A prognostic matrix code defines functional glioblastoma phenotypes and niches

Interactions among tumor, immune and vascular niches play major roles in driving glioblastoma (GBM) malignancy and treatment responses. The composition, heterogeneity, and localization of extracellular core matrix proteins (CMPs) that mediate such interactions, however, are not well understood. Here, we characterize functional and clinical relevance of genes encoding CMPs in GBM at bulk, single cell, and spatial anatomical resolution. We identify a "matrix code" for genes encoding CMPs whose expression levels categorize GBM tumors into matrisome-high and matrisome-low groups that correlate with worse and better patient survival, respectively. The matrisome enrichment is associated with specific driver oncogenic alterations, mesenchymal state, infiltration of pro-tumor immune cells and immune checkpoint gene expression. Anatomical and single cell transcriptome analyses indicate that matrisome gene expression is enriched in vascular and leading edge/infiltrative anatomic structures that are known to harbor glioma stem cells driving GBM progression. Finally, we identified a 17-gene matrisome signature that retains and further refines the prognostic value of genes encoding CMPs and, importantly, potentially predicts responses to PD1 blockade in clinical trials for GBM. The matrisome gene expression profiles provide potential biomarkers of functionally relevant GBM niches that contribute to mesenchymal-immune cross talk and patient stratification which could be applied to optimize treatment responses.

A prognostic matrix code defines functional glioblastoma phenotypes and niches

Interactions among tumor, immune and vascular niches play major roles in driving glioblastoma (GBM) malignancy and treatment responses. The composition, heterogeneity, and localization of extracellular core matrix proteins (CMPs) that mediate such interactions, however, are not well understood. Here, we characterize functional and clinical relevance of genes encoding CMPs in GBM at bulk, single cell, and spatial anatomical resolution. We identify a "matrix code" for genes encoding CMPs whose expression levels categorize GBM tumors into matrisome-high and matrisome-low groups that correlate with worse and better survival, respectively, of patients. The matrisome enrichment is associated with specific driver oncogenic alterations, mesenchymal state, infiltration of pro-tumor immune cells and immune checkpoint gene expression. Anatomical and single cell transcriptome analyses indicate that matrisome gene expression is enriched in vascular and leading edge/infiltrative anatomic structures that are known to harbor glioma stem cells driving GBM progression. Finally, we identified a 17-gene matrisome signature that retains and further refines the prognostic value of genes encoding CMPs and, importantly, potentially predicts responses to PD1 blockade in clinical trials for GBM. The matrisome gene expression profiles may provide biomarkers of functionally relevant GBM niches that contribute to mesenchymal-immune cross talk and patient stratification to optimize treatment responses.

Abstract 5871: Pan-cancer myeloid cell analysis at the single cell level reveals the influence of distinct organ sites in myeloid cell phenotypes and support targeting S100A4 to reverse immune suppression

With abundant pro-tumorigenic myeloid cells and few tumoricidal tumor-infiltrating lymphocytes (<5%), GBM is representative of “immune cold” tumors. As such, many different types of immunotherapies have failed to show significant benefits for most glioma patients. Hence, a better understanding of drivers of the immune suppressive microenvironment in GBM and other immune cold tumors is urgently needed to guide future immunotherapy development and application. We recently analyzed 201,986 human glioma and immune cells from 44 tissue fragments from 18 human glioma patients, and present a comprehensive and high-resolution cellular, molecular, and spatial heterogeneity atlas of human glioma. We report an extensive spatial and molecular heterogeneity of glioma and immune cells within the same patient. In addition, we discovered that cell:cell communication between glioma:myeloid cells is considerably more robust than glioma:T-cells, indicating that myeloid cells form a communication hub in vivo. To gain a deeper understanding of these important immune cells, we analyzed 83,479 glioma-infiltrating myeloid cells and identified 9 molecularly distinct myeloid subtypes: 3 microglia subtypes, 3 bone marrow-derived macrophage (BMDM) subtypes, MDSCs, neutrophils, and dendritic cells. Notably, we found that five of these myeloid cell subtype gene signatures are significant predictors of glioma patient survival, independent of glioma cell mutational profiles or gene expression patterns. Leveraging our dataset, we also identified a novel immunotherapy target that is highly expressed in immune-suppressive macrophages and T cells but not in anti-tumor leukocytes: S100A4. We provide both in vitro and in vivo evidence that S100a4 deletion in stromal cells is sufficient to reprogram the immune microenvironment and significantly extend the survival of two independent glioma models. To broaden the potential impact of targeting S100A4 as a selective modulator of immune suppressive leukocytes, we compared the molecular signatures of glioma-associated myeloid cells to those from 12 other cancer types and peripheral blood myeloid cells. We found that S100A4 expression pattern is highly consistent among all tumor types, where its expression is highest in the monocytes and MDSCs and low in most DCs and tissue-resident macrophages. Our preliminary analysis also shows that myeloid cells in gliomas are molecularly distinct from corresponding cell types in other cancers, strongly indicating the role brain microenvironment in influencing the infiltrating BMDM maturation and polarization.

