This work was supported by grants from Institut National du Cancer (INCA) (ET), Ligue contre le Cancer (ET), Universit&#233; Sorbonne Paris Cit&#233; (ET), ANR (Selectimmunco) (ET), Labex Immuno-Oncology (ET), SIRIC CARPEM (CG, ET). EdG was funded by a fellowship of Fondation ARC. EV and CD were funded by a fellowship of APHP (bourse ann&#233;e recherche). ChB is funded by a fellowship of Universit&#233; Sorbonne Paris Cit&#233; (contrat doctoral). The authors thank Bristol Myers Squibb for their funding in this project. The authors thank the department of Pathology of Hopital Europ&#233;en Georges Pompidou and Necker (Laurianne Chambolle, Elodie Michel and Gis&#232;le Legall). The authors thank the Histology platform of PARCC, Hopital Europ&#233;en Georges Pompidou (Corinne Lesaffre).

This study was conducted in accordance with the Declaration of Helsinki and was approved by the local ethics committee (CPP Ile de France nr. 2012-05-04). Informed consent was obtained from the participant included in the cohorts.
1. Tissue Material
<ol>
	<li>Collect RCC tissue samples on the day of surgery. Handle the surgical specimen at room temperature (pathology department).</li>
	<li>Collect a tumor sample of approximately 0.5 cm x 0.5 cm x 0.5 cm size in a dry tube. Snap freeze in liq...

