Alexander Joseph Lazar

ATRX is one of the most frequently altered genes in sarcoma and encodes an ATP-dependent chromatin remodeler implicated in maintaining heterochromatin. However, ATRX alterations have not been leveraged for sarcoma treatment. We observed loss of ATRX protein in 14% of soft tissue leiomyosarcoma (STLMS, n =127), 53% of uterine leiomyosarcoma (ULMS, n = 95), 37% of undifferentiated pleomorphic sarcoma (UPS, n = 82), and 8% of dedifferentiated liposarcoma (DDLPS, n = 84). ATRX loss was associated with significantly worse outcomes in ULMS, UPS, and DDLPS. ATRX knockout in sarcoma cells increased proliferation in cooperation with TP53 deletion, chromatin remodeling, and enrichment of PRDM4 and NFIX transcription factor motifs. PRDM4 and NFIX knockdown in ATRX -mutant sarcoma lines resulted in reduced proliferation and invasion, suggesting an epistatic relationship. Consistent with the known and re-demonstrated functional relationship between PRMD4 and YAP1, ATRX loss activated YAP1-TEAD signaling, and ATRX -deficient cells and sarcoma xenografts were more sensitive to the TEAD inhibitors VT103 and IAG933. Overall, our results identify ATRX loss as a prognostic factor of worse outcomes, implicate the ATRX-PRDM4-YAP1-TEAD axis as an underlying mechanism, and suggest use of TEAD inhibition as a potential therapeutic strategy for ATRX -deficient sarcomas.

Supplementary Figures and Tables

The 6th edition of the World Health Organization Classification of Soft Tissue and Bone Tumors (STB6) integrates the latest scientific and molecular discoveries with decades of pathological expertise to establish a globally accepted common language for diagnosis and clinical behavior. In this volume, the “essential” and “desirable” diagnostic criteria have been refined, considering different resource settings, ensuring accuracy while maintaining flexibility. A tumor type (entity) is a tumor in which multiple parameters (eg, clinical, histopathological, and/or genetic features) differ from those of other tumor types. In total, 19 new entities met these criteria and were added. A subtype is different in at least one dimension from the main tumor type (clinical, histopathological, or genetic), preferably resulting in a different treatment or outcome. A morphological pattern (no longer “variant”) is important for pathologists to be aware of to facilitate recognition but is not associated with different clinical behavior. The classification was drafted by 203 editors and authors from 27 countries, representing genetics, medical oncology, surgical oncology, orthopedic surgery, and radiology, in addition to pathology. STB6 includes soft tissue tumors (n=116), bone tumors (n=46), vascular tumors of soft tissue and bone (n=18), undifferentiated spindle and round cell sarcomas (n=4), hematopoietic and dendritic cell neoplasms (n=6), and genetic syndromes (n=6). In total, 62 sarcomas are included. A consensus was reached among the expert editorial board. In this review, we highlight changes in tumor classification in STB6, including recently described tumor types, novel diagnostic markers, recent discoveries in molecular genetics, and improvements in prognostication.

Neoadjuvant immune checkpoint inhibitors (ICIs) improve event-free survival in metastatic melanoma, yet resistance and recurrence remain common. Here we evaluated pepinemab, a Semaphorin 4D (SEMA4D)–blocking antibody, in combination with anti-PD1 nivolumab and/or anti-CTLA4 ipilimumab in a pilot biomarker-driven neoadjuvant trial (NCT03769155) for patients with resectable metastatic melanoma. The primary endpoint was to determine if pepinemab combined with ICIs modulates phenotypic properties within the tumor microenvironment in a manner that enhances T effector cell infiltration. Secondary endpoints included safety and tolerability, pathological response rates and radiographical response. Patients received two neoadjuvant doses followed by curative-intent surgery and one year of adjuvant nivolumab. Pepinemab-containing regimens demonstrated manageable toxicity profiles and did not delay or preclude curative-intent surgical resection in the 38 patients treated. The trial met its primary endpoint, as enrichment of transcripts associated with activated dendritic cells and immune recruitment pathways was observed in tumors from patients receiving pepinemab-containing regimens. Further, immune remodeling was evident by formation of mature lymphoid aggregates resembling tertiary lymphoid structures that contained clonally expanded T cell receptor repertoires. While this study was not powered to assess clinical efficacy, our findings do support further evaluation of SEMA4D blockade as a strategy to modulate the tumor microenvironment and potentially augment immunotherapy in melanoma and other solid malignancies.

