Quantifying T- and B-cell immune receptor distribution diversity to uncover their clinical relevance in clear cell renal cell carcinoma

Immune-modulating systemic therapies are often used to treat metastatic clear cell renal cell carcinoma (ccRCC). Used alone, sequence-based biomarkers neither accurately capture patient dynamics nor the tumor-immune microenvironment. To better understand the tumor ecology of this immune microenvironment, we used complementarity determining region-3 (CDR3) sequence recovery counts of the tumor infiltrating lymphocytes, and quantified tumor infiltration by sequences recovered from patient tumors by applying a generalized diversity index (GDI) to CDR3 sequence distributions across two distinct ccRCC cohorts. GDI can be understood as a curve over a continuum of diversity scales and allows sensitive characterization of distributions to capture richness, evenness, and subsampling uncertainty, along with other important metrics. For example, richness quantifies the total unique sequence count, while evenness quantifies similarities across sequence frequencies. We observed significant differences in receptor sequence diversity across gender and race. Further, our analysis revealed that patients with larger and more clinically aggressive tumors had increased richness of recovered tumoral CDR3 sequences, specifically in those from T-cell receptor alpha and B-cell immunoglobulin lambda light chain. We identified a novel and robust measure of distribution evenness, using GDI's inflection point (IP). High IP values associated with improved overall survival, suggesting that normal-like sequence distributions lead to better outcomes. Our results propose a new quantitative tool that can be used to better characterize patient-level differences related to immune cell infiltration and, can be used to identify unique characteristics of tumor-infiltrating lymphocyte heterogeneity in ccRCC and other malignancies.