Citation Format: Nourhan Abdelfattah, Parveen Kumar, Caiyi Wang, Jia-Shiun Leu, David Baskin, William Flynn, Ruli Gao, Kumar Pichumani, Omkar Ijare, Stephanie Wood, Suzanne Powell, David Haviland, Brittany Parker Kerrigan, Frederick Lang, Sujit Prabhu, Kristin Huntoon, Wen Jiang, Betty Kim, Joshy George, Kyuson Yun. Pan-cancer myeloid cell analysis at the single cell level reveals the influence of distinct organ sites in myeloid cell phenotypes and support targeting S100A4 to reverse immune suppression. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5871.

TMIC-63. SELECTIVE TARGETING OF IMMUNE-SUPPRESSIVE LEUKOCYTES TO REPROGRAM THE GBM IMMUNE LANDSCAPE

A significant barrier to immunotherapy efficacy is GBM’s immunosuppressive microenvironment composed of few tumor-infiltrating lymphocytes (TILs; < 5%) but abundant myeloid cells, making it an “immune cold” tumor. To enhance immunotherapy efficacy, a better molecular and functional understanding of the heterogeneous cell types in the GBM microenvironment and their function is urgently needed. Single cell RNA-sequencing offers high-resolution cellular and molecular data to elucidate cancer and stromal cell phenotypes at the single cell level to identify the most relevant cell types to target to enhance immune activation. We recently reported an integrated, multi-regional and -dimensional single-cell transcriptomic analysis of 201,986 human glioma and immune cells derived from 44 tissue fragments from 18 human glioma patients. In doing so, we mapped GBM cellular heterotypia and spatial, molecular, and functional heterogeneity of glioma associated immune cells. We observed an extensive spatial and molecular heterogeneity of glioma cells, microglia, macrophages, and T cells within the same tumor samples in low-grade gliomas (LGGs), primary GBMs, and recurrent GBMs. Importantly, our analysis of 83,479 glioma infiltrating myeloid cells identifies 9 molecularly distinct myeloid subtypes: 4 microglia, 4 bone marrow-derived macrophage (BMDM), and dendritic cell subtypes. Importantly, five of these myeloid cell subtype gene signatures were independent predictors of patient survival in multiple datasets, demonstrating the importance of immune cells in disease progression and aggressiveness. Here, we report evidence for heterogeneous cell:cell communication between glioma and immune cells in different regions within a patient, using CellChat, Cellphone DB, and NicheNet tools. We also nominate immune modulators other than PD1/PDL1 and CTLA3 as more promising targets in GBM. Finally, we provide evidence that S100A4 is a promising novel immunotherapy target since its high-level expression is required for immune-suppressive macrophages and Tregs to block T cell infiltration and DC maturation.

Abstract 3961: Cancer stem cells, not bulk tumor cells, predict mechanisms of resistance to SMO inhibitors in SHH medulloblastoma

