Science Immunology

The PDF file includes:

  • Fig. S1. Optimization of screen conditions using B2M KO cells.
  • Fig. S2. Library representation is sufficiently maintained throughout the screen, allowing detection of depleted and enriched sgRNAs.
  • Fig. S3. CRISPR KO screen for growth modifiers in MC38 cells identifies a high proportion of core essential genes.
  • Fig. S4. Genetic inactivation of autophagy genes does not inhibit growth of MC38 cells.
  • Fig. S5. The cytotoxic function of preactivated T cells is not limited by TNFα blockade.
  • Fig. S6. Map3k7 KO increases tumor cell killing by T cells.
  • Fig. S7. Rbck1 KO increases tumor cell killing by T cells.
  • Fig. S8. Rela KO increases tumor cell killing by T cells.
  • Fig. S9. NF-κB signaling pathway is active in cell lines resistant to TNFα-mediated killing.
  • Fig. S10. Atg9a KO increases tumor cell killing by T cells.
  • Fig. S11. Atg12 KO increases tumor cell killing by T cells.
  • Fig. S12. KO of autophagy genes in MC38 cells does not affect cell surface MHC-I levels or presentation of OVA peptide.
  • Fig. S13. TNFα does not induce MLKL phosphorylation in Rb1cc1 KO cells.
  • Fig. S14. Inactivation of autophagy does not increase the levels of key TNFα pathway components.
  • Fig. S15. Inactivation of autophagy does not impair TNFα-mediated induction of NF-κB target genes.
  • Fig. S16. Pharmacologic blockade of autophagy sensitizes human cancer cells to TNFα- and TRAIL-mediated killing.
  • Fig. S17. Pharmacologic blockade of autophagy sensitizes several mouse and human cancer cell lines to TNFα-mediated killing.
  • Fig. S18. Treating MC38 tumors early with PD-1/CTLA-4 antibodies results in complete tumor regression.
  • Fig. S19. Genetic inactivation of autophagy in tumors affects leukocyte infiltration.

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Other Supplementary Material for this manuscript includes the following:

  • Table S1. Gene-level MAGeCK analysis of genome-wide CRISPR KO screen in MC38 cells to identify genes that modulate killing by T cells (Excel spreadsheet).
  • Table S2. Normalized read counts for genome-wide CRISPR KO screen in MC38 cells grown in vitro without addition of T cells (Excel spreadsheet).
  • Table S3. Raw data file (Excel spreadsheet).