Single-cell transcriptomic insights into tumor and immune dynamics driving resistance to ixazomib combined with gemcitabine and doxorubicin in SMARCB1-deficient renal medullary carcinoma

SMARCB1 -deficient renal medullary carcinoma (RMC) is a highly aggressive kidney cancer characterized by replication stress and proteotoxic vulnerabilities, yet the molecular determinants of therapy response remain poorly understood. To delineate the mechanisms of response and resistance, we performed integrative single-cell and bulk multi-omic profiling of tumor samples from patients with RMC treated with a combination of the proteasome inhibitor ixazomib, gemcitabine, and doxorubicin. Analysis of 33,410 single cells from 11 patients revealed pronounced intratumoral and microenvironmental heterogeneity. Responding tumors displayed immune-inflamed microenvironments enriched for CD8⁺ cytotoxic T cells, effector-like and Tfh CD4⁺ T cells, NK cells, plasmacytoid (pDC) and conventional dendritic cells (cDC1/cDC2), and S100A8 ⁺ monocytes, consistent with enhanced antigen presentation and effector activation. In contrast, non-responders exhibited abundant macrophages, regulatory T cells, plasma cells, and inflammatory and myofibroblastic cancer-associated fibroblasts (iCAFs/mCAFs), forming immunosuppressive stromal-myeloid circuits that impeded cytotoxic infiltration and response. Malignant cells segregated into six transcriptional states, including proliferative, hypoxia-responsive, epithelial-mesenchymal, and neuroendocrine-squamous hybrid lineages. A proliferative state marked by replication stress, unfolded-protein-response activation, and proteasome component upregulation was enriched in non-responders and persisted at progression, suggesting adaptive proteostasis-driven resistance. Copy-number analyses identified focal gains in BAG4 , UBE4B , and UBE2W that may enhance apoptosis evasion and p53 degradation, reinforcing proteotoxic resilience. In contrast, well-differentiated and immune-mimicry tumor states correlated with improved survival. Integrative cell-cell communication analysis highlighted stromal-immune signaling through BMP4/5 and WNT4/6 as a hallmark of resistant tumors, whereas BMP6 expression associated with dendritic-cell activation and favorable immune remodeling. Together, these findings define molecular and cellular programs underlying therapeutic response in RMC and nominate actionable stress-adaptation and stromal-immune circuits as potential targets for future biomarker-guided combination strategies.