Amplifications at 9p24 have been identified in breast cancer and other malignancies, but the genes within this locus casually associated with oncogenicity or tumor progression remain unclear. Targeted next-generation sequencing of post-chemotherapy triple-negative breast cancers (TNBC) identified a group of 9p24-amplified tumors, which contained focal amplification of the Janus kinase-2 (JAK2) gene. These patients had markedly inferior recurrence-free and overall survival compared to patients with TNBC without JAK2 amplification. Presence of JAK2/9p24 amplifications occurred at higher rates in chemotherapy-treated TNBCs than in untreated TNBCs or basal-like breast cancers, or in other subtypes. Similar rates of JAK2 amplification were confirmed in patient-derived TNBC xenografts. In patients where longitudinal specimens were available, JAK2 amplification was selected for during neoadjuvant chemotherapy and eventual metastatic spread, suggesting a role in tumorigenicity and chemoresistance, phenotypes often attributed to a cancer stem-like cell population. In TNBC cell lines with JAK2 copy gains or amplification, specific inhibition of JAK2-STAT6 signaling reduced mammosphere formation and cooperated with chemotherapy in reducing tumor growth in vivo. In these cells, inhibition of JAK1-STAT3 signaling had little effect or, in some cases, counteracted JAK2-specific inhibition. Collectively, these results suggest that JAK2-specific inhibitors are more efficacious than dual JAK1/2 inhibitors against JAK2-amplified TNBCs. Furthermore, JAK2 amplification is a potential biomarker for JAK2-dependence which, in turn, can be used to select patients for clinical trials with JAK2 inhibitors.

Bristol-Myers Squibb, and Genentech. JAS is a compensated member of the advisory boards of Bristol-Myers Squibb, Pfizer, Array, Genentech, Incyte, and Curis and has received research support from Pfizer, Bristol-Myers Squibb, and Curis. PBF receives research funding from Incyte. JMB, MES, MVE, VS, and DBJ are coauthors on a patent pending for use of MHC-II to predict responses from immunotherapy (15/376,276). RSD, DMS, DBJ, and JMB are coauthors on a patent pending for use of FCRL6 antibodies for cancer therapy (62/584,458). JB and JYK are employees of Navigate BioPharma Services and receive compensation as such.

Immunotherapies targeting programmed cell death protein 1 (PD-1) or its ligand, programmed cell death ligand 1 (PD-L1), dramatically improve the survival of melanoma patients. However, only ∼40% of treated patients demonstrate a clinical response to single-agent anti-PD-1 therapy. An intact tumor response to type-II interferon (i.e. IFN-γ) correlates with response to anti-PD-1, and patients with de novo or acquired resistance may harbor loss-of-function alterations in the JAK/STAT pathway, which lies downstream of the interferon gamma receptor (IFNGR1/2). In this study, we dissected the specific roles of individual JAK/STAT pathway members on the IFN-γ response, and identified JAK1 as the primary mediator of JAK/STAT signaling associated with IFN-γ-induced expression of antigen-presenting molecules MHC-I and MHC-II, as well as PD-L1 and the cytostatic response to IFN-γ. In contrast to the crucial role of JAK1, JAK2 was largely dispensable in mediating most IFN-γ effects. In a mouse melanoma model, inhibition of JAK1/2 in combination with anti-PD-L1 therapy partially blocked anti-tumor immunologic responses, while selective JAK2 inhibition appeared to augment therapy. Amplification of JAK/STAT signaling in tumor cells through genetic inhibition of the negative regulator PTPN2 potentiated IFN-γ response in vitro and in vivo, and may be a target to enhance immunotherapy efficacy.

Triple-negative breast cancers (TNBCs) are heterogeneous and aggressive, with high mortality rates. TNBCs frequently respond to chemotherapy, yet many patients develop chemoresistance. The molecular basis and roles for tumor cell–stromal crosstalk in establishing chemoresistance are complex and largely unclear. Here we report molecular studies of paired TNBC patient–derived xenografts (PDXs) established before and after the development of chemoresistance. Interestingly, the chemoresistant model acquired a distinct KRAS Q61R mutation that activates K-Ras. The chemoresistant KRAS -mutant model showed gene expression and proteomic changes indicative of altered tumor cell metabolism. Specifically, KRAS -mutant PDXs exhibited increased redox ratios and decreased activation of AMPK, a protein involved in responding to metabolic homeostasis. Additionally, the chemoresistant model exhibited increased immunosuppression, including expression of CXCL1 and CXCL2, cytokines responsible for recruiting immunosuppressive leukocytes to tumors. Notably, chemoresistant KRAS- mutant tumors harbored increased numbers of granulocytic myeloid-derived suppressor cells (gMDSCs). Interestingly, previously established Ras/MAPK-associated gene expression signatures correlated with myeloid/neutrophil-recruiting CXCL1/2 expression and negatively with T cell–recruiting chemokines (CXCL9/10/11) across patients with TNBC, even in the absence of KRAS mutations. MEK inhibition induced tumor suppression in mice while reversing metabolic and immunosuppressive phenotypes, including chemokine production and gMDSC tumor recruitment in the chemoresistant KRAS-mutant tumors. These results suggest that Ras/MAPK pathway inhibitors may be effective in some breast cancer patients to reverse Ras/MAPK-driven tumor metabolism and immunosuppression, particularly in the setting of chemoresistance.

No abstract