The emergence of primary and acquired treatment resistance significantly reduces the clinical utility of many effective targeted therapies. Both genetic and epigenetic mechanisms of drug resistance have been reported in literature; however, whether these mechanisms are stochastically selected in individual tumors or governed by a predictable underlying principle is unknown.Here, we report that one can predict a priori the resistance mechanism that will arise in individual SMO inhibitor (SMOi)-resistant SHH medulloblastoma (MB), based on different CSC phenotypes in each tumor. We show that the dependence of cancer stem cells (CSCs), not bulk tumor cells, on the targeted pathway (sonic hedgehog (SHH) pathway) determines the molecular mechanism of resistance in individual tumors. Using both spontaneous (Fsmo;GFAP-cre) and transplantable (Ptch+/-;p53) mouse models of SHH MB treated with a Smoothened inhibitor, sonidegib/LDE225, we show that genetic-based resistance occurs only when the CSCs depend on the targeted pathway. In contrast, SHH MBs containing SHH-dependent bulk tumor cells but SHH-independent CSCs (SI-CSCs), acquire resistance through epigenetic reprogramming. Mechanistically, we discovered that the elevated proteasome activity in SMOi-resistant SI-CSC MBs alters the tumor cell maturation trajectory through enhanced degradation of specific epigenetic regulators, including the histone acetylation machinery. Consequently, SMOi-resistant SI- SMOi-resistant SI-CSC exhibit a global reduction of H3K9Ac, H3K14Ac, H3K56Ac, H4K5Ac, and H4K8Ac marks and gene expression changes. These results provide new insights into how selective pressure on distinct tumor cell populations contributes to different mechanisms of resistance to targeted therapies and implicate histone acetylation in the process. This information can be clinically exploited to understand responses and resistance to SMOis and other targeted therapies.

Citation Format: Joshy George, Yaohui Chen, Nourhan Abdelfattah, Keiko Yamamoto, Scott Adamson, Jong Min Choi, Brad Rybinski, Anuj Srivastava, Parveen Kumar, Min Gyu Lee, David S. Baskin, Wen Jiang, Betty Y. Kim, William Flavahan, Jeffrey H. Chuang, Sung Yun Jung, Kyuson Yun. Cancer stem cells, not bulk tumor cells, predict mechanisms of resistance to SMO inhibitors in SHH medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3961.

Abstract 1331: Elucidating cell-to-cell communication and immunotherapy responses in deeply characterized mouse models of human glioma subtypes

Immunotherapy is a promising treatment modality for highly invasive gliomas; however, clinical trials thus far have failed to provide significant clinical benefit to most GBM patients. GBM is one of the “immune cold” tumors characterized by poor infiltration of T cells even though greater than 40% of glioma cells are composed of immune cells in some patients. The majority of immune cells in GBM are immune-suppressive myeloid cells that block T cell infiltration and/or activation. To elucidate the mechanisms of immune evasion and to understand how the immune system interacts with glioma and stromal cells that shape the immune-suppressive landscape in GBM, there is an urgent need for immune-competent preclinical models that recapitulate the human disease. Human GBM is divided into three molecular subtypes (proneural:PR, classical:CL, and mesenchymal:MES) based on specific gene expression patterns and signature mutational profiles. Here, we report multi-dimensional analyses of six different transplantable mouse glioma models in the C57BL6/J background that represent all three human GBM molecular subtypes. We performed whole-exome sequencing as well as STR fingerprinting of each primary tumorsphere line and also performed immune phenotyping of each glioma model with flow cytometry. To gain molecular insights and determine cellular heterogeneity, we also performed single-cell RNA sequencing from the six models. Glioma cell analysis at the single-cell level revealed that cell-of-origin rather than the oncogenic driver (such as EGFRviii) plays a dominant role in determining the molecular phenotypes of glioma cells, driving their classification into a molecular subtype defined by human studies. In addition, we identified eight molecular subtypes of glioma-associated myeloid (GAMs), seven different subtypes of T cells, and provide molecular definitions of glioma-associated pericytes and endothelial cells in murine gliomas. In addition, we performed cross-species comparisons of glioma and immune cell subtypes between humans and mice at the single-cell level. Furthermore, we report qualitative and quantitative differences in the cell-to-cell communication among different stromal cells and glioma cells in each model, and propose that these interactions shape the local niche and functional neighborhoods. Finally, we leverage these preclinical models to elucidate underlying molecular mechanisms that drive differential sensitivities of each model to immunotherapies: anti-PD1, CTLA4, and 4-1BB in vivo. In summary, we report deeply characterized mouse models of human GBM subtypes and highlight their utility as preclinical models for immunotherapy evaluation and foundational tumor immunology studies.

Citation Format: Caiyi Wang, Jose Maldonado, Thomas D. Gallup, Nourhan Abdelfattah, Jia-Shiun Leu, Nithin Joshy, joshy George, Jihye Paik, Massimo Squatrito, Kyuson Yun. Elucidating cell-to-cell communication and immunotherapy responses in deeply characterized mouse models of human glioma subtypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1331.