<ol>
	<li>Borghaei, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nivolumab+versus+Docetaxel+in+Advanced+Nonsquamous+Non-Small-Cell+Lung+Cancer.">Nivolumab versus Docetaxel in Advanced Nonsquamous Non-Small-Cell Lung Cancer.</a> N Engl J Med. 373 (17), 1627-1639 (2015).</li><li>Granier, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cancer+immunotherapy:+Rational+and+recent+breakthroughs.">Cancer immunotherapy: Rational and recent breakthroughs.</a> Rev Med Interne. 37 (10), 694-700 (2016).</li><li>Motzer, R. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nivolumab+for+Metastatic+Renal+Cell+Carcinoma:+Results+of+a+Randomized+Phase+II+Trial.">Nivolumab for Metastatic Renal Cell Carcinoma: Results of a Randomized Phase II Trial.</a> J Clin Oncol. 33 (13), 1430-1437 (2015).</li><li>Robert, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nivolumab+in+previously+untreated+melanoma+without+BRAF+mutation.">Nivolumab in previously untreated melanoma without BRAF mutation.</a> N Engl J Med. 372 (4), 320-330 (2015).</li><li>Robert, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ipilimumab+plus+dacarbazine+for+previously+untreated+metastatic+melanoma.">Ipilimumab plus dacarbazine for previously untreated metastatic melanoma.</a> N Engl J Med. 364 (26), 2517-2526 (2011).</li><li>Rosenberg, J. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atezolizumab+in+patients+with+locally+advanced+and+metastatic+urothelial+carcinoma+who+have+progressed+following+treatment+with+platinum-based+chemotherapy:+a+single-arm,+multicentre,+phase+2+trial.">Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial.</a> Lancet. 387 (10031), 1909-1920 (2016).</li><li>Schadendorf, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pooled+Analysis+of+Long-Term+Survival+Data+From+Phase+II+and+Phase+III+Trials+of+Ipilimumab+in+Unresectable+or+Metastatic+Melanoma.">Pooled Analysis of Long-Term Survival Data From Phase II and Phase III Trials of Ipilimumab in Unresectable or Metastatic Melanoma.</a> J Clin Oncol. 33 (17), 1889-1894 (2015).</li><li>Ribas, A., Hu-Lieskovan, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=What+does+PD-L1+positive+or+negative+mean?.">What does PD-L1 positive or negative mean?.</a> J Exp Med. 213 (13), 2835-2840 (2016).</li><li>Rizvi, N. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cancer+immunology.+Mutational+landscape+determines+sensitivity+to+PD-1+blockade+in+non-small+cell+lung+cancer.">Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.</a> Science. 348 (6230), 124-128 (2015).</li><li>Roussel, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Composite+biomarkers+defined+by+multiparametric+immunofluorescence+analysis+identify+ALK-positive+adenocarcinoma+as+a+potential+target+for+immunotherapy.">Composite biomarkers defined by multiparametric immunofluorescence analysis identify ALK-positive adenocarcinoma as a potential target for immunotherapy.</a> OncoImmunology. 6 (4), e1286437 (2017).</li><li>Pages, F., Granier, C., Kirilovsky, A., Elsissy, C., Tartour, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biomarqueurs+pr&#233;dictifs+de+r&#233;ponse+aux+traitements+bloquant+les+voies+de+costimulation+inhibitrices.">Biomarqueurs pr&#233;dictifs de r&#233;ponse aux traitements bloquant les voies de costimulation inhibitrices.</a> Bull Cancer. 103, S151-S159 (2016).</li><li>Tumeh, P. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PD-1+blockade+induces+responses+by+inhibiting+adaptive+immune+resistance.">PD-1 blockade induces responses by inhibiting adaptive immune resistance.</a> Nature. 515 (7528), 568-571 (2014).</li><li>Fourcade, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Upregulation+of+Tim-3+and+PD-1+expression+is+associated+with+tumor+antigen-specific+CD8++T+cell+dysfunction+in+melanoma+patients.">Upregulation of Tim-3 and PD-1 expression is associated with tumor antigen-specific CD8+ T cell dysfunction in melanoma patients.</a> J Exp Med. 207 (10), 2175-2186 (2010).</li><li>Koyama, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adaptive+resistance+to+therapeutic+PD-1+blockade+is+associated+with+upregulation+of+alternative+immune+checkpoints.">Adaptive resistance to therapeutic PD-1 blockade is associated with upregulation of alternative immune checkpoints.</a> Nat Commun. 7, 10501 (2016).</li><li>Wherry, E. J., Kurachi, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+and+cellular+insights+into+T+cell+exhaustion.">Molecular and cellular insights into T cell exhaustion.</a> Nat Rev Immunol. 15 (8), 486-499 (2015).</li><li>Cai, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tim-3+expression+represents+dysfunctional+tumor+infiltrating+T+cells+in+renal+cell+carcinoma.">Tim-3 expression represents dysfunctional tumor infiltrating T cells in renal cell carcinoma.</a> World J Urol. 34 (4), 561-567 (2016).