The identification of defects in 3 fundamental determinants of antitumor immunity: reduced T-cell infiltration, phenotypically inappropriate CD8-positive T cells, and a lack of tumor-specific T-cell responses in chromophobe renal cell carcinoma (RCC) differentiate this histologic subtype from clear cell RCC and may account for the limited efficacy of existing immunotherapies in this rare histology, according to David A. Braun, MD, PhD.1,2
Results from a translational study published in the Journal of Clinical Oncology showed decreased immune infiltration in chromophobe RCC vs clear cell RCC (Wilcoxon P = .007), including a marked depletion of the proportion of tumor-infiltrating CD8-positive T cells from 44.6% in clear cell RCC to 9.6% in chromophobe RCC (Fisher’s exact P < .001). Immunohistochemistry evaluation showed lower immune checkpoint (ICI) expression, diminished clonal expansion, and decreased specificity of tumor-infiltrating CD8-positive T cells in chromophobe RCC.
Additional findings identified alpha intercalated cells as the cellular origin of renal oncocytic neoplasms, downregulation of HLA class I molecules, and the enrichment of potentially targetable pathways, such as ferroptosis and rapamycin.
“What this study suggests is that [chromophobe and clear cell RCC] really do have different biologies, and it’s critical to include that in our way of thinking,” said Braun, an assistant professor of medical oncology, Louis Goodman and Alfred Gilman Yale Scholar, and member of the Center of Molecular and Cellular Oncology at Yale Cancer Center in New Haven, Connecticut. “Essentially, chromophobe RCC is defective in all 3 of those critical axes that you need for an effective T-cell response.”
In an interview with OncLive®, Braun discussed the importance of understanding the unique biology and immune phenotypes of varying kidney cancer histologies; described how machine learning and single-cell RNA sequencing were leveraged for deep molecular characterization; and shared results from the study that elucidate the basic biology, oncogenesis, and mechanisms of immune evasion of these tumors.
Braun expanded on the implications and next steps for this research in a subsequent article.
OncLive: What was the rationale for evaluating tumor-intrinsic determinants of effective antitumor immunity for chromophobe RCC vs clear cell RCC?
Braun: Many groups that study the biology and immunology of kidney cancer have largely focused on clear cell RCC, the most common type of kidney cancer. By far, it is the one we know the most about. However, when it comes to the clinic, there can be a lot of difficulty treating those less common kidney cancers; in part, that’s because we don’t understand their biology. Understanding the basic biology of these tumors is going to be critical for developing therapies.
We focused on a type of kidney cancer that has gotten much less attention, called chromophobe RCC,[as well as] a related group of oncocytic neoplasms. These are ones that people sometimes associate with having a very favorable prognosis. Although that’s true to some extent in a very localized or early disease setting, I know from personal experience that metastasized chromophobe RCC is among the most difficult [RCC subtypes] to treat. [These patients], at least anecdotally, seem like they respond poorly to our current ICIs.
The rationale for this study was to try to understand the biology of these tumors, the cells that they come from, and their immune interactions, so that we might be able to learn why current therapies do or do not work and ultimately guide future therapeutic development.
What methods and tools were utilized to compare and contrast tumor characteristics, composition, and immune responses in this study?
The idea behind this was to take a small group of tumor samples from patients with chromophobe kidney cancer–related oncocytic neoplasms and do a deep dive into the biology and molecular characterization of these tumors. Thinking about this as a spectrum, we had a tumor that was a benign entity in an oncocytoma, so a benign oncocytic neoplasm. We had something that was a little bit in between, called a low-grade oncocytic tumor, which was something with malignant potential, but very little. It typically does not cause much in the way of problems, [although] it does have invasive behavior. Then we had true renal cell carcinomas, chromophobe renal cell carcinomas, that are malignant, metastasize, and can cause problems.
We used single-cell RNA sequencing in our lab. Rather than taking a tumor that is composed of a complex and heterogeneous population of different cells—not just the tumor cells, but also different immune cells, fibroblasts, and endothelial cells—we broke it down to individual cells and sequenced one cell at a time. We did single-cell RNA sequencing to understand the composition of those tumors, where they come from, and how that might inform whether they do or do not respond to immune therapy.
For each of these tumors, we performed single-cell RNA sequencing, sequenced the T-cell receptors for the T cells that were there, and also sequenced some normal kidneys that were adjacent to or next to the tumors. The goal was to learn where these cells come from and how their immune microenvironments are similar to or different from other forms of kidney cancer.
