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Innate resistance of PD-1 blockade through loss of function mutations in JAK resulting in inability to express PD-L1 upon interferon exposure
  1. Daniel Shin1,
  2. Angel Garcia-Diaz1,
  3. Jesse Zaretsky2,
  4. Helena Escuin-Ordinas1,
  5. Siwen Hu-Lieskovan3,
  6. Nicolaos J Palaskas1,
  7. Willy Hugo1,
  8. Marie Sara Komenan1,
  9. Bartosz Chmielowski4,
  10. Grace Cherry1,
  11. Beata Berent-Maoz1,
  12. Thomas G Graeber1,
  13. Roger Lo1,
  14. Begonya Comin-Anduix5 and
  15. Antoni Ribas6
  1. Aff1 grid.19006.3e0000000096326718UCLA Los Angeles CA USA
  2. Aff2 grid.19006.3e0000000096326718UCLA Molecular and Medical Pharmacology Los Angeles CA USA
  3. Aff3 grid.19006.3e0000000096326718David Geffen School of Medicine at UCLA Los Angeles CA USA
  4. Aff4 grid.19006.3e0000000096326718Division of Hematology - Medical OncologyUCLA Jonsson Comprehensive Cancer Center Los Angeles CA USA
  5. Aff5 grid.19006.3e0000000096326718UCLA, School of Medicine LA CA USA
  6. Aff6 grid.413083.d0000000091428600University of California at Los Angeles Medical Center Los Angeles CA USA

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Meeting abstracts


PD-L1-negative tumors assessed by immunohistochemistry often still respond to PD-1 blockade. PD-L1 is inducible by interferon, therefore, absolute negative tumors are the ones unable to up-regulate PD-L1 in response to interferons. Genetic mutations in the interferon receptor signaling pathway leading to loss of PD-L1 up-regulation were hypothesized to exhibit innate resistance to PD-1 blockade.

Experimental procedures

After optimization, 50 primary human melanoma cell lines were exposed to interferons (alpha, beta and gamma) and PD-L1 expression was measured. Interferon signaling was assessed by single cell phospho-proteomics, pSTAT1 (Y701), pSTAT3, pSTAT5, pSTAT6 expression level by flow cytometry (FACS LSRII). Western blot assessed JAK1/JAK2/IRF1 as well as STAT/pSTAT expression and Whole exome sequencing was performed by next generation sequencing for three selected melanoma cell lines and on biopsies from 25 patients with advanced melanoma treated with anti-PD-1 therapy.


Three out of 50 melanoma cell lines were unable to up-regulate PD-L1 in response to interferon gamma; two of them had disruptive mutations in JAK1 or JAK2, and a third one had a defect in expression of IRF1 in response to interferons. Western blot analysis confirmed loss of function for the JAK1/JAK2 mutations and loss of downstream IRF1/STAT1/3/5 phosphorylation events. Whole exome sequencing of biopsies from 15 patients with metastatic melanoma who had objective response to PD-1 blockade (pembrolizumab) showed no homozygous inactivating mutations in interferon signaling pathway genes. Interestingly, one patient with the highest mutational load out of 10 patients without clinical response to PD-1 blockade had an amplified allele of JAK1 with a P429S mutation in the src-homology (SH2) domain. A cell line derived from this patient showed lack of sustained up-regulating of PD-L1 expression in response to interferon gamma by, and Western blot confirmed loss of JAK1 expression. Immunohistochemistry of tumor biopsy for this patient showed few CD8+ T cells.


This study has defined genetic mechanisms of innate resistance to PD-1 blockade which lead to inhibition of adaptive PD-L1 expression in patients with advanced melanoma. This work suggests lack of interferon-gamma induced PD-L1 upregulation has the potential to be a negative selective marker for PD-1 blockade therapy.