</li><li>Sakuishi, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+Tim-3+and+PD-1+pathways+to+reverse+T+cell+exhaustion+and+restore+anti-tumor+immunity.">Targeting Tim-3 and PD-1 pathways to reverse T cell exhaustion and restore anti-tumor immunity.</a> J Exp Med. 207 (10), 2187-2194 (2010).</li><li>Stack, E. C., Wang, C., Roman, K. A., Hoyt, C. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplexed+immunohistochemistry,+imaging,+and+quantitation:+a+review,+with+an+assessment+of+Tyramide+signal+amplification,+multispectral+imaging+and+multiplex+analysis.">Multiplexed immunohistochemistry, imaging, and quantitation: a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis.</a> Methods. 70 (1), 46-58 (2014).</li><li>Bethmann, D., Feng, Z., Fox, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunoprofiling+as+a+predictor+of+patient's+response+to+cancer+therapy-promises+and+challenges.">Immunoprofiling as a predictor of patient's response to cancer therapy-promises and challenges.</a> Curr Opin Immunol. 45, 60-72 (2017).</li><li>Badoual, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PD-1-expressing+tumor-infiltrating+T+cells+are+a+favorable+prognostic+biomarker+in+HPV-associated+head+and+neck+cancer.">PD-1-expressing tumor-infiltrating T cells are a favorable prognostic biomarker in HPV-associated head and neck cancer.</a> Cancer Res. 73 (1), 128-138 (2013).</li><li>Nizard, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Induction+of+resident+memory+T+cells+enhances+the+efficacy+of+cancer+vaccine.">Induction of resident memory T cells enhances the efficacy of cancer vaccine.</a> Nat Commun. 8, 15221 (2017).</li><li>Nghiem, P. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PD-1+Blockade+with+Pembrolizumab+in+Advanced+Merkel-Cell+Carcinoma.">PD-1 Blockade with Pembrolizumab in Advanced Merkel-Cell Carcinoma.</a> N Engl J Med. 374 (26), 2542-2552 (2016).</li><li>Roussel, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Composite+biomarkers+defined+by+multiparametric+immunofluorescence+analysis+identify+ALK-positive+adenocarcinoma+as+a+potential+target+for+immunotherapy.">Composite biomarkers defined by multiparametric immunofluorescence analysis identify ALK-positive adenocarcinoma as a potential target for immunotherapy.</a> Oncoimmunology. (4), (2017).</li><li>Woods, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mismatch+in+epitope+specificities+between+IFNgamma+inflamed+and+uninflamed+conditions+leads+to+escape+from+T+lymphocyte+killing+in+melanoma.">Mismatch in epitope specificities between IFNgamma inflamed and uninflamed conditions leads to escape from T lymphocyte killing in melanoma.</a> J Immunother Cancer. 4, 10 (2016).</li><li>Granier, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tim-3+Expression+on+Tumor-Infiltrating+PD-1+CD8++T+Cells+Correlates+with+Poor+Clinical+Outcome+in+Renal+Cell+Carcinoma.">Tim-3 Expression on Tumor-Infiltrating PD-1+CD8+ T Cells Correlates with Poor Clinical Outcome in Renal Cell Carcinoma.</a> Cancer Res. 77 (5), 1075-1082 (2017).</li><li>Feng, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multispectral+Imaging+of+T+and+B+Cells+in+Murine+Spleen+and+Tumor.">Multispectral Imaging of T and B Cells in Murine Spleen and Tumor.</a> J Immunol. 196 (9), 3943-3950 (2016).</li><li>Feng, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multispectral+imaging+of+formalin-fixed+tissue+predicts+ability+to+generate+tumor-infiltrating+lymphocytes+from+melanoma.">Multispectral imaging of formalin-fixed tissue predicts ability to generate tumor-infiltrating lymphocytes from melanoma.</a> J Immunother Cancer. 3, 47 (2015).</li><li>Fridman, W. H., Pages, F., Sautes-Fridman, C., Galon, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+immune+contexture+in+human+tumours:+impact+on+clinical+outcome.">The immune contexture in human tumours: impact on clinical outcome.</a> Nat Rev Cancer. 12 (4), 298-306 (2012).</li><li>Nizard, M., Roussel, H., Tartour, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resident+Memory+T+Cells+as+Surrogate+Markers+of+the+Efficacy+of+Cancer+Vaccines.">Resident Memory T Cells as Surrogate Markers of the Efficacy of Cancer Vaccines.</a> Clin Cancer Res. 22 (3), 530-532 (2016).</li><li>Sandoval, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mucosal+imprinting+of+vaccine-induced+CD8(+)+T+cells+is+crucial+to+inhibit+the+growth+of+mucosal+tumors.">Mucosal imprinting of vaccine-induced CD8(+) T cells is crucial to inhibit the growth of mucosal tumors.</a> Sci Transl Med. 5 (172), 172ra120 (2013).</li><li>Carstens, J. 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Modifications and Troubleshooting:
The tissue quality is an important parameter; it can be easily checked by hematoxylin and eosin coloration.
One advantage of the technique is the possibility of multiplexed stainings, but to avoid fluorophore spillover, it recommended to choose emission wavelengths with delta of 10 nm minimum. Here, because we had 4 stainings including DAPI, we chose to spread out the wavelengths (DAPI: 460 nm, AF488: 519 nm, Cyani...

