A5035384698- Cancer Immunotherapy and Biomarkers
- Renal cell carcinoma treatment
- CAR-T cell therapy research
- Mathematical Biology Tumor Growth
- Single-cell and spatial transcriptomics
- Renal and related cancers
- Immune Cell Function and Interaction
- Cancer Genomics and Diagnostics
- Immunotherapy and Immune Responses
- Biosimilars and Bioanalytical Methods
- Bladder and Urothelial Cancer Treatments
University of Helsinki
2022-2023
Helsinki University Hospital
2022-2023
Renal cell carcinoma (RCC) is considered as an immunogenic cancer. Because not all patients respond to current immunotherapies, we aimed investigate the immunological heterogeneity of RCC tumors. We analyzedthe immunophenotype circulating, tumor, and matching adjacent healthy kidney immune cells from 52 nephrectomy with multi-parameter flow cytometry. Additionally, studied transcriptomic mutation profiles 20 clear (ccRCC) tumors bulk RNA sequencing a customized pan-cancer gene panel. The...
While the abundance and phenotype of tumor-infiltrating lymphocytes are linked with clinical survival, their spatial coordination its significance remain unclear. Here, we investigated immune profile intratumoral peritumoral tissue clear cell renal carcinoma patients (n = 64). We trained a classifier to detect from hematoxylin eosin stained slides. Using unsupervised classification, were further classified into cold, hot excluded topographies reflecting lymphocyte localization. The...
The successful use of expanded tumor-infiltrating lymphocytes (TIL) in adoptive TIL therapies has been reported, but the effects expansion, immunophenotype, function, and T cell receptor (TCR) repertoire infused products relative to tumor microenvironment (TME) are not well understood. In this study, we analyzed samples (
<div><p>The successful use of expanded tumor-infiltrating lymphocytes (TIL) in adoptive TIL therapies has been reported, but the effects expansion, immunophenotype, function, and T cell receptor (TCR) repertoire infused products relative to tumor microenvironment (TME) are not well understood. In this study, we analyzed samples (<i>n</i> = 58) from treatment-naïve patients with renal carcinoma (RCC), “pre-rapidly expanded” TILs (pre-REP TIL, <i>n</i> 15)...
<p>Figure S2 shows representative flow gating strategies for the immunophenotyping of various sample types (tumor, healthy kidney, pre-REP TILs and REP TILs), as well co-culture assays.</p>
<p>Figure S3 shows representative gating strategies for the immune subset populations and T-cell subtypes healthy kidney, tumor, pre-REP TIL REP samples.</p>
<p>Figure S9 shows the correlation of overlapping clonotypes between REP TILs and pre-REP TILs.</p>
<p>Figure S1 shows a schematic of the TIL expansion protocol.</p>
<p>Figure S10 shows correlation of overlapping clonotypes between the tumor and pre-REP TILs.</p>
<p>Figure S13 shows analyses from the scRNA+TCRab-seq data, including different UMAP clusters, differentially expressed genes and canonical marker gene expressions.</p>
<p>Figure S15 shows pathway enrichment analyses for the pre-REP TILs and REP TILs, as well abundance of RCC-associated motifs found in UMAP T-cell clusters each tumor sample.</p>
<p>Figure S7 shows analyses of the co-culture assays involving CD107a/b, IFN-y,TNF-a and GzB expressions.</p>
<p>Figure S1 shows a schematic of the TIL expansion protocol.</p>
<p>Supplementary Table S3 shows the sample availability, usage and TIL expansion potentials.</p>
<p>Supplementary Table S3 shows the sample availability, usage and TIL expansion potentials.</p>
<p>Figure S8 shows the analyses of different clonotype sizes and tracking their abundancies found in bulk TCRb-seq data.</p>
<p>Figure S6 shows the flow cytometric analyses of immune cell subsets, T-cell phenotypes, and marker expressions, as well correlation between subsets expansion potential (fold-change REP TILs/pre-REP TILs).</p>
<p>Figure S15 shows pathway enrichment analyses for the pre-REP TILs and REP TILs, as well abundance of RCC-associated motifs found in UMAP T-cell clusters each tumor sample.</p>
<p>Figure S2 shows representative flow gating strategies for the immunophenotyping of various sample types (tumor, healthy kidney, pre-REP TILs and REP TILs), as well co-culture assays.</p>
<p>Figure S4 shows representative gating strategies for the different marker expressions in CD4+ and CD8+ T-cells samples (healthy kidney, tumor, pre-REP TIL REP TIL).</p>
<p>Figure S11 shows treemaps of various clonotypes found in the patient samples and matches to viral-specific TCRs.</p>
<p>Figure S8 shows the analyses of different clonotype sizes and tracking their abundancies found in bulk TCRb-seq data.</p>
<p>Figure S14 shows the clonalities, expression scores and size of clonotypes represented in T-cell UMAP clusters.</p>
<p>Figure S4 shows representative gating strategies for the different marker expressions in CD4+ and CD8+ T-cells samples (healthy kidney, tumor, pre-REP TIL REP TIL).</p>
<p>Figure S7 shows analyses of the co-culture assays involving CD107a/b, IFN-y,TNF-a and GzB expressions.</p>