP1-positive lysosomes in vitro; its effect was predominantly cytostatic, with minimal NK cell–mediated cytotoxicity. Clinically, panitumumab-based therapy achieved a 53.9% objective response rate, including 15.4% complete responses, with median progression-free and overall survival rates of 5.8 and 9.5 months, respectively. Conclusions: WT EGFR is a foundational dependency in RMC that is effectively targeted by panitumumab-based therapy. These findings, derived from a nonrandomized registry, provide a biological and clinical rationale for further prospective validation.

Purpose: Ablative radiotherapy (RT) improves clinical outcomes in patients with unresectable intrahepatic cholangiocarcinoma (ICC). Applicability to “supermassive” ICC remains uncertain given smaller tumor diameters in previous studies. We hypothesize that supermassive ICCs are not mutationally or histopathologically different from nonsupermassive ICCs and so would respond favorably to ablative RT. Experimental Design: This is a retrospective study of patients with supermassive ICC treated at the University of Texas MD Anderson Cancer Center (MDACC) and the National Cancer Database (NCDB). Patients treated at MDACC with unresectable ICC, ≥10 cm in diameter, treated with ablative RT or chemotherapy alone were included. Among NCDB patients, patients treated with chemotherapy alone were included. We analyzed overall survival (OS), tumor-related liver failure (TRLF), and treatment toxicity. We further analyzed mutational status and histopathology in supermassive and nonsupermassive ICC tumors. Results: We identified 63 patients treated at MDACC. Patients treated with RT showed improved OS compared with patients treated with chemotherapy alone (median OS: 28.7 vs. 11.9 months; adjusted HR = 0.4; P = 0.02). Patients treated with chemotherapy alone had a higher rate of TRLF compared with those who received RT (47.1% vs. 12.1%; P = 0.01). The RT cohort had improved OS compared with a frequency-matched NCDB chemotherapy-only cohort of supermassive ICC (37.6 vs. 8.9 months, P < 0.001). No major differences in mutational status or histopathology were noted between supermassive and nonsupermassive ICC tumors. Conclusions: Patients with supermassive ICC did not show a distinct mutational or histopathologic profile compared with those with nonsupermassive ICC and had promising outcomes with manageable toxicity when treated with ablative RT.

Background/Objectives: Uveal melanoma is the most common primary ocular cancer in adults. Patients with metastatic uveal melanoma (mUM) have limited treatment options and poor prognosis. mUM is characterized by high oxidative phosphorylation (OXPHOS), which may be a therapeutic vulnerability for this disease. ONC206 is an imipridone compound that can inhibit OXPHOS indirectly and is currently being evaluated in clinical trials. Thus, we tested the effects of ONC206 on human uveal melanoma cell lines and patient-derived xenografts (PDXs) in vitro and in vivo. Methods: The effects of ONC206 on cell survival, apoptosis, autophagy, oncogenic signaling pathways, and metabolic networks were assessed in vitro using human melanoma cell lines. ONC206 was then tested for safety and anti-tumor activity in vivo using two mUM PDX models. Results: ONC206 treatment produced dose-dependent inhibition of mUM cell growth in vitro, with induction of varying levels of apoptosis and autophagy. ONC206 treatment also downregulated OXPHOS effector proteins and metabolites, thereby impairing mitochondrial OXPHOS. Treatment with ONC206 significantly reduced tumor burden and improved survival in two UM PDX mouse models in vivo. Conclusions: Our findings position ONC206 as a mechanistically distinct agent to target mitochondrial metabolism and to inhibit mUM. As ONC206 is currently being evaluated in multiple clinical studies, our data support further evaluation as a potential new therapeutic strategy for mUM.