In the past few years, immunotherapy has emerged as a very promising treatment for many types of cancers, including RCC. Particularly, immunotherapy based on the inhibition of inhibitory checkpoints like PD-1 and CTLA-4 has been reported to be clinically effective1,2,3,4,5,6. Monoclonal antibodies against CTLA-4, PD-1, or Program Death Ligand 1 (PD-L1) are already approved in several cancers and lead to long lasting clinical responses in more than 20% of patients7. Nevertheless, not all patients are responders, the cost of the treatment is high, and these treatments are toxic, leading to potential serious autoimmune-like side effects. Therefore, the current challenge is to identify predictive markers to those new immunotherapies. The rate of mutations in the tumor, the expression of PD-L1, or the levels of intratumoral CD8+ T cell infiltration have been reported to correlate with clinical response. However, this association is still too weak to recommend the use of these clinical biomarkers in clinical practice except for the companion test for PD-L1 before the administration of Pembrolizumab in non-small cell lung cancer (NSCLC) patients8,9,1011,12. It has been demonstrated that the co-expression of many inhibitory receptors like PD-1, Tim-3, Lag-3, and CTLA-4, induces a cell exhaustion phenotype and resistance to therapy13,14,15. Since peripheral blood is not representative of the tumor microenvironment, it is of high interest to analyze the phenotypic features of the cells in situ. PD-1 and Tim-3 co-expressing T cells are known to be functionally impaired cells in several contexts13,16,17. In this study, the prognostic impact of the co-expression of the two inhibitory receptors PD-1 and Tim-3 on CD8+ T cells was assessed.
Up until now, studying the co-expression of multiple markers on tumor infiltrating lymphocytes (TILs) has mainly been performed by flow cytometry analysis, making it necessary to work on fresh tumors and therefore precluding retrospective analyses. With conventional in situ staining, only one staining at a time can be performed, and the characterization of the cell type that co-expresses the markers is not possible. For example, PD-L1 is expressed by many cell types of the tumoral microenvironment, making it difficult to define by conventional immunohistochemistry analysis which cells expressing PD-L1 are the more relevant for correlative studies. In this work, we developed an innovative in situ multiparametric immunofluorescence method with computer-counting to correlate the co-expression of PD-1 and Tim-3 by tumor infiltrating CD8+ T-cells with clinical outcomes in RCC. This technique has several advantages, including the possibility to analyze at a single cell level and multiple markers at the same time using a multispectral camera that can capture restricted intervals &#62;10 nm through liquid crystal filters18. Moreover, the procedure is automatic which enables an inter-operator reproducibility and a shortened analysis compared to manual techniques19. In the cancer field, several studies reported convincing multiple stainings of immune molecules like PD-1, PD-L1, and CD8 in Merkel-cell carcinoma, lung cancer, and head and neck cancer20,21,22,23. The automated cell count is possible with training by the user (phenotyping step). The fluorescence is measured in the different cell compartments (nuclei, cytoplasm, and membrane).
Here, different subsets of tumor-infiltrating CD8+ T cells expressing PD-1 and/or Tim-3 in a large cohort of RCC were counted and the results were correlated with clinical gravity scores and survival parameters. It was also possible to analyze membrane fluorescence intensity at the cellular resolution with Mean Fluorescence Intensity (MFI) data like in cytometry. As far as we know, this represents the first study reporting prognostic results using this multispectral imaging based count technique.

