Project description:A mutation that results in tumor rejection activity in a neoepitope (which is a poor binder of Kd) influences the immunogenicity of the tumor as a whole. Our results demonstrate the activity in vivo of a poorly-MHC I-binding cancer neoepitope.
Project description:By using >36,000 immunogenicity assay results, we developed a method to identify peptide-MHC complexes whose structural alignment facilitates T cell reaction. Our method accurately predicted neoepitopes for MHC II as well as MHC I that were responsive to checkpoint blockade when applied to >1,200 samples of various tumor types and on-therapy melanoma samples. To investigate selection by spontaneous immunity at the single epitope level, we analyzed the frequency spectrum of >25 million mutations in >9,000 treatment-naïve tumors in association with >100 immune phenotypes. MHC II immunogenicity specifically lowered variant frequencies in tumors under high immune pressure particularly with high TCR clonality and MHC II expression.
Project description:Cancer immunotherapy has revolutionized patient outcomes by enhancing immune responses, with major histocompatibility complex class II (MHC-II) playing a pivotal role. While MHC-II is classically expressed by professional antigen-presenting cells (pAPCs), emerging evidence highlights its expression by cancer cells, where it correlates with enhanced immune infiltration and favorable clinical outcomes. However, the regulatory mechanisms of cancer cell-intrinsic MHC-II remain unclear. Here, using genome-wide CRISPR-Cas9 screens, we identify the aryl hydrocarbon receptor (AhR) and its nuclear translocator (ARNT) as key regulators of MHC-II expression in human melanoma cells. The expression level and ligand-dependent activity of AhR and ARNT significantly correlate with cancer cell-intrinsic MHC-II expression. Multi-omics analyses reveal that this regulation is mediated through transcriptional activation of the MHC-II transactivator, CIITA, via binding of AhR-ARNT to its second promoter, pII. Our findings uncover a previously unrecognized regulatory axis for MHC-II expression in tumors, presenting new targets for enhancing immunotherapy.
Project description:Cancer immunotherapy has revolutionized patient outcomes by enhancing immune responses, with major histocompatibility complex class II (MHC-II) playing a pivotal role. While MHC-II is classically expressed by professional antigen-presenting cells (pAPCs), emerging evidence highlights its expression by cancer cells, where it correlates with enhanced immune infiltration and favorable clinical outcomes. However, the regulatory mechanisms of cancer cell-intrinsic MHC-II remain unclear. Here, using genome-wide CRISPR-Cas9 screens, we identify the aryl hydrocarbon receptor (AhR) and its nuclear translocator (ARNT) as key regulators of MHC-II expression in human melanoma cells. The expression level and ligand-dependent activity of AhR and ARNT significantly correlate with cancer cell-intrinsic MHC-II expression. Multi-omics analyses reveal that this regulation is mediated through transcriptional activation of the MHC-II transactivator, CIITA, via binding of AhR-ARNT to its second promoter, pII. Our findings uncover a previously unrecognized regulatory axis for MHC-II expression in tumors, presenting new targets for enhancing immunotherapy.
Project description:The immune response against tuberculosis relies, at least in part, on CD4+ T cells. Protective vaccines require the induction of antigen-specific CD4+ T cells via mycobacterial peptides presented by MHC class-II in infected macrophages. We have purified MHC class-I and MHC-II peptides and analysed them by mass spectrometry. We have successfully identified 97 mycobacterial peptides presented by MHC-II and 54 presented by MHC-I, from 76 and 41 antigens, respectively. The sequences of selected peptides were confirmed by spectral match validation and immunogenicity evaluated by IFN-gamma ELISpot against peripheral blood mononuclear cells from volunteers vaccinated with BCG, M.tb latently infected subjects or patients with tuberculosis disease. Three antigens were expressed in viral vectors, and evaluated as vaccine candidates alone or in combination in a murine aerosol M.tb challenge model. When delivered in combination, the three candidate vaccines conferred significant protection in the lungs and spleen compared with BCG alone, demonstrating proof-of-concept for this unbiased approach to identifying novel candidate antigens.