Abstract 2540: A multi-dimensional analysis of human gliomas at the single cell level identifies immune suppressive macrophage molecular signatures and a novel immunotherapy target for GBM

Glioblastoma (GBM) is the most prevalent primary brain malignancy in adults. The current standard of care includes maximal surgical resection followed by radio- and chemotherapy with temozolomide. Yet <5% of GBM patients survive more than five years. This indicates a desperate need for more effective treatments, such as immunotherapy for GBM patients. Unfortunately, most immunotherapy trials, including vaccines, adoptive cellular therapy, CAR-T cells, and checkpoint blockade, showed only modest benefits in GBM patients. A major barrier to immunotherapy efficacy is GBM’s immunosuppressive microenvironment composed of few tumor infiltrating lymphocytes (TILs; <5%) but abundant myeloid cells, making it an immune cold tumor. By contrast, immune hot tumors, characterized by abundant tumoricidal effector T cells necessary to mount a meaningful attack, have consistently responded better to immunotherapy. Hence, a better definition of the heterogeneous cell types in the GBM microenvironment and their function is urgently needed. Fortunately, single cell transcriptomics approaches provide comprehensive and high-resolution cellular and molecular understanding to resolve this heterogeneity. Here we report an integrated, multiregional and -dimensional single cell transcriptomic analysis of 201,986 human glioma and immune cells derived from 44 tissue fragments from 18 human glioma patients. In doing so, we map GBM cellular heterotypia and spatial, molecular, and functional heterogeneity of glioma associated immune cells. We report extensive spatial and molecular heterogeneity of glioma cells, microglia, macrophages, and T cells within the same tumor samples in low grade gliomas, primary GBMs, and recurrent GBMs. Importantly, our analysis of 83,479 glioma infiltrating myeloid cells identifies 9 molecularly distinct myeloid subtypes: 4 microglial, 4 bone marrow derived macrophage and dendritic cells subtypes. Importantly, in multiple independent glioma patient cohorts, 5 of these myeloid cell subtype gene signatures were independent predictors of patient survival. We also provide evidence that cell:cell communication between glioma and immune cells is more robust than glioma:Tcells, indicating that myeloid cells form a communication hub in vivo. Additionally, we identified S100A4 as highly expressed in immunosuppressive macrophages and T cells, and provide in vitro and in vivo evidence that S100a4 plays a critical role in promoting immunosuppressive phenotypes in glioma associated leukocytes. This study not only provides the first comprehensive single cell atlas of GBM to include both glioma and immune cells from same samples but also demonstrates its utility in elucidating cell:cell communication among different cell types in vivo and discovering new therapeutic targets for this poorly immunogenic cancer.

Citation Format: Nourhan Abdelfattah, Parveen Kumar, Caiyi Wang, Jia-Shiun Leu, William W. Flynn, Ruli Gao, David S. Baskin, Kumar Pichumani, Omkar B. Ijare, Stephanie Wood, Suzanne Powell, David Haviland, Frederick F. Lang, Sujit Prabhu, Kristin Huntoon, Brittany C. Parker Kerrigan, Wen Jiang Jiang, Betty Y. Kim, Joshy George, Kyuson Yun. A multi-dimensional analysis of human gliomas at the single cell level identifies immune suppressive macrophage molecular signatures and a novel immunotherapy target for GBM [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2540.

Cancer stem cells, not bulk tumor cells, determine mechanisms of resistance to SMO inhibitors

The emergence of treatment resistance significantly reduces the clinical utility of many effective targeted therapies. Although both genetic and epigenetic mechanisms of drug resistance have been reported, whether these mechanisms are stochastically selected in individual tumors or governed by a predictable underlying principle is unknown. Here, we report that the dependence of cancer stem cells (CSCs), not bulk tumor cells, on the targeted pathway determines the molecular mechanism of resistance in individual tumors. Using both spontaneous and transplantable mouse models of sonic hedgehog (SHH) medulloblastoma (MB) treated with an SHH/Smoothened inhibitor, sonidegib/LDE225, we show that genetic-based resistance occurs only in tumors that contain SHH-dependent CSCs (SD-CSCs). In contrast, SHH MBs containing SHH-dependent bulk tumor cells but SHH-independent CSCs (SI-CSCs) acquire resistance through epigenetic reprogramming. Mechanistically, elevated proteasome activity in SMOi-resistant SI-CSC MBs alters the tumor cell maturation trajectory through enhanced degradation of specific epigenetic regulators, including histone acetylation machinery components, resulting in global reductions in H3K9Ac, H3K14Ac, H3K56Ac, H4K5Ac, and H4K8Ac marks and gene expression changes. These results provide new insights into how selective pressure on distinct tumor cell populations contributes to different mechanisms of resistance to targeted therapies. This insight provides a new conceptual framework to understand responses and resistance to SMOis and other targeted therapies.