<table>
	<tbody>
		<tr>
			<td>Vectra 3 Automated Quantitative Pathology Imaging&#160;</td>
			<td>Perkin Elmer</td>
			<td>CLS142338</td>
			<td></td>
		</tr>
		<tr>
			<td>inForm cell analysis 2.1.</td>
			<td>Perkin Elmer</td>
			<td>CLS135781</td>
			<td></td>
		</tr>
		<tr>
			<td>R software</td>
			<td>https://www.r-project.org</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Dakopen delimiting pen</td>
			<td>Dako</td>
			<td>S2002</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris Buffer Salin TBS Tablets</td>
			<td>Takara, Bio Inc.</td>
			<td>TAKT9141Z</td>
			<td>pH7.6 100 tablet</td>
		</tr>
		<tr>
			<td>Tris Buffer Salin Tween 20 TBS(+Tween20)</td>
			<td>Takara, Bio Inc.</td>
			<td>TAKT9142Z</td>
			<td>pH 7.6 100 tablets</td>
		</tr>
		<tr>
			<td>Biotin blocking system</td>
			<td>Dako</td>
			<td>X0590</td>
			<td>Avidin 0.1% and Biotin 0.01%</td>
		</tr>
		<tr>
			<td>normal donkey serum</td>
			<td>Jackson Immunoresearch</td>
			<td>017-000-001</td>
			<td>5% vol./vol. concentration</td>
		</tr>
		<tr>
			<td>Fluoroshield with DAPI</td>
			<td>Sigma-aldrich</td>
			<td>F6057</td>
			<td>1.5 &#181;g/mL concentration&#160;</td>
		</tr>
		<tr>
			<td>Knittel glass coverslip</td>
			<td>Knittel&#160;Gl&#228;ser,</td>
			<td>100039</td>
			<td>24x60 mm 100 cover slips</td>
		</tr>
		<tr>
			<td>Rabbit anti-CD8 Clone P17-V</td>
			<td>novus</td>
			<td>NBP1-79055</td>
			<td>use at 4&#181;g/mL</td>
		</tr>
		<tr>
			<td>Mouse anti-PD-1 Clone NAT</td>
			<td>abcam</td>
			<td>ab52587</td>
			<td>use at 2 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Goat anti-Tim-3</td>
			<td>R&#38;D</td>
			<td>AF2365</td>
			<td>use at 3 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Rabbit anti-PD-L1 Clone SP142</td>
			<td>Roche</td>
			<td>7309457001</td>
			<td>use at 1 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Mouse AF647 labeled pan- Keratin Clone C11&#160;</td>
			<td>Cell Signalling</td>
			<td>4528</td>
			<td>use at 0.5 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Goat anti-human gal9&#160;</td>
			<td>R&#38;D</td>
			<td>AF2045</td>
			<td>use at 0.3 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Cyan 5 conjugated donkey anti-rabbit&#160;</td>
			<td>Jackson Immunoresearch</td>
			<td>711-175-152</td>
			<td>use at 5 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Biotinylated F(ab&#8217;2) donkey anti-mouse IgG</td>
			<td>Jackson Immunoresearch</td>
			<td>715-066-150</td>
			<td>use at 3 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Alexa Fluor488 conjugated donkey anti-goat IgG</td>
			<td>abcam</td>
			<td>ab150133</td>
			<td>use at 5 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Cy3 labeled streptavidin&#160;</td>
			<td>Amersham</td>
			<td>PA43001</td>
			<td>use at 3 &#181;g/mL</td>
		</tr>
		<tr>
			<td>negative control mouse IgG1</td>
			<td>Dako</td>
			<td>X0931</td>
			<td>use at 2 &#181;g/mL</td>
		</tr>
		<tr>
			<td>IgG from goat serum</td>
			<td>Sigma-aldrich</td>
			<td>I5256</td>
			<td>use at 3 &#181;g/mL</td>
		</tr>
		<tr>
			<td>IgG from rabbit serum</td>
			<td>Sigma-aldrich</td>
			<td>I5006</td>
			<td>use at 4&#181;g/mL</td>
		</tr>
	</tbody>
</table>