Project description:Through analyzing publicly available single-cell and bulk sequencing data from ICI-treated cohorts, ZNF180-regulome was predictive of ICI responses in independent bulk sequencing cohorts, and ZNF180+ tumors persisted after the therapy with immune-suppressive features such as MHC-I loss and CD155 expressions, the primary ligand to TIGIT inhibitory receptor. To investigate regulatory roles of ZNF180 to confer these immune suppressive phenotypes, we performed ZNF180 knock-down in melanoma cells in vitro with different genetic backgrounds, namely A375 (BRAF-mutant) and SKMEL147 (NRAS-mutant) cells, and performed RNA- and ATAC-sequencing. The integrative analysis revealed ZNF180 silencing promoted tumor immunogenicity through gain of accessibility on MHC-I/-II coding genes, CD155 down-regulation to avoid TIGIT/CD155 checkpoint signaling, and suppressed AP-1 transcription factor activities as the drivers of melanoma reprogramming towards MITFlowAXLhigh de-differentiated cells. Further, ZNF180 silencing increased CD4 helper T-cell infiltrations in tumors and regressed the tumors in vivo. Collectively, these results indicate ZNF180 is a tumor intrinsic regulator of melanoma plasticity to drive de-differentiated phenotypes with immune-suppressive features including loss of immunogenicity, T-cell inhibitory signals through TIGIT/CD155 checkpoint and exclusion of CD4 helper T-cells. As ZNF180-regulome manifests in non-metastatic melanoma in contrast to the current focus of standard-of-care ICI on the metastatic disease, these results establish ZNF180-regulome as a biomarker and novel therapeutic avenue for early stage melanoma to intervene ICI resistance.
Project description:Cancer immunotherapy has revolutionized patient outcomes by enhancing immune responses, with major histocompatibility complex class II (MHC-II) playing a pivotal role. While MHC-II is classically expressed by professional antigen-presenting cells (pAPCs), emerging evidence highlights its expression by cancer cells, where it correlates with enhanced immune infiltration and favorable clinical outcomes. However, the regulatory mechanisms of cancer cell-intrinsic MHC-II remain unclear. Here, using genome-wide CRISPR-Cas9 screens, we identify the aryl hydrocarbon receptor (AhR) and its nuclear translocator (ARNT) as key regulators of MHC-II expression in human melanoma cells. The expression level and ligand-dependent activity of AhR and ARNT significantly correlate with cancer cell-intrinsic MHC-II expression. Multi-omics analyses reveal that this regulation is mediated through transcriptional activation of the MHC-II transactivator, CIITA, via binding of AhR-ARNT to its second promoter, pII. Our findings uncover a previously unrecognized regulatory axis for MHC-II expression in tumors, presenting new targets for enhancing immunotherapy.
Project description:Cancer immunotherapy has revolutionized patient outcomes by enhancing immune responses, with major histocompatibility complex class II (MHC-II) playing a pivotal role. While MHC-II is classically expressed by professional antigen-presenting cells (pAPCs), emerging evidence highlights its expression by cancer cells, where it correlates with enhanced immune infiltration and favorable clinical outcomes. However, the regulatory mechanisms of cancer cell-intrinsic MHC-II remain unclear. Here, using genome-wide CRISPR-Cas9 screens, we identify the aryl hydrocarbon receptor (AhR) and its nuclear translocator (ARNT) as key regulators of MHC-II expression in human melanoma cells. The expression level and ligand-dependent activity of AhR and ARNT significantly correlate with cancer cell-intrinsic MHC-II expression. Multi-omics analyses reveal that this regulation is mediated through transcriptional activation of the MHC-II transactivator, CIITA, via binding of AhR-ARNT to its second promoter, pII. Our findings uncover a previously unrecognized regulatory axis for MHC-II expression in tumors, presenting new targets for enhancing immunotherapy.
Project description:This mathematical model describes interactions between glioma tumors and the immune system that may occur following direct intra-tumoral administration of ex-vivo activated alloreactive cytotoxic-T-lymphocytes (aCTLs) as part of adoptive immunotherapy. The model includes descriptions of aCTL, neoplastic cells, MHC class I and II molecules, TGF-beta and IFN-gamma.