Genome-wide CRISPR/Cas9 screens reveal shared and cell-specific mechanisms of resistance to SHP2 inhibition

SHP2 (PTPN11) acts upstream of SOS1/2 to enable RAS activation. Allosteric SHP2 inhibitors (SHP2i) in the clinic prevent SHP2 activation, block proliferation of RTK- or cycling RAS mutant-driven cancers, and overcome “adaptive resistance.” To identify SHP2i resistance mechanisms, we performed genome-wide CRISPR/Cas9 knockout screens on two SHP2i-sensitive cell lines, recovering genes expected to cause resistance (NF1, PTEN, CDKN1B, LZTR1, and RASA2) and novel targets (INPPL1, MAP4K5, epigenetic modifiers). We screened 14 additional lines with a focused CRISPR library targeting common “hits” from the genome-wide screens. LZTR1 deletion conferred resistance in 12/14 lines, followed by MAP4K5 (8/14), SPRED2/STK40 (6/14), and INPPL1 (5/14). INPPL1, MAP4K5, or LZTR1 deletion reactivated ERK signaling. INPPL1-mediated sensitization to SHP2i required its NPXY motif but not lipid phosphatase activity. MAP4K5 acted upstream of MEK through a kinase-dependent target(s); LZTR1 had cell-dependent effects on RIT and RAS stability. INPPL1, MAP4K5, or LZTR1 deletion also conferred SHP2i resistance in vivo. Defining the SHP2i resistance landscape could suggest effective combination approaches.

J Exp Med (2023) 220 (5)

Creating MHC-restricted neoantigens with covalent inhibitors that can be targeted by immune therapy

Intracellular oncoproteins can be inhibited with targeted therapy, but responses are not durable. Immune therapies can be curative, but most oncogene-driven tumors are unresponsive to these agents. Fragments of intracellular oncoproteins can act as neoantigens presented by the major histocompatibility complex (MHC) but recognizing minimal differences between oncoproteins and their normal counterparts is challenging. We have established a platform technology that exploits hapten-peptide conjugates generated by covalent inhibitors to create distinct neoantigens that selectively mark cancer cells. Using the FDA-approved covalent inhibitors sotorasib and osimertinib, we developed “HapImmuneTM” antibodies that bind to drug-peptide conjugate/MHC complexes but not to the free drugs. A HapImmuneTM-based bispecific T cell engager selectively and potently kills sotorasib-resistant lung cancer cells upon sotorasib treatment. Notably, it is effective against KRASG12C mutant cells with different HLA supertypes, HLA-A*02 and A*03/11, suggesting loosening of MHC restriction. Our strategy creates targetable neoantigens by design, unifying targeted and immune therapies.

Cancer Discov CD-22-1074


Combined Inhibition of SHP2 and CXCR1/2 Promotes Anti-Tumor T Cell Response in NSCLC


Clinical trials of SHP2 inhibitors (SHP2i) alone and in various combinations are ongoing for multiple tumors with over-activation of the RAS/ERK pathway. SHP2 plays critical roles in normal cell signaling; hence, SHP2is could influence the tumor microenvironment. We found that SHP2i treatment depleted alveolar and M2-like macrophages and promoted B and T lymphocyte infiltration in Kras- and Egfr-mutant non-small cell lung cancer (NSCLC). However, treatment also increased intratumor gMDSCs via tumor-intrinsic, NF-kB-dependent production of CXCR2 ligands. Other RAS/ERK pathway inhibitors also induced CXCR2 ligands and gMDSC influx in mice, and CXCR2 ligands were induced in tumors from patients on KRASG12C-inhibitor trials. Combined SHP2(SHP099)/CXCR1/2(SX682) inhibition depleted a specific cluster of S100a8/9high gMDSCs, generated Klrg1+ CD8+ effector T cells with a strong cytotoxic phenotype but expressing the checkpoint receptor NKG2A, and enhanced survival in Kras-and Egfr-mutant models. Our results argue for testing RAS/ERK pathway/CXCR1/2/NKG2A inhibitor combinations in NSCLC patients.


Our study shows that inhibiting the SHP2/RAS/ERK pathway triggers NF-kB-dependent up-regulation of CXCR2 ligands and recruitment of S100A8high gMDSCs, which suppress T cells in NSCLC. Combining SHP2 and CXCR2 inhibitors blocks this gMDSC immigration, resulting in enhanced Th1 polarization, induction of CD8+ KLRG1+ effector T cells with high cytotoxic activity and improved survival in multiple NSCLC models.

SHP2 Inhibition Prevents Adaptive Resistance to MEK Inhibitors in Multiple Cancer Models

The RAS/ERK MAP kinase pathway is aberrantly activated in a large percentage of human cancers, and promotes malignant behavior.  Inhibitors of MEK, one of the key intermediates in this pathway, have had limited utility in the clinic, often due to the rapid development of “intrinsic resistance.”  Intrinsic resistance is due to up regulation of multiple growth factor receptors and their ligands, and previous work by the lab and by others has shown that is required for RAS activation by these receptors.  Here we found that combining MEK and SHP2 inhibitors shows broad efficacy against a wide range of malignancies, and also that SHP2 inhibitors as single agents can antagonize certain types of RAS mutations (fast cycling mutants).

SHP2 Inhibition Prevents Adaptive Resistance to MEK Inhibitors in Multiple Cancer Models.
Cancer Discov. 2018 Oct;8(10):1237-1249.



Vitamin C in Stem Cell Reprogramming and Cancer

Mutations of one copy of TET2, whose protein product promotes DNA (and RNA) hydroxymethylation (and eventually, DNA and RNA de-methylation, are commonly associated with myelodyspastic syndromes (MDS) and acute myeloid leukemia, among other hematopoietic neoplasms. Previous work had suggested that Vitamin C, an essential co-factor of TET2, can promote TET2 activation as well.  We found that high dose vitamin C, acting via residual TET2 and TET3, had potent anti-neoplastic effects in mouse and human models of MDS/AML. Molecular analysis confirmed that this treatment promotes demethylation of key leukemia-associated genes, including base excision repair genes. The latter result suggested that PARP inhibitors might further increase Vitamin C efficacy, which we also demonstrated.

Vitamin C in Stem Cell Reprogramming and Cancer
Trends Cell Biol. 2018 Sep;28(9):698-708.