The antidepressant imipramine inhibits breast cancer growth by targeting estrogen receptor signaling and DNA repair events

Aberrant activities of various cell cycle and DNA repair proteins promote cancer growth and progression and render them resistant to therapies. Here, we demonstrate that the anti-depressant imipramine blocks growth of triple-negative (TNBC) and estrogen receptor-positive (ER+) breast cancers by inducing cell cycle arrest and by blocking heightened homologous recombination (HR) and non-homologous end joining-mediated (NHEJ) DNA repair activities. Our results reveal that imipramine inhibits the expression of several cell cycle- and DNA repair-associated proteins including E2F1, CDK1, Cyclin D1, and RAD51. In addition, we show that imipramine inhibits the growth of ER + breast cancers by inhibiting the estrogen receptor- α (ER-α) signaling. Our studies in preclinical mouse models and ex vivo explants from breast cancer patients show that imipramine sensitizes TNBC to the PARP inhibitor olaparib and endocrine resistant ER + breast cancer to anti-estrogens. Our studies suggest that repurposing imipramine could enhance routine care for breast cancer patients. Based on these results, we designed an ongoing clinical trial, where we are testing the efficacy of imipramine for treating patients with triple-negative and estrogen receptor-positive breast cancer. Since aberrant DNA repair activity is used by many cancers to survive and become resistant to therapy, imipramine could be used alone and/or with currently used drugs for treating many aggressive cancers.

M6A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression

Osteosarcoma is the most common malignancy of the bone, yet the survival for osteosarcoma patients is virtually unchanged over the past 30 years. This is principally because development of new therapies is hampered by a lack of recurrent mutations that can be targeted in osteosarcoma. Here, we report that epigenetic changes via mRNA methylation holds great promise to better understand the mechanisms of osteosarcoma growth and to develop targeted therapeutics. In osteosarcoma patients, the RNA demethylase ALKBH5 was amplified and higher expression correlated with copy number changes. ALKBH5 was critical for promoting osteosarcoma growth and metastasis, yet it was dispensable for normal cell survival. Me-RIP-seq analysis and functional studies showed that ALKBH5 mediates its pro-tumorigenic function by regulating m6A levels of histone deubiquitinase USP22 and the ubiquitin ligase RNF40. ALKBH5-mediated m6A deficiency in osteosarcoma led to increased expression of USP22 and RNF40 that resulted in inhibition of histone H2A monoubiquitination and induction of key pro-tumorigenic genes, consequently driving unchecked cell cycle progression, incessant replication and DNA repair. RNF40, which is historically known to ubiquitinate H2B, inhibited H2A ubiquitination in cancer by interacting with and affecting the stability of DDB1-CUL4-based ubiquitin E3 ligase complex. Taken together, this study directly links increased activity of ALKBH5 with dysregulation of USP22/RNF40 and histone ubiquitination in cancers. More broadly, these results suggest that m6A RNA methylation works in concert with other epigenetic mechanisms to control cancer growth.

Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target

A major rate-limiting step in developing more effective immunotherapies for GBM is our inadequate understanding of the cellular complexity and the molecular heterogeneity of immune infiltrates in gliomas. Here, we report an integrated analysis of 201,986 human glioma, immune, and other stromal cells at the single cell level. In doing so, we discover extensive spatial and molecular heterogeneity in immune infiltrates. We identify molecular signatures for nine distinct myeloid cell subtypes, of which five are independent prognostic indicators of glioma patient survival. Furthermore, we identify S100A4 as a regulator of immune suppressive T and myeloid cells in GBM and demonstrate that deleting S100a4 in non-cancer cells is sufficient to reprogram the immune landscape and significantly improve survival. This study provides insights into spatial, molecular, and functional heterogeneity of glioma and glioma-associated immune cells and demonstrates the utility of this dataset for discovering therapeutic targets for this poorly immunogenic cancer.

