Profiling antigen specificity concurrently with protein and mRNA quantification using high throughput single-cell multiomics reveal surprising similarities between bystander and tumor specific CD8+ tumor-infiltrating lymphocytes (TILs) in renal cell carcinoma (RCC).

e15014 Background: Recently, using human colorectal and lung cancer, we showed that CD8+ T cells infiltrating tumor tissue (TILs) are not only specific for tumor antigens, but are also composed of CD8+ TILs specific for cancer unrelated epitopes – called bystander – such as HCMV, EBV or flu epitopes. We also showed that the surface marker CD39 can be useful for discriminating bystander (CD39−) from tumor-specific (CD39+) CD8+ TILs (Simoni et al, Nature, 2018). Methods: Here, our aim was to test these findings in human Renal cell Carcinoma (RCC) and to better understand the biology of these bystander CD8+ TILs. Results: Surprisingly, our primary CYTOF analyses showed heterogeneity within bystander CD8 TILs that possess various phenotypes including effector (CD45RO+), memory (CD45RO+ CCR7+), Trm (CD69+ CD103+/–), and senescent (CD57+ KLRG1+) cell features. Using targeted mRNA single-cell sequencing combined with BD AbSeq assay, we analyzed sorted CD8+ TILs from RCC patients and identified bystander CD8+ TILs using oligo-tagged tetramers. Gene signature analysis of these different subsets revealed transcriptomic similarities with the tumor-specific CD8+ TILs. Conclusions: Our data provide a comprehensive perspective of cancer unrelated CD8+ TILs in RCC and suggest functional roles for these cells in tumor immune responses, which could lead to new diagnostic and therapeutic strategies.

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Identification Of Gene Signature For Renal Cell Carcinoma-Associated Fibroblasts Mediating Cancer Progression And Affecting Prognosis

10.21203/rs.3.rs-49601/v1 ◽

2020 ◽

Author(s):

Bitian Liu ◽

Xiaonan Chen ◽

Yunhong Zhan ◽

Bin Wu ◽

Shen Pan

Keyword(s):

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Single Cell ◽

Clinical Significance ◽

Cell Lines ◽

Cancer Progression ◽

Renal Cell ◽

Gene Signature ◽

Pathological Grade ◽

Single Cell Sequencing

Abstract Background: Cancer-associated fibroblasts (CAFs) are most abundant in stroma and are critically involved in cancer progression. However, the specific signature of CAFs and related clinicopathological parameters in renal cell carcinoma (RCC) remain unclear. Methods: In this work, methods using recognized gene signatures were employed to roughly assess the infiltration level of the stroma and CAFs in RCC based on the data in The Cancer Genome Atlas. Weighted gene co-expression network analysis (WGCNA) was used to cluster transcriptomes and correlate with CAFs to identify specific markers. A comparison of fibroblast versus urothelial carcinoma cell lines and correlation with previously reported CAF markers were performed to demonstrate the specific expressed of the gene signature. The gene signature was used to compare fibroblast infiltration of each sample through single sample gene set enrichment analysis, and the clinical significance of fibroblasts was analyzed via Cox risk assessment and the chi-square test. Finally, we used validation data to verify the clinical significance of the fibroblast gene signature in RCC. Results: Roughly calculated tumor matrix and CAF levels were significantly higher in kidney cancer than in normal tissues. More than 85% of fibroblast-specific markers identified by WGCNA were consistent with markers obtained via single-cell sequencing. These markers were more highly expressed in fibroblast cell lines and were significantly correlated with canonical CAFs makers. Data validation also showed that CAFs were significant correlation with survival and pathological grade. Conclusions: In summary, our findings indicate that the gene signature potentially serves as a biomarker of CAFs in RCC and that infiltration of fibroblasts in RCC is an independent prognostic factor associated with pathological grade and stage of tumor. The ability to recognize specific CAF markers using WGCNA is comparable to single-cell sequencing.

