High risk clear cell renal cell carcinoma microenvironments contain protumour immunophenotypes lacking specific immune checkpoints

Abstract

Perioperative immune checkpoint inhibitor (ICI) trials for intermediate high-risk clear cell renal cell carcinoma (ccRCC) have failed to consistently demonstrate improved patient outcomes. These unsuccessful ICI trials suggest that the tumour infiltrating immunophenotypes, termed here as the immune cell types, states and their spatial location within the tumour microenvironment (TME), were unfavourable for ICI treatment. Defining the tumour infiltrating immune cells may assist with the identification of predictive immunophenotypes within the TME that are favourable for ICI treatment. To define the immunophenotypes within the ccRCC TME, fresh para-tumour (pTME, n = 2), low-grade (LG, n = 4, G1-G2) and high-grade (HG, n = 4, G3-G4) tissue samples from six patients with ccRCC presenting at a tertiary referral hospital underwent spatial transcriptomics sequencing (ST-seq). Within the generated ST-seq datasets, immune cell types and states, termed here as exhausted/pro-tumour state or non-exhausted/anti-tumour state, were identified using multiple publicly available single-cell RNA and T-cell receptor sequencing datasets as references. HG TMEs revealed abundant exhausted/pro-tumour immune cells with no consistent increase in expression of PD-1, PD-L1 and CTLA4 checkpoints and angiogenic genes. Additional HG TME immunophenotype characteristics included: pro-tumour tissue-resident monocytes with consistently increased expression of HAVCR2 and LAG3 checkpoints; an exhausted CD8+ T cells sub-population with stem-like progenitor gene expression; and pro-tumour tumour-associated macrophages and monocytes within the recurrent TME with the expression of TREM2. Whilst limited by a modest sample size, this study represents the largest ST-seq dataset on human ccRCC. Our study reveals that high-risk ccRCC TMEs are infiltrated by exhausted/pro-tumour immunophenotypes lacking specific checkpoint gene expression confirming that HG ccRCC TME are immunogenic but not ICI favourable.

Microphysiological systems as models for immunologically ‘cold’ tumors

“…However, a notable proportion of patients experience disease progression shortly after initiating systemic treatment. Additionally, outcomes from adjuvant ICI trials for localized ccRCC have not shown improvements in survival ( Raghubar et al, 2023 ). These unsuccessful trials suggest that the types, states, and spatial distribution of tumor-infiltrating immune cells within the TME may not favor ICI treatment.…”

Spatial transcriptomics in cancer research and potential clinical impact: a narrative review

“… (Davidson et al 2023 ) Renal cell carcinoma Visium 6 patients, 10 samples Mechanisms explaining lack of response to immunotherapy in high-risk patients, including exhausted immune cells and lack of expression of PD-1 , PD-L1 and CTLA4 genes. (Raghubar et al 2023 ) Prostate cancer GeoMx DSP Tissue microarray (TMA) TMA constructed from 27 patients, in total, 168 tumor cores from 56 tumors used. Metastatic prostate cancer immune infiltrate lacks PD1, PD-L1 and CTLA4 .…”

“…Kidney cancer is known to be responsive to immunotherapy, and spatial analysis has revealed that the underlying mechanisms may include myofibroblastic cancer-associated fibroblasts (myCAFs) (Davidson et al 2023 ). Elucidating the immune phenotype of high-risk clear cell renal cell carcinoma (ccRCC) with ST has also provided insights into the immunogenic TME of tumors that have abundant exhausted/pro-tumor immune cells and provided clues to mechanisms explaining the infrequent lack of response to immunotherapy, including exhausted immune cells and lack of expression of the PD-1 , PD-L1 and CTLA4 genes (Raghubar et al 2023 ).…”

PD1/PD-L1 blockade in clear cell renal cell carcinoma: mechanistic insights, clinical efficacy, and future perspectives

“…Research has analyzed the TME of intermediate- to high-risk ccRCC patients using spatial transcriptome sequencing (ST-seq) and found that a high-level TME is rich in exhausted/pro-tumor immune cells and lacks specific checkpoint gene expression, suggesting its immunogenicity but unfavorable response to ICIs therapy. The types and status of immune cells infiltrating tumors may help predict responses to ICI therapy [ 133 ]. In ccRCC patients responding to ICI therapy, higher densities of tumor-infiltrating T cells, CTLs, and PD1-positive immune cells are observed [ 134 ].…”