Autophagy Promotes Growth of High Tumor Mutational Burden Tumors by Inhibiting a T Cell Immune Response [Exome-seq]

Autophagy degrades and recycles intracellular components to sustain metabolism and survival during starvation. Tumor cells upregulate and require autophagy to support their metabolism and enhance their proliferation and malignancy, and host autophagy also promotes tumor growth by providing essential tumor nutrients such as arginine in the circulation or alanine in the local tumor microenvironment. In addition to its metabolic role, autophagy regulates immune cell homeostasis and function, and suppresses inflammation, which may also play a role in cancer. Although host autophagy does not promote a T cell anti-tumor immune response in tumors with low tumor mutational burden (TMB), whether this was the case in tumors with high TMB was not known. Here we show that in contrast to low TMB tumors, host-specific deletion of the essential autophagy gene Atg7 induces a pro-inflammatory cytokine response and limits the growth of high TMB tumors, which is rescued by T-cell depletion. Expression of immune-related genes is increased in tumors from Atg7?/? hosts in a T-cell dependent manner. Tumors from Atg7?/? hosts also have decreased T regulatory cells (Tregs), and depletion of Tregs phenocopies the reduced tumor growth observed in Atg7?/? hosts. Moreover, loss of Stimulator of interferon genes (Sting) or IFNg restores growth of high TMB tumors on Atg7?/? hosts. Finally, similar to whole-body loss of autophagy, specific loss of autophagy in the liver is sufficient to limit tumor growth. Thus, autophagy, especially in the liver, promotes tumor immune tolerance by limiting STING, T cells, and IFNg, which enables tumor growth. We have designated this: Hepatic Autophagy Immune Tolerance (HAIT). Autophagy thereby promotes tumor growth through both metabolic and immune mechanisms depending on mutational load, and autophagy inhibition is an effective means to promote an anti-tumor T-cell response in high TMB tumors. Genomic DNA Profiling using Agilent SureSelect Mouse All Exon kit and sequencing using Illumina NextSeq550 Overall design: DNA was extracted from MB49, YUMM 1.1 and UV YUMM 1.1-9 cell lines using the QIAsymphony DSP DNA midi kit (937255, Qiagen). Mouse whole exome libraries were constructed using Agilent SureSelect Mouse All Exon kit according to the manufacturer's protocol. The resulting sequencing libraries were analyzed using Agilent D1000 screentape and quantified using KAPA qPCR. Libraries were then normalized and pooled into one pool. The library pool was then clustered and sequenced on the Illumina NextSeq550 instrument using 2x151bp paired end reads to a mean death of 80X, following the manufacturer's protocols 4 samples