Andrew Katims, MD, MPH, urologic oncology fellow, Memorial Sloan Kettering Cancer Center, discusses the feasibility of using single-cell RNA-sequencing (scRNA-seq) in 

-mutated upper tract urothelial carcinoma.

At the 2023 American Urological Association Annual Meeting, Katims and colleagues presented findings from an investigation on the use of scRNA-seq to characterize the immune phenotype of 

-mutated upper tract urothelial carcinoma. Using 7 individual tissue samples obtained from patients who were treatment naïve, researchers identified 19 immune cell clusters with unique biologic functions, including 8 T-cell clusters, which were categorized into 

-mutated disease had a T-cell phenotype characterized by a high frequency of active/exhausted Th17-like CD4 cells, lower levels of regulatory T cells, and increased amounts of CD8/cytotoxic cells in naïve state.

Although single-cell sequencing currently has a role in a research setting, it is not practical to use in a clinical setting at this point, Katims explains. He notes that several factors currently limit the practicality of scRNA-seq in a clinical setting, including its high cost.

However, the costs of bulk RNA sequencing are steadily falling, and results from bulk testing have been similar to those seen with scRNA-seq, Katims continues. Although scRNA-seq can provide a more granular picture, the targeted gene sequencing, followed by RNA sequencing, appear to be the current trajectory for testing patients with upper urothelial tract carcinoma, Katims notes. scRNA-seq could have a role; however, it will be important to validate these results in bulk RNA sequencing, which can be more affordable and have a more practical clinical application, Katims concludes.

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Andrew Katims, MD, MPH, discusses the feasibility of using single-cell RNA-sequencing in FGFR3-mutated upper tract urothelial carcinoma


Dr Katims on the Feasibility of scRNA-seq in FGFR3+ Upper Tract Urothelial Carcinoma

Andrew Katims, MD, MPH, urologic oncology fellow, Memorial Sloan Kettering Cancer Center, discusses the rationale for investigating immune responses in the tumor microenvironment of 

-mutated upper tract urothelial carcinoma using single-cell RNA-sequencing (scRNA-seq).

At the 2023 American Urological Association Annual Meeting, findings from a study utilizing scRNA-seq to better characterize the immune phenotype of upper tract urothelial carcinoma showed that 19 immune cell clusters with unique biologic functions were identified, including 8 T-cell clusters, which were categorized into 

-mutated disease had a T-cell phenotype characterized by a high frequency of active/exhausted Th17-like CD4 cells, lower levels of regulatory T-cells, and increased amounts of CD8/cytotoxic cells in naïve state.

Although prior research has been conducted to evaluate immune responses in the tumor microenvironment of bladder cancer, upper tract urothelial carcinoma is a unique disease state, Katims says. This is due to the disease’s different mutational patterns, responses to drugs, and origin, despite bladder cancer and upper tract urothelial carcinoma sharing the same cancer cell type, Katims explains.

The original goal of this study was to define the overall tumor microenvironment and immune phenotype of patients with all types of upper tract urothelial carcinoma who have not received chemotherapy, Katims expands. However, 

 mutations became the focus of the study because they are the most common mutation found in these patients. Additionally, there has been controversy surrounding what the 

mutations mean for the disease’s immune phenotype, Katims says.

–mutated upper tract urothelial carcinoma is T-cell depleted, explaining why there is not a robust response to immunotherapy, Katims continues. However, a more recent study demonstrated that it this tumor type is infiltrated with CD8+ T-cells. The most recent study aimed to get a clearer picture of the tumor microenvironment for 

–mutated upper tract urothelial carcinoma, Katims concludes.

Andrew Katims, MD, MPH, discusses the rationale for investigating immune responses in the tumor microenvironment of FGFR3-mutated upper tract urothelial carcinoma using single-cell RNA-sequencing.

Dr Katims on the Goal for Investigating the Immune Phenotype of FGFR3+ Upper Tract Urothelial Carcinoma

Andrew Katims, MD, MPH, urologic oncology fellow, Memorial Sloan Kettering Cancer Center, discusses research characterizing immune responses in the tumor microenvironment of 

Patients with upper tract urothelial carcinoma commonly harbor 

 mutations. As patients with this tumor type often experience poor responses to immune checkpoing blockade, 

 mutations have been implicated in the impairment of T-cell responses in the tumor microenvironment.

