Detection of immune cell checkpoint and functional markers in the tumor microenvironment by the RNA in situ hybridization RNAscope assay

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1 pplication Note Immunotherapy Detection of immune cell checkpoint and functional markers in the tumor microenvironment by the RN in situ hybridization RNscope assay Ming-Xiao He, Na Li, Courtney nderson, Yuling Luo, Nan u, Xiao-Jun Ma, Emily Park he RNscope assay is a unique RN IH technology that identifies RN expression at the single cell level with morphological context. Here we present the use of RNscope for the detection of RN targets in the tumor microenvironment (ME) that are involved in tumor immunology and immunotherapy: Checkpoint markers Immune cell markers Cytokines and chemokines Detection of these RN targets with the RNscope assay can aid in: Localization of specific immune cell types (i.e., cytotoxic lymphocytes and regulatory cells) in the ME Determining spatial relationships between different cell types in the ME Characterization of secreted proteins (i.e., cytokines and chemokines) Evaluation of immune function in ME beyond enumeration of tumor infiltrating lymphocytes Introduction he field of cancer immunotherapy has expanded rapidly in recent years with immune checkpoint inhibitors and other therapeutic approaches such as cancer vaccines and chimeric antigen receptor (CR) therapy showing promising clinical results. Despite the dramatic and durable responses seen in many patients, our understanding of the immune response to cancer is still limited, and we cannot reliably predict who will or will not benefit from these new interventions. o better stratify patients for immunotherapy treatments, the series of events and biomarkers involved in the cancer immunity cycle need to be better understood (1-3). In addition, spatially mapped expression data at the single-cell level is crucial to understanding the cellular organization and cell-to-cell interactions in the tumor and its complex microenvironment (ME). RNscope is a unique RN IH technology that provides single-cell gene expression resolution with spatial and morphological context. he RNscope assay detects mrn and long noncoding RNs in fresh frozen, fresh fixed, and formalin-fixed paraffin-embedded (FFPE) cells and tissues by utilizing a unique double Z probe design and signal amplification strategy that allows for visualization of target RN as a single dot, where each dot is an individual RN molecule (4). he RNscope strategy offers the key benefits of high sensitivity due to the signal amplification method, and high specificity because of the double Z probe design, resulting in a high signal-to-noise ratio in many tissues. In this report we examined 50 selected immune checkpoint and functional markers (summarized in Figure 1) to demonstrate the utility of the RNscope assay for tumor immunology applications. With the RNscope 2.5 HD duplex assay we demonstrate localization of PD-L1 and several immune markers in ovarian and lung cancers (Figures 2-4). Detection of 12 immune checkpoint markers, 14 immune cell markers, and 24 immune function markers, such as cytokines and chemokines, in multiple human tumors is also demonstrated by the RNscope brown assay (Figures 5-7; ppendix). he complete data set can be viewed in the appendix available online at 1

2 Checkpoint markers Immune cell markers Cytokines and chemokines L (CD272) CD3 CCL5 IL10 CL4 CD8α (CD8) CCL7 IL12 IDO1 CD27 CX3CL1 IL13 IM3 (HVCR2) CD40 CX3CR1 IL17 LG3 CD40L (CD40LG) CXCL9 IL18 MIC CD70 CXCL10 IL20 MIC FOXP3 CXCL13 IL21 PD-1 (PDCD1) Granulysin (GNLY) IFN1 IL33 PD-L1 (CD274) ICM1 IFNγ (IFNG) GFβ (GF1) PD-L2 (PDCD1LG2) ICO IL1 NFα (NF) 4-1/CD137 (NFRF9) Perforin (PRF1) IL4 VEGF- (VEGF) 7-H4 (VCN1) OX40L (NFF4) IL6 OX40 (NFRF4) IL7 HVEM (NFRF14) FIGURE 1. Immune markers examined in this study by the RNscope assay. Fifty immune system markers were examined in this study, including 12 immune checkpoint markers, 14 immune cell markers, and 24 cytokines and chemokines. Ovarian cancer Lung cancer PD-L1/CD8α FIGURE 2. imultaneous detection of PD-L1 and CD8α mrns. he manual RNscope 2.5 HD Duplex assay was used to detect expression of the immune checkpoint marker PD-L1 (green chromogen) and the immune cell marker CD8α (red chromogen) in human ovarian () and lung () tumors. Inset shows enlarged region outlined in white. sterisk denotes PD-L1+/CD8- cells; arrowhead denotes PD-L1+/CD8+ cells. Note that in the lung cancer sample () PD-L1 is profusely expressed in both tumor cells and immune cells, with abundant CD8+ immune cell infiltration. However, in the ovarian cancer sample () PD-L1 expression is primarily restricted to the immune cells., stroma;, tumor. White line delineates tumor margin. 40x magnification. 2 pplication Note

3 Ovarian cancer Lung cancer CD3/IFNγ D CD8α/IFNγ C F CD4/IFNγ E FIGURE 3. imultaneous detection of IFNγ and immune cell markers CD3, CD8α and CD4 mrns. he manual RNscope 2.5 HD Duplex assay was used to detect expression of the immune function marker IFNγ and the immune cell markers CD3 (-), CD8α (C-D), or CD4 (E-F) in human ovarian (, C, E) and lung (, D, F) tumors. CD3, CD8α, and CD4 were detected using green chromogen and IFNγ was detected using red chromogen. Inset shows enlarged region outlined in white. sterisk denotes CD+/IFNγ- cells; arrowhead denotes CD+/IFNγ+ cells; arrow denotes CD-/IFNγ+ cells., stroma;, tumor. White line delineates tumor margin. 40x magnification. Ovarian cancer Lung cancer CD4/FOXP3 FIGURE 4. imultaneous detection of FOXP3 and CD4 mrns. he manual RNscope 2.5 HD Duplex assay was used to detect expression of the immune cell markers CD4 (green chromogen) and FOXP3 (red chromogen) in human ovarian () and lung () tumors. Inset shows enlarged region outlined in white. sterisk denotes CD4+/FOXP3- cells; arrowhead denotes CD4+/FOXP3+ regulatory cells., stroma;, tumor. White line delineates tumor margin. 40x magnification. Immunotherapy 3