OTME-10. Integrated analysis of human gliomas at the single cell level identifies S100A4 as a novel immunotherapy target

Understanding the immune composition of a given tumor is critical to assess its potential responsiveness to cancer immunotherapy. This is especially true for tumors that are intrinsically resistant to immunotherapies, such as GBM. Unfortunately, studies on the functional heterogeneity and associated molecular targets of immune-suppressive cells in vivo have been lacking. Here we report an integrated multi-dimensional analysis of the mutational profiles and single-cell transcriptomics of 60,024 glioma and stromal cells from 16 human samples. We identified molecular signatures of seven distinct macrophage subtypes, each with prognostic clinical value. The three inflammatory subtypes showed hallmarks of TNF/NFκB pathway enrichment and are associated with good outcomes; in contrast, four immunosuppressive subtypes with metabolic pathway hallmarks (oxidative phosphorylation, PI3K/AKT/mTOR, fatty acid metabolism) are associated with poor survival. In addition, we resolved an ongoing controversy in the field regarding the roles of brain resident macrophages, microglia, vs. bone marrow derived macrophages (BMDM) in gliomas. Our data show compelling evidence that microglia are pro-inflammatory and are associated with good survival while BMDMs are mostly immune-suppressive and associated with poor survival. In addition, deciphering immune-suppressive macrophage and Treg molecular signatures enabled us to identify previously unknown immunotherapy targets. In a proof of principle study, we showed that S100A4, a calcium binding protein previously shown to mediate metastasis, was universally upregulated in both innate and adaptive immune suppressor cells, and implantation of gliomas in S100a4-/- host mice significantly extended survival and resulted in pro-inflammatory immune landscape, compared to same glioma cells implanted in B6 control hosts. This functional validation study shows that S100A4 is a highly promising therapeutic target for GBM immunotherapy.

EMBR-33. YAP1 FUNCTION IN SHH MEDULLOBLASTOMA PROGRESSION AND IMMUNE EVASION

Our incomplete understanding of the key players in Medulloblastoma (MB) development and progression, and their roles in modulating highly Immune desert-like microenvironment in MBs present major hurdles in successfully applying existing therapies and developing new therapies for MBs. Here, we demonstrate that Yap1 acts as a critical modulator of SHH MB (fSmoM2; GFAPcre (SG) and Ptch;p53 SHH-MB mouse models) progression and immune evasion. Yap1 genetic deletion in SG mice significantly extends survival and normalizes brain development by increasing neuronal differentiation. Both bulk and single-cell RNA sequencing analyses show that Yap1 deleted tumors contain cells with more differentiated molecular signatures similar to late CGNPs and differentiating neurons, and less stem-like cells, compared to SG tumors. Additionally, integrated analyses of ChiPseq, RNAseq, and scRNAq data suggest that Yap1 directly binds to the Super enhancer region containing Sox2 and promotes Sox2 expression in SHH MB cells. We postulate that Yap1 expression is maintained or re-activated in SHH MB cells to generate long-term self-renewing tumor cells. Consistently, Yap1-deleted SHH MB or Verteporfin (a small molecule inhibitor of Yap1) -treated Ptch;p53 MB cells lose self-renewal ability in vitro. Furthermore, we hypothesize that a molecular mechanism underlying this stemness promoting function is mediated through Sox2 expression. Intriguingly, Yap1 deletion in SG MBs is accompanied by a significant change in the immune microenvironment, when compared to age-matched SG MBs. There is a significant increase in the number of bone marrow-derived immune cells (including cytotoxic T-cells, neutrophils, and macrophages). RNAseq analysis of rescued tumors shows marked enrichment of interferon-gamma response genes and pro-inflammatory cytokines. This study highlights Yap1 as a crucial mediator of MB progression and a molecular regulator of inflammatory immune cell infiltration into SHH MBs. Consequently, our work paves the way for improving immunotherapy treatments in brain malignancies.

