Chromophobe renal cell carcinoma (RCC) was shown to have an immune-cold environment that impedes patient response to immunotherapy, although ferroptosis induction may be a promising target for managing tumor resistance in this subtype, according to findings from a study of the tumor-intrinsic and microenvironmental mechanisms of impaired antitumor immunity in patients with chromophobe RCC, which were published in the Journal of Clinical Oncology.
Investigators found that α-intercalated cells (ICA) are the cellular origin of renal oncolytic neoplasms. Additionally, HLA class I molecule downregulation occurs in chromophobe RCC, coupled with the enrichment of pathways that may be targetable, such as ferroptosis and rapamycin.
Furthermore, following the tumor microenvironment (TME) of chromophobe RCC was shown to have decreased immune infiltration compared with that of clear cell RCC (ccRCC; Wilcoxon P = .007), including a marked depletion of the proportion of tumor-infiltrating CD8-positive T cells (9.6% vs 44.6% in ccRCC; Fisher’s exact P < .001). The proportion of CD4-positive T cells was also lower in chromophobe RCC (3.2%) vs ccRCC (12.3%; Fisher’s exact P < .001). Conversely, chromophobe RCC displayed a higher proportion of B-lineage (20.6% vs 1.4%; Fisher’s exact P < .001) and myeloid (34.7% vs 17.7%; Fisher’s exact P < .001) cells compared with ccRCC. These findings demonstrate the distinct tumor-infiltrating immune repertoire of chromophobe RCC.
Notably, an immunohistochemistry (IHC) evaluation of 4 chromophobe RCC samples and 3 ccRCC samples showed that chromophobe RCC–infiltrating CD8-positive T cells had lower immune checkpoint expression, as well as decreased tumor specificity and clonal expansion compared with ccRCC cells, indicating that the few T cells that do exist in these disease subtypes are nonspecific bystanders, rather than active mediators of antitumor immunity. Additionally, the density ratio of PD-1 expression to CD8 expression trended lower in chromophobe RCC vs ccRCC (Wilcoxon P = .11), indicating that the CD8-positive T cells in chromophobe RCC have a distinct immune phenotype, including lower expression of PD-1, a clinically actionable immune checkpoint.
Moreover, a real-world clinical analysis showed that patients with metastatic chromophobe RCC who received immune-based therapies had poor survival outcomes compared with patients with ccRCC.
“Our study confirms the cellular origin of chromophobe RCC and identified several differentially expressed pathways, supporting the investigation of new targets for chromophobe RCC therapy, including ferroptosis, mTORC1 signaling, and IL-15 signaling,” lead study author Chris Labaki, MD, and coauthors wrote. “Our work also provides the first in-depth look at the immune characteristics of chromophobe RCC and renal oncolytic tumors, identifying key areas of immune dysfunction that provide a mechanistic basis for the poor responses to ICI therapies observed in chromophobe RCC.”
Labaki is an internal medicine resident at Beth Israel Deaconess Medical Center and a research associate at Dana-Farber Cancer Institute and the Broad Institute of Massachusetts Institute of Technology and Harvard in Boston, Massachusetts.
Summarizing the Study Rationale
Chromophobe RCC is the second most common type of non-ccRCC and is associated with poor clinical outcomes compared with other RCC histologies. Although immune checkpoint inhibition is a standard of care (SOC) for patients with metastatic ccRCC, these regimens have not been as effective in patients with advanced chromophobe RCC, although this has only been studied in small patient populations. Overall, however, the optimal treatment strategy for patients with chromophobe RCC is an unmet need for this population, partly because the underlying biology of the disease is poorly understood.
Although prior studies have attempted to define the TME and phenotypic states of immune cell populations in chromophobe RCC and renal oncolytic tumors, these are still not well characterized. In addition, the exact cellular origin of these diseases has not been comprehensively identified.
Due to these unanswered questions, investigators conducted a study to evaluate the tumor-intrinsic and immune microenvironment characteristics of chromophobe RCC and renal oncolytic neoplasms, as well as determine the clinical outcomes of patients with advanced chromophobe RCC treated with systemic antineoplastic therapies.
Outlining the Study Design
Investigators performed single-cell transcriptomic and T-cell receptor profiling on fresh tumor and adjacent healthy tissue specimens from 5 patients with chromophobe RCC and renal oncolytic neoplasms. Machine learning was used to evaluate the cellular origin of the renal oncolytic neoplasms and assess associated oncogenic pathways. Investigators also used IHC to compare immune infiltration between ccRCC and renal oncolytic neoplasms.
Additionally, the study compared immune checkpoint expression, tumor specificity, and clonal expansion between chromophobe RCC and ccRCC. Furthermore, the investigators used the IMDC dataset to compare clinical outcomes with first-line systemic therapies in patients with metastatic chromophobe RCC vs those with ccRCC.
Expanding on the Findings
Four of the 5 tumor samples included in this analysis originated from the primary kidney tumor. The other sample originated from a positive retroperitoneal lymph node for chromophobe RCC. At the time of sample collection, no patients had been treated with systemic antineoplastic therapies.
Inferred copy number variations (CNV) from scRNA sequencing (scRNA-seq) data showed full-chromosome deletions in the 3 chromophobe RCC samples, which is consistent with the known genomic profile of this disease. Conversely, the low-grade oncolytic tumors (LOT) and renal oncocytoma (RO) cells did not contain large CNV events, which was also consistent with previously reported findings.
The machine-learning analysis of scRNA-seq data from matched normal samples in the study cohort (n = 784) showed that the chromophobe RCC, RO, and LOT tumor cells shared the highest level of predicted similarity with ICA cells. External scRNA-seq data of chromophobe RCC cells further validated these findings.
