172MO - Novel regulators of antigen presentation and therapeutic reactivation of MHC-I to overcome immune evasion in small cell lung cancer

Background

Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine cancer and the addition of immune checkpoint blockade (ICB) to first-line chemotherapy for SCLC has shown modest benefits. SCLCs evade anti-tumor immunity by repressing MHC-I expression and antigen presentation (AP). We comprehensively analyzed SCLC clinical samples to identify SCLC molecular subtypes associated with MHC repression.

Methods

Molecular profiling of 5056 NSCLCs and 944 SCLC tumors was performed using DNA and RNA sequencing, and IHC. We performed single-cell RNA sequencing of SCLC clinical samples and genetically engineered mouse models (GEMMs).

Results

We identified novel repressed AP genes and gene networks associated with HLA repression. We generated canonical (MHC-I and II) and non-canonical expression scores in SCLC clinical samples that measure the spectrum of AP repression across SCLC subtypes. The MHC-I score was correlated with RNA expression of key genes and previously validated immune signatures (T cell-inflamed, NK cell, and STING pathway) and was correlated with the outcome of immunotherapy. We identified transcriptional regulators associated with our MHC-I-score using enhancer networks and correlative gene expression analyses. CRISPR knockout studies in SCLC cell lines identified that expression of the non-homologous end-joining (NHEJ) gene, PRKDC (DNAPKCs), is negatively correlated with HLA-A/B/C. Ablation of DNAPKCs significantly upregulated the expression of MHC-I, HLA-A/B/C, TAP1, and TAP2 in SCLC. Pharmacological inhibition of DNAPKCS enhanced MHC-I expression and significantly augmented the anti-tumor immune response of PD-L1 blockade in multiple GEMMs.

Conclusions

We provide novel insight into the mechanisms of immunotherapy resistance and MHC repression in SCLC. We established the heterogeneity of MHC repression across SCLC tumors and identified networks and pathways that can be targeted to de-repress MHC-I in SCLC. We establish the direct role of DNAPKCs as a therapeutic target that can augment the anti-tumor immune response of PD-L1 blockade by induction of MHC-I expression in SCLC. Our findings have important implications for harnessing NHEJ regulators for immunotherapy in SCLC.

Legal entity responsible for the study

The authors.

Funding

Has not received any funding.

Disclosure

All authors have declared no conflicts of interest.