multiplexed immunofluorescence analysis and quantification of intratumoral pd-1+ tim-3+ cd8+ t cells

Immune cells are important components of the tumor microenvironment and influence tumor growth and evolution at all stages of carcinogenesis. Notably, it is now well established that the immune infiltrate in human tumors can correlate with prognosis and response to therapy. The analysis of the immune infiltrate in the tumor microenvironment has become a major challenge for the classification of patients and the response to treatment.
The co-expression of inhibitory receptors such as Program Cell Death Protein 1 (PD1; also known as CD279), Cytotoxic T Lymphocyte Associated Protein 4 (CTLA-4), T-Cell Immunoglobulin and Mucin Containing Protein-3 (Tim-3; also known as CD366), and Lymphocyte Activation Gene 3 (Lag-3; also known as CD223), is a hallmark of T cell exhaustion. We developed a multiparametric in situ immunofluorescence staining to identify and quantify at the cellular level the co-expression of these inhibitory receptors. On a retrospective series of frozen tissue of renal cell carcinomas (RCC), using a fluorescence multispectral imaging technology coupled with an image analysis software, it was found that co-expression of PD-1 and Tim-3 on tumor infiltrating CD8+ T cells is correlated with a poor prognosis in RCC. To our knowledge, this represents the first study demonstrating that this automated multiplex in situ technology may have some clinical relevance.

