FIGURE 4 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu 
Published: July 2023

<p>Identification and validation of RCC-associated TCR motifs. <b>A,</b> Strategy for the identification of RCC-associated motifs. First, GLIPH2 was separately run on the RCC TCRβ-seq samples: tumor (<i>n</i> = 42), healthy kidney (<i>n</i> = 24), and PB (<i>n</i> = 32) samples. The overlap of the motifs is shown on the Venn diagrams. We subsequently pruned the motifs found in other datasets to increase the likeliness of finding RCC-associated motifs. We retained motifs that were only exclusive to or enriched to the tumor, resulting in a total of 7,435 RCC-associated motifs (<a href="#SMT4" target="_blank">Supplementary Table S4</a>). RA = Rheumatoid arthritis. <b>B,</b> Validation of RCC-associated TCR motifs. From TCGA cohort (<a href="#bib48" target="_blank">48</a>), we selected samples with at least 100 TCR reads and were left with RCC samples (<i>n</i> = 148), as well as samples from 25 different tumors (<i>n</i> = 1,042). The <i>P</i> value was calculated using the two-sided Wilcoxon test. Tumor sample abbreviations and sample numbers are shown in <a href="#SMT4" target="_blank">Supplementary Table S4</a>. Additional validation results are presented in <a href="#SMF8" target="_blank">Supplementary Fig. S8</a>. <b>C,</b> Proportion of TCRs with RCC-associated motifs in different tissues (left). TCRs with RCC-associated motifs were calculated in samples from our cohort [patients with RCC sampled from PB (<i>n</i> = 32), healthy kidney (<i>n</i> = 24), tumor (<i>n</i> = 42), pre-REP TIL (<i>n</i> = 7), REP TIL (<i>n</i> = 7), and two comparison cohorts (Emerson and colleagues (<a href="#bib46" target="_blank">46</a>), PB samples (<i>n</i> = 786); Huuhtanen and collegaues (<a href="#bib47" target="_blank">47</a>), melanoma biopsy samples (<i>n</i> = 216)]. The proportion of anti-viral TCRs was also calculated using TCRGP (ref. <a href="#bib32" target="_blank">32</a>; right). <i>P</i> values were calculated with the Wilcoxon test. Raw data are presented in <a href="#SMT4" target="_blank">Supplementary Table S4</a>. <b>D,</b> Stacked barplot showing the proportion of TCRs with RCC-associated motifs and anti-viral TCRs in RCC tumors predicted with TCRGP (<a href="#bib32" target="_blank">32</a>). <b>E,</b> Stacked barplot showing the proportion of TCRs with RCC-associated motifs and TCRGP (<a href="#bib32" target="_blank">32</a>)-predicted anti-viral TCRs in the REP TIL samples. <b>F,</b> The expansion and number of RCC-associated motifs in REP TIL samples. On the left, each colored bar denotes the proportion of individual RCC-associated motifs in each REP TIL sample. The legend for the colors is not shown, as there are 1,790 RCC-associated motifs (please refer to <a href="#SMT4" target="_blank">Supplementary Table S4</a> for all). The right panel shows the total number of different RCC-associated motifs in each REP sample.</p>