Supplementary Methods file contains extended methods, including the processing and analysis of multiple sequencing datasets.

Supplementary Tables file contains key information and supporting datasets. Table S1 | Clinicopathological features of the 22 MIBC patients. Table S2 | The top 50 most significantly differentially expressed genes between the 15 single cell clusters. Table S3 | GSEA pathway enrichment results for 4 spatial clusters. Table S4 | Clinical characteristics and spatial tumor state composition across samples. Table S5 | Bootstrap-based robustness analysis of spatial tumor state proportions. Table S6 | The top 50 most significantly differentially expressed genes between the 4 spatial clusters.

Supplementary Figures file contains Supplementary Figures S1–S15. Figure S1 | Pathology-guided spatial annotation across 22 MIBC tumors. Figure S2 | Validation of spatial deconvolution accuracy and cell-type compartmentalization. Figure S3 | Additional tumors demonstrating spatial CNV-based subclones and transcriptional divergence. Figure S4 | Cross-platform concordance of CNV profiles inferred from spatial transcriptomics and WES. Figure S5 | Transcriptional and functional features across the luminal-to-basal differentiation continuum. Figure S6 | Single-cell analysis recapitulates the spatial luminal-to-basal differentiation continuum. Figure S7 | Spatial validation of lineage-associated EGFR and FGFR3 expression patterns. Figure S8 | Lineage-associated expression of FGFR3–EGFR signaling and transcriptional regulators across normal tissue, tumor states, and independent cohorts. Figure S9 | Pathology-guided spatial annotation across all MIBC tumors. Figure S10 | Spatial tumor states associate with chemotherapy response and stress-related gene expression. Figure S11 | NECTIN4 expression is enriched in luminal tumors and declines at the tumor-normal boundary. Figure S12 | Subtype-associated genomic alterations and their relationship with basal program activity. Figure S13 | Associations between basal signature scores and clinical or molecular features across MIBC cohorts. Figure S14 | Pathologist-guided TLS annotation confirms spatial transcriptomic predictions. Figure S15 | Lineage-associated chemokine programs and tumor–TLS interactions.

Objectives: Synovial sarcoma (SS) mostly arises in the extremities, yet data focused exclusively on primary extremity tumors remain limited. Therefore, we evaluated survival outcomes in patients with localized extremity SS treated at a large sarcoma referral center. Methods: A retrospective chart review of patients diagnosed with primary extremity SS between 2000 and 2020 with localized disease was conducted. Overall survival (OS), local recurrence-free survival (LRFS), and metastasis-free survival (MFS) were evaluated. Results: The study included 287 patients (median age: 35 y; follow-up: 5.3 y). Most tumors arose in the lower extremity (75%), and the median tumor size was 6 cm (range: 0.4 to 24). The median OS was 14 years, with a 10-year OS of 57%. Ten-year LRFS was 76%, and 10-year MFS was 51%. Tumors ≥5 cm (aHR: 2.06, 95% CI: 1.12-3.79), and the poorly differentiated subtype (aHR: 1.93, 95% CI: 1.01-3.69) were associated with inferior OS. For LRFS, positive/unknown margins were strongly associated with elevated local-recurrence risk (aHR: 4.09, 95% CI: 2.30-7.28), whereas perioperative radiation therapy significantly improved LRFS (aHR: 0.38, 95% CI: 0.22-0.68). For MFS, in a subgroup of patients with tumors ≥4 cm, perioperative chemotherapy was independently associated with improved MFS (aHR: 0.54, 95% CI: 0.34-0.86). Conclusions: Outcomes in extremity SS are driven by tumor size, subtype, and margin status. Perioperative radiation is recommended as it is associated with superior local control, and perioperative chemotherapy is highly recommended, particularly in patients with a tumor size of ≥4 cm, as it is associated with improved MFS.

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.