Investigators then conducted a differential gene expression analysis between chromphobe RCC and its cell of origin (i.e., ICA cells) using scRNA-seq data to further understand the transcriptional changes related to chromphobe RCC tumorigenesis. The most upregulated genes in chromophobe RCC cells vs ICA cells were KLK1, NUPR1, FTL, and FTH1. Notably, NUPR1, FTL, and FTH1 have all been shown to inhibit ferroptosis, a key molecular axis in chromophobe RCC pathogenesis that may have therapeutic vulnerabilities.
The most downregulated genes in chromophobe RCC cells vs ICA cells were ADGRF5, HSPA1A, HSPA1B, HLA-A, HLA-B, HLA-C, HSPA8, HSPA5, and HSPA6. Notably, downregulation of HLA-A, HLA-B, HLA-C is associated with immunotherapy resistance. HSPA5, HSPA6, HSPA8, HSPA1A, and HSPA1B are known to suppress ferroptosis.
To determine whether the T cells present in chromophobe RCC had antitumor specificity to inform targeted therapy approaches, the investigators compared single-cell T-cell receptor sequencing profiling data from chromophobe RCC vs ccRCC samples. The proportion of unexpanded T-cell clones, which are usually observed when T cells do not encounter a cognate antigen, was significantly higher in chromophobe RCC vs ccRCC (P = .05). Furthermore, chromophobe RCC trended toward having a lower proportion of expanded clonotypes compared with ccRCC. These findings are evident of low tumor specificity in chromophobe RCC.
To further investigate the adaptive immune capabilities in chromophobe RCC, the investigators conducted an analysis of the isolated T-cell compartment in 12,688 chromophobe RCC and oncolytic tumor cells. This analysis showed that T cells that were isolated from chromophobe RCC and other renal oncolytic neoplasms had a low tumor-specific signature expression but a high viral-specific signature expression.
A signature expression assessment of CD8-positive T cells alone showed that chromophobe CD8-positive T cells had significantly decreased tumor-specific signature expression (Wilcoxon P < .001) and increased viral-specific signature expression (Wilcoxon P < .001) compared with ccRCC CD8-positive T cells. Similar expression patterns were seen regarding CD4-positive T-cell specificity across these 2 disease subtypes. These results support the finding that the T-cell infiltrate in chromophobe RCC cells has bystander properties.
Clinical Analysis Findings and Next Steps
Investigators then performed a clinical analysis using real-world data from the International metastatic RCC Database Consortium from 229 patients with chromophobe RCC; among these patients, 31 had received SOC immune checkpoint inhibitor (ICI)–based therapy, including dual ICI regimens (n = 12) or ICI/VEGF-targeted regimens (n = 19) in the frontline setting. This population was compared against a real-world population of 8931 patients with ccRCC, 856 of whom had received ICI-based therapies (dual ICI, n = 503; ICI/VEGF-targeted therapies, n = 353) in the first-line setting.
At a median follow-up of 58.6 months, patients with metastatic chromophobe RCC who had received ICI-based treatment achieved a median overall survival (OS) of 24.7 months (95% CI, 16.0-not reached [NR]) vs 50.5 months (95% CI, 42.5-67.4) in those with metastatic ccRCC (adjusted HR, 2.80; 95% CI, 1.51-5.18). The median time to treatment failure (TTF) was also worse in the chromophobe population, at 4.5 months (95% CI, 2.4-16.0) vs 11.0 months (95% CI, 9.8-13.6) in the ccRCC population (adjusted HR, 2.23; 95% CI, 1.43-3.48). The overall response rates (ORRs) in these respective populations were 12.0% vs 47.1% (adjusted odds ratio [OR], 95% CI, 2.95-64.84). No patients with metastatic chromophobe RCC who received first-line ICI therapy achieved a complete response compared with 4.9% of patients in the metastatic ccRCC population.
Notably, the investigators observed no major differences in survival outcomes between the 2 subgroups among patients who received frontline VEGF-targeted therapy. The median OS was 23.1 months (95% CI, 19.1-35.6) in the chromophobe population vs 26.4 months (95% CI, 25.5-27.7) in the clear cell population (adjusted HR, 1.25; 95% CI, 0.98-1.59). Moreover, the median TTF was 7.3 months (95% CI, 5.1-8.7) in the chromophobe subgroup vs 8.3 months (95% CI, 8.0-8.4) in the clear cell subgroup (HR, 1.25; 95% CI, 1.01-1.56).
Importantly, patients with metastatic chromophobe RCC who were treated with the first-line mTOR inhibitors everolimus (Afinitor) or temsirolimus (Torisel) achieved a higher median OS vs those with metastatic ccRCC, at 41.3 months (95% CI, 14.4-NR) vs 13.4 months (95% CI, 10.9-15.3), respectively (adjusted HR, 0.77; 95% CI, 0.48-1.25). Similarly, a median TTF benefit was observed in the chromophobe population at 7.84 months (95% CI, 5.29-16.6) vs 3.45 months (95% CI, 2.99-3.98) in the clear cell population (adjusted HR, 0.52; 95% CI, 0.33-0.82).
In general, OS and TTF outcomes were similar among patients with chromophobe RCC regardless of whether they received first-line ICI-based therapy, VEGF-targeted therapy, or an mTOR inhibitor.
“By identifying these key axes of immune dysfunction, these data provide a foundation for the rational design of future immunotherapy strategies for chromophobe RCC, including increasing tumor cell antigen presentation and expanding the repertoire of tumor-specific CD8-positive T cells that infiltrate the TME,” the authors concluded.
Reference
Labaki C, Saad E, Madsen KN, et al. Tumor-intrinsic and microenvironmental determinants of impaired antitumor activity in chromophobe renal cell carcinoma. J Clin Oncol. 2025;43(23):2639-2654. doi:10.1200/JCO-25-00234