Ontological analyses reveal clinically-significant clear cell renal cell carcinoma subtypes with convergent evolutionary trajectories into an aggressive type

Abstract

Background: Clear cell renal cell carcinoma (ccRCC) is a particularly challenging tumor type because of its extensive phenotypic variability as well as intra-tumoral heterogeneity (ITH). Clinically, this complexity has been reduced to a handful of pathological variables such as stage, grade and necrosis, but these variables fail to capture the breadth of the disease. How different phenotypes affect patient prognosis and influence therapeutic response is poorly understood. Extensive ITH illustrates remarkable plasticity, providing a framework to study tumor evolution. While multiregional genomic analyses have shown evolution from an ancient clone that acquires metastatic competency over time, these studies have been conducted agnostic to morphological cues and phenotypic plasticity. Methods: We established a systematic ontology of ccRCC phenotypic variability by developing a multiscale framework along three fundamental axes: tumor architecture, cytology and the microenvironment. We defined 33 parameters, which we comprehensively evaluated in 549 consecutive ccRCCs retrospectively. We systematically evaluated the impact of each parameter on patient outcomes, and assessed their contribution through multivariate analyses. We measured therapeutic impact in the context of antiangiogenic therapies. We applied dimensionality reduction by t-distributed stochastic neighbor embedding (t-SNE) algorithms to tumor architectures for the study of tumor evolution superimposing tumor size and grade vectors. Evolutionary models were refined through empirical analyses of directed evolution of tumor intravascular extensions, and metastatic competency (as determined by tumor reconstitution in a heterologous host). Findings: We discovered several novel ccRCC phenotypes, developed an integrated taxonomy, and identified features that improve current prognostic models. We identified a subset of ccRCCs refractory to anti-angiogenic therapies. We developed a model of tumor evolution, which revealed converging evolutionary trajectories into an aggressive type. Interpretation: This work serves as a paradigm for deconvoluting tumor complexity and illustrates how morphological analyses can improve our understanding of ccRCC pleiotropy. We identified several subtypes associated with aggressive biology, and differential response to targeted therapies. By analyzing patterns of spatial and temporal co-occurrence, intravascular tumor extensions and metastatic competency, we were able to identify distinct trajectories of convergent phenotypic evolution.

Pancreatic tropism of metastatic renal cell carcinoma

“…These analyses centered on the UTSW cohort (n = 18), for which extensive pathology slides were available. While ccRCC are notoriously heterogeneous and multiple architectures have been reported (19,20), we found that 83% of primary tumors were dominated by a single architecture -small, compact nests ( Figure 2A). In contrast, a dominant compact nest pattern was found in only 25% of primary tumors leading to metastases outside the pancreas (P < 0.0001).…”

“…The compact, small nest pattern consists of well-circumscribed, small acini of tumor cells with clear cytoplasm, compact nuclei, and indistinct, low-grade nucleoli. This pattern is characteristically associated with low-grade tumors and is the predominant pattern in nonmetastatic ccRCC (47% of primary tumors without metastases) (20). The pattern is quite different from more aggressive patterns found in metastatic RCC patients without PM ( Figure 2C).…”

“…The morphologic architecture, cytologic pattern, and tumor microenvironment in each sample were centrally reviewed and characterized by a genitourinary pathologist after preparing H&E-stained slides. Morphologic patterns were evaluated according to a recently developed classification system that correlates with tumor aggressiveness and prognosis (20).…”

Altered Tissue and Plasma Levels of Fibroblast Activation Protein-α (FAP) in Renal Tumours

“…The current state of the art in the diagnosis relies on the histologic findings and immunohistochemical profile of the tumours. Since radiotherapy and chemotherapy are inefficient therapies in renal tumours, only surgery has demonstrated a real impact in improving patients’ survival [ 3 , 4 ]. Then, RCC is far from being a single disease and research to discover new tumour markers of clinical significance is needed.…”

“…Due to its phenotypic variability and intratumoural heterogeneity, CCRCC is considered to be one of the most challenging of human neoplasms [ 4 ]. Metastatic disease is present at diagnosis in around 30% of patients, and another third relapses and progresses to metastatic disease after nephrectomy [ 3 ].…”