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Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy
Anna Reustle1,2, Moreno Di Marco3, Carolin Meyerhoff1,2
1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
Background:
Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy.
Methods:
We analyzed HLA-presented peptides by MS-based ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues, and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate targets with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from The Cancer Genome Atlas (TCGA KIRC, n = 452). DNA methylation (TCGA KIRC, n = 273), somatic mutations (TCGA KIRC, n = 392), and gene ontology (GO) and correlations with tumor metabolites (cohort 1, n = 30) and immune-oncological markers (cohort 1, n = 37) were analyzed to characterize regulatory and functional involvements. CD8+ T cell priming assays were used to identify immunogenic peptides. The candidate gene EGLN3 was functionally investigated in cell culture.
Results:
A total of 34,226 HLA class I- and 19,325 class II-presented peptides were identified in ccRCC tissue, of which 443 class I and 203 class II peptides were ccRCC-specific and presented in ≥ 3 tumors. One hundred eighty-five of the 499 corresponding source genes were involved in pathways activated by ccRCC tumors. After validation in the independent cohort from TCGA, 113 final candidate genes remained. Candidates were involved in extracellular matrix organization, hypoxic signaling, immune processes, and others. Nine of the 12 peptides assessed by immunogenicity analysis were able to activate naïve CD8+ T cells, including peptides derived from EGLN3. Functional analysis of EGLN3 revealed possible tumor-promoting functions.
Conclusions:
Integration of HLA ligandomics, transcriptomics, genetic, and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is recommended to expand the treatment landscape of ccRCC.
Insights
Researchers identified novel drug targets for clear cell renal cell carcinoma (ccRCC) immunotherapy by integrating multi-omics data. These ccRCC-specific HLA-presented peptides show potential for developing new treatments for advanced kidney cancer.
Area of Science:
- Oncology
- Immunology
- Genetics
Background:
- Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer subtype.
- Current therapies offer limited cure rates for advanced or metastatic ccRCC.
- Novel therapeutic targets are crucial for improving ccRCC treatment outcomes.
Purpose of the Study:
- To identify ccRCC-specific HLA-presented peptides as potential drug targets for immunotherapy.
- To develop an integrated multi-omics workflow for target discovery.
- To validate candidate targets in independent cohorts and assess their immunogenicity.
Main Methods:
- Mass spectrometry-based ligandomics of ccRCC tumors and normal tissues.
- Transcriptome and gene set enrichment analyses to identify ccRCC-activated pathways.
- Integration of -omics data (ligandomics, transcriptomics, genomics, epigenetics) for target identification and validation.
- Analysis of DNA methylation, somatic mutations, and correlation with metabolites and immune markers.
- CD8+ T cell priming assays to assess peptide immunogenicity.
Main Results:
- Identified 34,226 HLA class I and 19,325 class II peptides; 443 class I and 203 class II peptides were ccRCC-specific.
- 113 final candidate genes remained after validation, involved in pathways like ECM organization and hypoxic signaling.
- Nine of 12 assessed peptides activated naïve CD8+ T cells, including those from EGLN3.
- EGLN3 was identified as a potential tumor-promoting gene.
Conclusions:
- The integrated approach successfully identified novel, functionally relevant therapeutic targets for ccRCC immunotherapy.
- The identified HLA-presented peptides represent promising candidates for ccRCC drug development.
- Further validation of these targets is recommended to expand the therapeutic landscape for ccRCC.