Using the general protocol described above, we aimed to quantify intratumoral CD8+ T cells co-expressing the inhibitory receptors PD-1 and Tim-3 in frozen tissues from patients with RCC, and to correlate the results with clinical outcomes25.
Optimization of the CD8/PD-1/Tim-3 Staining:
Different species of antibodies ...

Watch this Scientific Journal Video about Multiplexed Immunofluorescence Analysis and Quantification of Intratumoral PD-1+ Tim-3+ CD8+ T Cells at JoVE.com

Multiplexed Immunofluorescence Analysis and Quantification of Intratumoral PD-1+ Tim-3+ CD8+ T Cells

Studying tumor microenvironment may identify prognostic or predictive biomarkers of clinical response to immunotherapy. Presented here, is an innovative method based on in situ fluorescence multispectral imaging to analyze and count automatically various subpopulations of CD8+ T cells. This reproducible and reliable technique is suitable for large cohort analyses.

Multiplexed Immunofluorescence Analysis and Quantification of Intratumoral PD-1+ Tim-3+ CD8+ T Cells

Immune cells are important components of the tumor microenvironment and influence tumor growth and evolution at all stages of carcinogenesis. Notably, it ...

The overall goal of this multiplexed immunofluorescence analysis is to automatically count cells based on their phenotype. This method allows multifluorescence and automatic cell counting to analyze the phenotype and function of tumor immune cells within a tumor microenvironment. This technology facilitated the generation of two types of composite prognosis for predicted by your markers derived directly from the tumor microenvironment.Generally, individuals new to this method may struggle because the pheno typing procedure is very long and the resulting raw data requires further processing. We first had the idea for this method when we attempting to characterize the phenotype and immunological interactions of annhodge miranty cells. After thawing, use a paper towel to carefully dry the slides around the tissue sections and then circle the tissues with a hydrophobic barrier pen.When the barrier has dried, fix the samples in 100%acetone for five minutes, followed by two minutes of air drying, then wash the slides in TBS for 10 minutes. Pretreat the slides with 3 drops of 0.1%Avidin for 10 minutes in the dark, then tap or flick the slides to cover the tissue with the Avidin solution. Add 3 drops of 01%biotin to each sample, then tap or flick the biotin across the samples followed by a TBS wash as just demonstrated.Then block any nonspecific binding with 100 microliters of 5%normal serum in TBS for 30 minutes at room temperature. At the end of the incubation, tap the slides to remove the excess serum and incubate the slides in 100 microliters of the primary antibody cocktail of interest for one hour in a humidified chamber. Wash the antibodies labeled slides in TBST for five minutes.After drying, label the cells with 100 microliters of the secondary antibody cocktail of interest for 30 minutes in the humidified chamber, followed by a 10 minute wash in TBS. Incubate the dried secondary antibody labeled slides with 100 microliters of the tertiary antibody cocktail of interest for 30 minutes followed by 10 minutes of a TBS wash. At the end of the wash, dry the slides and mount the tissues with a dapi supplemented mounting medium.Then clover each slide with a cover slip and let the mounting medium set for at least two hours. To scan the slides, open the microscope software and load the image scanning protocol. Load the first slide onto the microscope stage.Then in the control bar, click set exposure and adjust the exposure time for each filter until a sufficient but not saturating signal is obtained. Click start in the upper panel and open the LabID folder. Enter the ID of the first slide and click next.To acquire the overview of the slide under bright field light at a 4x magnification, click monochrome imaging and find specimen. To select the are of tissue to be scanned, press the control key and use the cursor to select or deselect the regions of interest to be scanned at the 4x magnification. To obtain a fluorescent red/blue/green image of each region, click low power imagine.For high power field selection, press the control key and select at least five regions of interest that correspond to the areas of the tissue that will be scanned at the 20x magnification. Then, to obtain a multi spectral image acquisition of each field, click high power imagine, and click data storage to store the images in the appropriate lab ID folder. To create a new project under the file menu, select new project, under the find feature menu, select cell segmentation, and under the pheno typing menu, select pheno typing, then click configure.In image format, select multi spectral. In sample format, choose fluorescence. To integrate the representative images into the project, under the file menu click open image and select 10-30 representative images of the whole series.To remove the auto florescence, open the unstained slide, and select the library source and the appropriate fluorophores. Click auto florescence and select the area of auto florescence on the blank slide. To generate a composite image, select prepare all to integrate the fluorescence library and the auto fluorescent spectra.Click the eye icon to open the view editor panel and deselect autoflourescence to trim the autoflourescence signal. Select an appropriate color for each marker. To segment the cells, in the compartment menu, select nuclei and membrane.Under the nuclei menu, set DAPI as the nuclear counter stain. Click segment cells and check the segmentation of the nuclei in the cell membranes. To phenotype the cells, under the phenotype menu, click add.To create the cell phenotype categories, select more than five representative for Fluorophor and Fluorophor combination, and click train classifier. The classifier is creating an algorithm that attributes a phenotype for each cell with a confidence interval. Zoom and check the phenotypes of the cells.Then click phenotype all to save the phenotype algorithm and the image project, under the file menu select save project. Then name the project and save it. To perform a batch analysis of the series, select bath analysis and select the saved project.Select a folder for storing the batched data. Add the images to be analyzed then click run. At the end of the analysis check the quality of the composite image and verify the pheno typing of all of the images within the series.Analysis of the tumor infiltrating CD8 positive T-cells, on a clear renal cell carcinoma specimen by fluorescence multi spectral imaging reveals approximately half of the CD8 positive T-cells to be single positive for PD-1 and about 1/3 to be double positive for PD-1 and Tim-3. After integrating these various cell signals on a tissue section, measurement of the PD-1 florescence intensity on PD-1 positive Tim-3 positive versus PD-1 positive, Tim-3 negative CD8 positive T-cells, reveals that the PD-1 MFI is higher when Tim-3 is co expressed reinforcing the functional relevance of Tim-3 expression. In this representative experiment, 66%of the renal tumor patients were also positive for PD-1 Ligand expression and 100%were positive for the Tim-3 ligand Galactin-9.Clinical scoring of the tumor tissues from renal cell carcinoma patients, also demonstrated the positive correlation between the number and percentage of tumor infiltrating CD-8 positive T-cells expressing PD-1 and Tim-3 and the prognostic scoring parameters but not PD-1 positive CD-8 not expressing Tim-3. Interestingly, renal cell carcinoma patients with CD-8 positive T-cells co expressing PD1 with and Tim 3 above the median percentage were more likely to relapse while the expression of PD-1 without Tim-3 co expression was found not to be correlated with patient relapse. While I attempted this procedure it's important to remember to review the phenotype of the cells with two separated investigators including a pathologist if possible.Following this procedure other matters like for cytometry can be performed to answer additional questions about the functional impact of self phenotype after x-vivo stimulation. After it's development, this technique paved the way for researchers in the field of cancer to explore immune responses in effected organs.

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JoVE Journal

Cancer Research

14.3K vistas.  Université Paris Descartes. The overall goal of this multiplexed immunofluorescence analysis is to automatically count cells based on their phenotype. This method allows multifluorescence and automatic cell counting to analyze the phenotype and function of tumor immune cells within a tumor microenvironment. This technology facilitated the generation of two types of composite prognosis for predicted by your markers derived directly from the tumor microenvironment.Generally, individuals new to this method may strug...