As such, a study utilizing scRNA-seq was performed to better characterize the immune phenotype of these tumors. Seven individual tissue samples were obtained from patients who were treatment naïve. The phenotype of defined cell clusters and immune composition in the tumor tissue was analyzed using scRNA-seq.

A total of 19 immune cell clusters with unique biologic functions were identified, including 8 T-cell clusters, Katims reports. Clusters were categorized into 

-unmutated samples, he states. Overall, patients with 

-mutated disease had a T-cell phenotype characterized by a high frequency of active/exhausted Th17-like CD4 cells, lower levels of regulatory T cells, and increased amounts of CD8/cytotoxic cells in naïve state.

Findings from this study were consistent with previous data showing that 

-mutated tumors are associated with high T-cell infiltration, Katims continues. This was particularly noted in cluster 3 of the CD8 compartment. CD8 cells were primarily in a naïve state and were associated with lower exhausted/active markers, lower rates of cytotoxic activity, leukocyte apoptotic process, and alpha-beta T-cell differentiation regulation, Katims states. Accordingly, the tumor microenvironment appears to be less robust in these patients. Moreover, the high level of plasma cell infiltration and Th17 in the CD4 compartment potentially signals the presence of tertiary lymphoid structures in these tumors, he adds.

Although findings from this study do indicate specific functional traits of various T-cell compartments in urothelial carcinoma, the large amount of data produced by scRNA-seq requires substantial analysis and should be used to ask many more clinically relevant questions, Katims explains. Ultimately, these data could ultimately inform efforts to activate T-cell response and maximize therapeutic benefit for these patients, Katims concludes.

Andrew Katims, MD, MPH, discusses research characterizing immune responses in the tumor microenvironment of FGFR3-mutated upper tract urothelial carcinoma using single-cell RNA-sequencing 

Dr Katims on Characterizing Immune Phenotype in FGFR3-mutated Upper Tract Urothelial Carcinoma 

Andrew Katims, MD, MPH, urologic oncology fellow, Memorial Sloan Kettering Cancer Center, discusses the utility of a circulating tumor (ct)DNA assay (MSK-ACCESS) in patients with node-positive muscle-invasive bladder cancer (MIBC).

ctDNA is associated with disease progression, worse overall survival, and recurrence in patients with bladder cancer. As such, investigators sought to evaluate whether ctDNA sequencing could be used to predict pathologic response to neoadjuvant chemotherapy and metastatic recurrence in patients with node-positive MIBC undergoing radical cystectomy. Patients in the trial provided plasma samples, which were collected before, during, and after neoadjuvant chemotherapy, and 3 months following radical cystectomy. The samples were evaluated using MSK-ACCESS, an ultrasensitive ctDNA assay designed to identify somatic mutations in 129 cancer-associated genes.

The results indicated that the sensitivity of the assay in detecting disease was high, Katims says. Specifically, 80% of patients with node-positive disease had detectable ctDNA, and 90% of patients with metastatic disease had detectable ctDNA. When evaluated as a predictive biomarker, investigators demonstrated that the presence of ctDNA at any point during or after treatment with chemotherapy was a poor prognostic factor and was associated with shorter recurrence-free survival in both the localized and node-positive settings. These data support existing literature on the prognostic effect of ctDNA, Katims says.

Notably, positive ctDNA at the time of diagnosis was associated with pathologic nodal upstaging at the time of cystectomy. Moreover, in addition to seeing whether ctDNA is present or absent from the blood with a positive or negative result, the assay was also able to identify targetable gene mutations like 

, which distinguishes it from other from commercial assays on the market, Katims concludes.

Andrew Katims, MD, MPH, discusses the utility of a circulating tumor DNA assay (MSK-ACCESS) in patients with node-positive muscle-invasive bladder cancer.
 

Andrew Katims, MD, MPH

Articles

Dr Katims on the Feasibility of scRNA-seq in FGFR3+ Upper Tract Urothelial Carcinoma

Dr Katims on the Goal for Investigating the Immune Phenotype of FGFR3+ Upper Tract Urothelial Carcinoma

Dr Katims on Characterizing Immune Phenotype in FGFR3-mutated Upper Tract Urothelial Carcinoma

Dr Katims on the Utility of the MSK-ACCESS Assay in Node+ MIBC