A comprehensive immunogenomic analysis of over 10,000 tumors across 33 cancer types was conducted using data from the TCGA. Six immune subtypes were identified: Wound Healing, IFN-γ Dominant, Inflammatory, Lymphocyte Depleted, Immunologically Quiet, and TGF-β Dominant. These subtypes are characterized by distinct immune cell compositions, Th1:Th2 ratios, intratumoral heterogeneity, aneuploidy, neoantigen load, and prognosis. Driver mutations correlated with leukocyte levels, and multiple networks, including transcription, microRNAs, copy number, and epigenetic processes, were involved in tumor-immune interactions. The study provides a resource for understanding tumor-immune interactions and advancing immunotherapy research.
The six immune subtypes span multiple tumor types and are associated with different immune response patterns. C1 (Wound Healing) showed Th2 bias and high proliferation, while C2 (IFN-γ Dominant) had high M1/M2 macrophage polarization and TCR diversity. C3 (Inflammatory) had elevated Th17 and Th1 genes, and lower aneuploidy. C4 (Lymphocyte Depleted) had a macrophage signature and high M2 response. C5 (Immunologically Quiet) had low lymphocyte and high macrophage responses. C6 (TGF-β Dominant) had high lymphocytic infiltration and TGF-β signature. These subtypes have prognostic implications for cancer management.
The study characterized immune infiltrate composition, including leukocyte fraction, TILs, and immune cell types. Prognostic associations were found between immune subtypes and survival. C3 had the best prognosis, while C4 and C6 had the worst. Immune subtypes were associated with different immune responses, including Th17, Th1, and Th2. Tumor types showed varied immune responses, with some associated with better outcomes.
Somatic variations, such as mutations in driver genes, were linked to immune subtypes. C1 was enriched in TP53, PIK3CA, PTEN, and KRAS mutations. C2 was enriched in HLA-A, B, and CASP8. C3 had BRAF, CDH1, and PBRM1 mutations. C4 had CTNNB1, EGFR, and IDH1 mutations. C5 had IDH1, ATRX, and CIC mutations. C6 had KRAS G12 mutations. These mutations influenced immune infiltration and prognosis.
Demographic and germline variations, such as gender and ancestry, influenced immune cell content and PD-L1 expression. Women had higher PD-L1 expression in some cancers, while individuals of African ancestry had lower PD-L1 expression. These variations may impact the efficacy of immunotherapy.
Neoantigen loadA comprehensive immunogenomic analysis of over 10,000 tumors across 33 cancer types was conducted using data from the TCGA. Six immune subtypes were identified: Wound Healing, IFN-γ Dominant, Inflammatory, Lymphocyte Depleted, Immunologically Quiet, and TGF-β Dominant. These subtypes are characterized by distinct immune cell compositions, Th1:Th2 ratios, intratumoral heterogeneity, aneuploidy, neoantigen load, and prognosis. Driver mutations correlated with leukocyte levels, and multiple networks, including transcription, microRNAs, copy number, and epigenetic processes, were involved in tumor-immune interactions. The study provides a resource for understanding tumor-immune interactions and advancing immunotherapy research.
The six immune subtypes span multiple tumor types and are associated with different immune response patterns. C1 (Wound Healing) showed Th2 bias and high proliferation, while C2 (IFN-γ Dominant) had high M1/M2 macrophage polarization and TCR diversity. C3 (Inflammatory) had elevated Th17 and Th1 genes, and lower aneuploidy. C4 (Lymphocyte Depleted) had a macrophage signature and high M2 response. C5 (Immunologically Quiet) had low lymphocyte and high macrophage responses. C6 (TGF-β Dominant) had high lymphocytic infiltration and TGF-β signature. These subtypes have prognostic implications for cancer management.
The study characterized immune infiltrate composition, including leukocyte fraction, TILs, and immune cell types. Prognostic associations were found between immune subtypes and survival. C3 had the best prognosis, while C4 and C6 had the worst. Immune subtypes were associated with different immune responses, including Th17, Th1, and Th2. Tumor types showed varied immune responses, with some associated with better outcomes.
Somatic variations, such as mutations in driver genes, were linked to immune subtypes. C1 was enriched in TP53, PIK3CA, PTEN, and KRAS mutations. C2 was enriched in HLA-A, B, and CASP8. C3 had BRAF, CDH1, and PBRM1 mutations. C4 had CTNNB1, EGFR, and IDH1 mutations. C5 had IDH1, ATRX, and CIC mutations. C6 had KRAS G12 mutations. These mutations influenced immune infiltration and prognosis.
Demographic and germline variations, such as gender and ancestry, influenced immune cell content and PD-L1 expression. Women had higher PD-L1 expression in some cancers, while individuals of African ancestry had lower PD-L1 expression. These variations may impact the efficacy of immunotherapy.
Neoantigen load