4 7-H4 ovary L testicle D CL4 lung IDO1 esophagus C F MIC ovary MIC ovary E H PD-1 ovary PD-L1 ovary G FIGURE 5. Detection of immune checkpoint markers in human tumors. he RNscope manual brown assay was used to detect expression of several immune checkpoint markers in multiple human tumors. 40x magnification. 4 pplication Note

5 CD3 ovary CD8α breast D HVEM gastric FOXP3 stomach C F ICM1 lung ICO stomach E H Perforin stomach OX40L liver G FIGURE 6. Detection of immune cell markers in human tumors. he RNscope manual brown assay was used to detect expression of several immune cell markers in multiple human tumors. 40x magnification. Immunotherapy 5

6 CXCL9 stomach CCL5 esophagus D CX3CR1 liver CXCL13 stomach C F IFNγ vulva IL1 bladder E H IL6 bladder IL33 normal stomach G J NFα breast GF1 stomach I FIGURE 7. Detection of cytokines, chemokines, and their receptors in human tumors. he RNscope manual brown assay was used to detect expression of several cytokines, chemokines, and their receptors in multiple human tumors. 40x magnification. 6 pplication Note

7 Conclusions Detecting RN biomarker expression at the single-cell level while preserving spatial information is critical to understanding cellular organization and cell-to-cell interactions in the cancer-immunity cycle. Here we show that the RNscope assay is able to detect immune checkpoint markers and immune function markers in a variety of human tumors. Overall these results demonstrate the utility of the RNscope technology in studying tumor immunology and key targets of immunotherapy in the tumor and its complex microenvironment. ppendix containing all data discussed in this study is available at acdbio.com/immunotherapy Markers Probe name Cat No. Checkpoint markers 7-H4 (VCN1) Hs-VCN L (CD272) Hs-L CD137/4-1 (NFRF9) Hs-NFRF CL4 Hs-CL IDO1 Hs-IDO IM3 (HVCR2) Hs-HVCR LG3 Hs-LG MIC Hs-MIC MIC Hs-MIC PD-1 (PDCD1) Hs-PDCD PD-L1 (CD274) Hs-CD PD-L2 (PDCD1LG2) Hs-PDCD1LG Immune cell markers CD3 Hs-CD3-pool CD8α (CD8) Hs-CD CD27 Hs-CD CD40 Hs-CD CD40L (CD40LG) Hs-CD40LG CD70 Hs-CD FOXP3 Hs-FOXP Granulysin (GNLY) Hs-GNLY HVEM (NFRF14) Hs-NFRF ICM1 Hs-ICM ICO Hs-ICO Markers Probe name Cat No. Cytokines and chemokines CCL5 Hs-CCL CCL7 Hs-CCL CX3CL1 Hs-CX3CL CX3CR1 Hs-CX3CR CXCL9 Hs-CXCL CXCL10 Hs-CXCL CXCL13 Hs-CXCL IFN1 Hs-IFN IFN-γ (IFNG) Hs-IFNG IL1 Hs-IL IL4 Hs-IL IL6 Hs-IL IL7 Hs-IL IL10 Hs-IL IL12 Hs-IL IL13 Hs-IL IL17 Hs-IL IL18 Hs-IL IL20 Hs-IL IL21 Hs-IL IL33 Hs-IL GF-β (GF1) Hs-GF NF-α (NF) Hs-NF VEGF- (VEGF) Hs-VEGF OX40L (NFF4) Hs-NFF OX40 (NFRF4) Hs-NFRF Perforin (PRF1) Hs-PRF Immunotherapy 7

8 Probes for duplex assay Markers Probe name Cat # PD-L1/CD8 Hs-CD Hs-CD8-C C2 PD-L1/CD3 Hs-CD Hs-CD3-pool-C C2 CD3/IFNG Hs-CD3-pool Hs-IFNG-C C2 CD8a/IFNG Hs-CD Hs-IFNG-C C2 References 1. Pardoll DM. he blockade of immune checkpoints in cancer immunotherapy. Nat Rev Cancer. 2012; 12(4): Chen D and Mellman I. Oncology meets immunology: the cancer-immunity cycle. Immunity. 2013; 39(1): umeh PC et al. PD-1 blockade induces new responses by inhibiting adaptive immune response. Nature. 2014; 515(7528): Wang F, Flanagan J, u N, Wang LC, ui, Nielson, Wu X, Vo H, Ma XJ, Luo Y. RNscope: novel in situ RN analysis platform for formalin-fixed, paraffin-embedded tissues. J Mol Diagn. 2012; 14(1):22-9. DICLIMER ll samples used in this study have been qualified for RN integrity with PPI and dap control probes before target probe analysis. lways qualify your samples as describe in the getting started section You may observe a difference in staining pattern, due to variation in tissue preparation methods or associated biology within the tissue samples. CD4/IFNG Hs-CD Hs-IFNG-C C2 CD4/FOXP3 Hs-CD Hs-FOXP3-C C2 Data not included in this report. o read additional pplication Notes, visit For Research Use Only. Not for diagnostic use. RNscope is a registered trademark of dvanced Cell Diagnostics, Inc. in the United tates or other countries. ll rights reserved dvanced Cell Diagnostics, Inc. Doc #: /Rev/Effective Date03/31/2016 California, U

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