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Consensus NMF of 81 primary ependymoma samples at k = 3 delineates two posterior fossa subgroups in the study cohort.

Supplemental Figure Legends

STAT3, IL-6 and inflammatory response pathway signaling associated gene expression is upregulated in Group A EPN.

Experimentally determined STAT3 upregulated genes.

Ependymoma (EPN) in childhood is a brain tumor with substantial mortality. Inflammatory response has been identified as a molecular signature of high-risk Group A EPN. To better understand the biology of this phenotype and aid therapeutic development, transcriptomic data from Group A and B EPN patient tumor samples, and additional malignant and normal brain data, were analyzed to identify the mechanism underlying EPN Group A inflammation. Enrichment of IL6 and STAT3 pathway genes were found to distinguish Group A EPN from Group B EPN and other brain tumors, implicating an IL6 activation of STAT3 mechanism. EPN tumor cell growth was shown to be dependent on STAT3 activity, as demonstrated using shRNA knockdown and pharmacologic inhibition of STAT3 that blocked proliferation and induced apoptosis. The inflammatory factors secreted by EPN tumor cells were shown to reprogram myeloid cells, and this paracrine effect was characterized by a significant increase in pSTAT3 and IL8 secretion. Myeloid polarization was shown to be dependent on tumor secretion of IL6, and these effects could be reversed using IL6-neutralizing antibody or IL6 receptor–targeted therapeutic antibody tocilizumab. Polarized myeloid cell production of IL8 drove unpolarized myeloid cells to upregulate CD163 and to produce a number of proinflammatory cytokines. Collectively, these findings indicate that constitutive IL6/STAT3 pathway activation is important in driving tumor growth and inflammatory cross-talk with myeloid cells within the Group A EPN microenvironment. Effective design of Group A–targeted therapy for children with EPN may require reversal of this potentially immunosuppressive and protumor pathway. Cancer Immunol Res; 3(10); 1165–74. ©2015 AACR.

IL-6 is the driving cytokine for immune suppressive phenotype observed in 811 CM monocytes.

S3I-201 effects on cell cycle EPN cell line 811 and apoptosis in EPN cell line 723.

Ratio of Group A EPN IL6/STAT3 pathway genes in tumor versus the myeloid compartments.

Introduction: Acute myeloid leukemia (AML) is an aggressive disease with a dismal prognosis. This is largely due to high relapse rates, which stem from our inability to eliminate leukemia stem cells (LSCs) with conventional chemotherapy. As we have gained a deeper understanding of the biology of LSCs, new targets against these chemo-resistant cells have surfaced. One such example is treatment using venetoclax/azacititine, a therapy that has significantly improved the outcome for these patients. Notwithstanding, some patients show resistance to all treatments, and developing a larger repertoire of agents that target LSCs remains an unmet need in this disease. One key vulnerability of LSCs is their dependence on oxidative phosphorylation (OXPHOS). Although signal transducer and activator of transcription 3 (STAT3) has been classically studied as a transcription factor that regulates self-renewal and proliferation, it has also been shown to play an essential role in OXPHOS via regulation of the electron transport chain (ETC). Given that STAT3 is commonly overexpressed in AML, and LSCs are dependent on OXPHOS, we hypothesized that STAT3 may be an effective target for eradication of LSCs. Methods: We have developed a novel small molecule inhibitor of STAT3, SF25. This compound, as well as genetic knockdown of STAT3, was employed to test the functional role of STAT3 in primary AML specimens. Flow cytometry, colony-forming potential, and engraftment of primary samples in PDX mouse models were performed to assess therapeutic efficacy. RNA-seq, seahorse assays, and metabolomics experiments were also performed to determine molecular mechanisms linked to targeting STAT3. Results: Our data shows that inhibition of STAT3 in primary AML samples leads to decreased cell viability, colony-formation and engraftment potential in xenograft models, while not affecting normal hematopoietic stem cells. This effect appears to be a result of mitochondrial dysfunction in LSCs, as seen by a significant decrease in oxygen consumption rate of STAT3 depleted cells. The mitochondrial dysfunction and reduction in OXPHOS is mediated by the downregulation of several mitochondrial and nuclear encoded genes that are important for oxidative phosphorylation, including several electron transport chain complex genes. Inhibition of STAT3 also affects glutaminolysis, as noted by metabolomics analysis of leukemia stem cells treated with STAT3 inhibitor. We suspect this effect is mediated by down-regulation of Myc upon STAT3 inhibition, which blocks glutamine conversion to glutamate, and leads to further decrease in TCA cycle intermediates. Conclusions: Acute myeloid leukemia is an aggressive disease, largely due to the presence of a chemo-resistant population of leukemia stem cells. LSCs highly depend on proper mitochondrial function and OXPHOS, a process that is partly regulated by STAT3 via multiple mechanisms. We propose that inhibition of STAT3 is therefore an effective way of eliminating this population, making this a promising new target in the treatment of AML. Disclosures No relevant conflicts of interest to declare.

Ependymoma (EPN) in childhood is a brain tumor with substantial mortality. Inflammatory response has been identified as a molecular signature of high-risk Group A EPN. To better understand the biology of this phenotype and aid therapeutic development, transcriptomic data from Group A and B EPN patient tumor samples, and additional malignant and normal brain data, were analyzed to identify the mechanism underlying EPN Group A inflammation. Enrichment of IL6 and STAT3 pathway genes were found to distinguish Group A EPN from Group B EPN and other brain tumors, implicating an IL6 activation of STAT3 mechanism. EPN tumor cell growth was shown to be dependent on STAT3 activity, as demonstrated using shRNA knockdown and pharmacologic inhibition of STAT3 that blocked proliferation and induced apoptosis. The inflammatory factors secreted by EPN tumor cells were shown to reprogram myeloid cells, and this paracrine effect was characterized by a significant increase in pSTAT3 and IL8 secretion. Myeloid polarization was shown to be dependent on tumor secretion of IL6, and these effects could be reversed using IL6-neutralizing antibody or IL6 receptor–targeted therapeutic antibody tocilizumab. Polarized myeloid cell production of IL8 drove unpolarized myeloid cells to upregulate CD163 and to produce a number of proinflammatory cytokines. Collectively, these findings indicate that constitutive IL6/STAT3 pathway activation is important in driving tumor growth and inflammatory cross-talk with myeloid cells within the Group A EPN microenvironment. Effective design of Group A–targeted therapy for children with EPN may require reversal of this potentially immunosuppressive and protumor pathway. Cancer Immunol Res; 3(10); 1165–74. ©2015 AACR.