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Profiling the inhibitory receptors LAG-3, TIM-3, and TIGIT in renal cell carcinoma reveals malignancy

Nature Communications ◽

10.1038/s41467-021-25865-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Kimiharu Takamatsu ◽

Nobuyuki Tanaka ◽

Kyohei Hakozaki ◽

Ryohei Takahashi ◽

Yu Teranishi ◽

...

Keyword(s):

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Cell Count ◽

Single Cell ◽

Renal Cell ◽

Clinical Pathology ◽

Cutting Edge ◽

Inhibitory Receptors ◽

Histological Subtypes ◽

Human Renal Cell Carcinoma

AbstractA cutting edge therapy for future immuno-oncology is targeting a new series of inhibitory receptors (IRs): LAG-3, TIM-3, and TIGIT. Both immunogenomic analyses and diagnostic platforms to distinguish candidates and predict good responders to these IR-related agents are vital in clinical pathology. By applying an automated single-cell count for immunolabelled LAG-3, TIM-3, and TIGIT, we reveal that individual IR levels with exclusive domination in each tumour can serve as valid biomarkers for profiling human renal cell carcinoma (RCC). We uncover the immunogenomic landscape associated with individual IR levels in human RCC tumours with metastases in various organs and histological subtypes. We then externally validate our results and devise a workflow with optimal biomarker cut-offs for discriminating the LAG-3, TIM-3, and TIGIT tumour profiles. The discrimination of LAG-3, TIM-3, and TIGIT profiles in tumours may have a broad impact on investigations of immunotherapy responses after targeting a new series of IRs.

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Regulatory effects of interleukin-4 on tumor-infiltrating lymphocytes derived from human renal cell carcinoma

Journal of Surgical Research ◽

10.1016/0022-4804(92)90261-w ◽

1992 ◽

Vol 53 (6) ◽

pp. 602-609 ◽

Cited By ~ 1

Author(s):

Christian Peyret ◽

Bernard H. Bochner ◽

Tchun Y. Lee ◽

Alec S. Koo ◽

Jean B. deKernion ◽

...

Keyword(s):

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Renal Cell ◽

Tumor Infiltrating Lymphocytes ◽

Interleukin 4 ◽

Human Renal Cell Carcinoma ◽

Regulatory Effects ◽

Infiltrating Lymphocytes

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Profiling the inhibitory receptors LAG-3, TIM-3, and TIGIT in renal cell carcinoma reveals malignancy

10.21203/rs.3.rs-55869/v1 ◽

2020 ◽

Author(s):

Kimiharu Takamatsu ◽

Nobuyuki Tanaka ◽

Kyohei Hakozaki ◽

Ryohei Takahashi ◽

Shuji Mikami ◽

...

Keyword(s):

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Cell Count ◽

Single Cell ◽

Renal Cell ◽

Clinical Pathology ◽

Cutting Edge ◽

Inhibitory Receptors ◽

Histological Subtypes ◽

Human Renal Cell Carcinoma

Abstract A cutting edge therapy for future immuno-oncology is targeting a new series of inhibitory receptors (IRs): LAG-3, TIM-3, and TIGIT. Both immunogenomic analyses and diagnostic platforms to distinguish candidates and predict good responders to these IR-related agents are vital in clinical pathology. By applying an automated single-cell count for immunolabeled LAG-3, TIM-3, and TIGIT, we revealed that individual IR levels with exclusive domination in each tumour can be valid biomarkers for profiling human renal cell carcinoma (RCC). We uncovered the immunogenomic landscape associated with individual IR levels in human RCC tumours with metastases in various organs and histological subtypes. We then externally validated our results and devised a workflow with optimal biomarker cut-offs for discriminating the tumour profiles of LAG-3, TIM-3, and TIGIT. The discrimination of LAG-3, TIM-3, and TIGIT profiles in tumours may have a broad impact on investigations on immunotherapy responses after targeting a new series of IRs.

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