What specific aspects of immune response were evaluated, and why were they chosen?
[Several] axes of the immune system were markedly different in chromophobe vs clear cell RCC. Using the International Metastatic RCC Database Consortium, [IMDC], we looked at patients who were treated in the first-line setting with ICIs, and we saw that [those with] chromophobe tumors did substantially worse than those with clear cell RCC. [This was] not true for VEGF inhibitors. In fact, the opposite pattern [emerged] for mTOR inhibitors. [We then] questioned: why are they not responding to ICIs nearly as well? One reason is that [the chromophobe RCC tumor cells] actively downregulate their class I machinery and hide from the immune system. But when we think of the ingredients you need to form an effective immune response, [there are] 3 big points. We have to have T cells present, they have to be the right phenotype, meaning they have to express the receptors that we’re targeting, and they have to have the right specificity. We know that T cells have very specific targets that they recognize; just because T cells are in the tumor doesn’t mean they’re capable of recognizing the tumor. They could be bystanders. They could be there very nonspecifically, and they’re a T cell that recognizes the flu virus or some old viral infection, in which case they’re not helpful. Those are the 3 axes that we explored in this study.
Which of these determinants were found to impair immune responses in chromophobe RCC?
We contrasted [chromophobe RCC] with a more common type, which is clear cell RCC. We found that in each of those 3 axes, there was a severe immune defect within chromophobe RCC. The first is that there were fewer immune cells there to begin with than clear cell RCC, but even among the few immune cells that were there, and even lower proportion were CD8-positive T cells, which we think of as being the sort of most beneficial cells for antitumor immunity. There were virtually no CD8-positive T cells to begin with. That’s one problem.
Second, when we looked at the CD8-positive T cells that were there, they were the wrong phenotype. They were not expressing PD-1 or any other immune checkpoint receptors, and so they look like they wouldn’t be necessarily capable of responding to an anti–PD-1 agent. We validated that using a larger-scale dataset within The Cancer Genome Atlas.
The last question is whether they are actually tumor-specific. We use a number of different sorts of approaches for this, looking at the clonality of the T-cell receptors and looking at signatures for tumor specificity or bystander effects. [This confirmed that] the few T cells that are there are not only the wrong phenotype, but they’re actually largely bystanders and are not capable of recognizing the tumor.
How was machine learning utilized to identify the cells of origin for chromophobe RCC and related oncocytic neoplasms? What findings did this elucidate?
A key question is, where do these cells come from? Where do they originate? For certain common types of kidney cancer, such as clear cell RCC, the most common type, or papillary RCC, the second most common type, it is known that these arise from proximal tubule epithelial cells, which are located early in the tubule of the normal kidney. There were some thoughts, certainly, that chromophobe RCC arises from the distal tubule.
In this study, a combination of single-cell RNA sequencing and a machine learning–based approach was used to pinpoint the exact cell of origin for these tumor cells and related oncocytic neoplasms. The findings showed that they were most highly similar to, or related to, the alpha intercalated cell, [which is] a relatively rare subtype of cells within the distal tubule of the kidney.
This is important for several reasons. First, it helps in understanding the basic biology of these tumors and their origins. Second, it provides insight into the programs, genes, and gene expression pathways responsible for oncogenesis, tumor behavior, and potentially immune evasion. Once the cell of origin was identified, it became possible to determine which genes and gene programs differed in the tumor cells compared with the alpha intercalated cell.
Using the machine learning–based approach, it was found that there was much higher activity in certain signaling pathways, such as mTOR signaling, which could have therapeutic implications given the role of mTOR inhibitors in kidney cancer. Additionally, there was a marked downregulation of antigen presentation, particularly of HLA class I molecules, suggesting that the tumors might be actively evading or hiding from T cells. This combined approach of single-cell RNA sequencing, machine learning, and comparative analysis with the cell of origin provides critical insights into tumor biology and potential therapeutic strategies.
References
- 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
- Hazell, N. Novel insights into chromophobe renal cell carcinoma biology and potential therapeutic strategies. News Release. Yale School of Medicine. July 2, 2025. Accessed August 13, 2025. https://medicine.yale.edu/news-article/novel-insights-into-chromophobe-renal-cell-carcinoma-biology-and-potential-therapeutic-strategies/