Abstract PS19-14: Matrin3 inhibits breast cancer growth by suppressing microtubule nucleation protein MZT2B

Despite improvement in overall survival, many patients with breast cancers still succumb to this disease. Identification of new biomarkers and safe therapeutic targets are urgently needed to improve the overall clinical outcome of breast cancer patients. Our studies discovered a RNA binding protein, MATRIN3 (MATR3), as a novel tumor suppressor. MATR3 is expressed at a significantly reduced levels in breast tumors. MATR3 inhibited short and long-term viability as well as migration and invasion of breast cancer cells. Further, MATR3 overexpression suppressed tumor growth, while its depletion induced tumor growth in orthotopic mouse tumor models. RNA seq and RNA immunoprecipitation analyses revealed that MATR3 binds and directly regulates the expression of several microtubule-associated proteins. Mechanistic studies identified MZT2B, a mitotic spindle organizing protein as a down stream effector of MATR3. MZT2B knockdown or knockout using CRISPR-CAS9 resulted in significantly decreased short and long term viability as well as reduced migration and invasion of breast cancer cells. Notably, MZT2B overexpression rescued the inhibitory effect of MATR3 overexpression on breast cancer growth. Furthermore, MATR3 overexpression downregulated expression of key microtubule nucleation protein complex including γ-tubulin and γ-tubulin ring complex protein (TUBGCP). Our data suggest that MATR3 inhibits breast cancer growth and progression by inhibiting MZT2B and consequently microtubule nucleation in breast cancers.

Citation Format: Panneerdoss Subbarayalu, Subapriya Rajamanickam, Suryavathi Viswanadhapalli, Fuyang Li, Vijay Eedunuri, Pooja Yadav, Esha Reddy, Santosh Timilsina, Saif SR Nirzhor, Benjamin C Onyeagucha, Li-Ju Wang, Yu-Chiao Chiu, Tabrez Mohammad, Nourhan Abdelfattah, Nicholas Dybdal-Hargreaves, Yidong Chen, Ratna Vadlamudi, Manjeet Rao. Matrin3 inhibits breast cancer growth by suppressing microtubule nucleation protein MZT2B [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS19-14.

STEM-18. DISTINCT BUT PREDICTABLE MECHANISMS DRIVE GENETIC VS. EPIGENETIC RESISTANCE TO TARGETED THERAPY

Emergence of therapy resistance greatly reduces long-term utility of effective targeted therapies, including SMO/SHH pathway inhibitors. SHH signaling is activated in ~25% of human medulloblastomas (MB) and FDA approved SMOi (to treat basal cell carcinoma (BCC)) are currently in clinical trials for MBs and acute myeloid leukemia (AML). Accumulating clinical experience suggests that a significant number of BCC patients treated with SMOi develop acquired resistance over time and some show de novo resistance. A similar pattern is observed in MB patients, indicating the need to elucidate resistance mechanisms, particularly those driving de novo vs. acquired resistance, and develop new strategies to overcome both de novo and acquired resistance to SMOi. We report that we have discovered a novel, epigenetic mechanism of therapy resistance to SMOi that underlie de novo resistance. Using two different mouse models of SHH MB, we tested our original hypothesis that the selective pressure on cancer stem cells (CSCs), but not bulk tumor cells, will determine the resistance mechanism at the molecular level. We show that acquired mutations in the SHH pathway genes (previously reported mechanism of resistance) occur only in tumors that contain CSCs that depend on the SHH pathway. In tumors where only the bulk tumor cells, but not CSCs, depend on SHH signaling, no acquired mutations in the SHH pathway genes are detected. Instead, in these tumors, epigenetic reprogramming through selective degradation of specific histone modifiers results in global changes in the epigenetic cell state and gene expression patterns. Importantly, we can predict the mechanism of resistance in individual tumors prior to treatment based on CSC phenotypes. Finally, we also report biomarkers that can be used to identify tumors with CSCs that are independent of SHH pathway, which can be exploited to design anticipatory combination therapies in the future.

PDTM-09. Yap1 FUNCTION IN SEX-BIASED MEDULLOBLASTOMA FORMATION AND ANTI-TUMOR IMMUNITY

Immunotherapies offer remarkable potential to provide robust therapeutic benefit. Patients suffering from medulloblastoma (MB), the most frequent pediatric brain malignancy, can especially benefit from this approach, minimizing the devastating side effects of aggressive radiation and chemotherapies that disrupt normal brain development. However, regulators of the immune landscape remain poorly understood and no effective immunotherapies exist yet for MB. Here, we describe a sex-dependent Yap1 function in fSmoM2;GFAPcre SHH-MB (SG) mouse model. We show that Yap1 is both a cell-autonomous regulator of MB stem-cells and a non-cell-autonomous regulator of immune infiltrates in SHH-MB. Yap1 deletion in SG mice results in increased neuronal differentiation, significantly extended survival, and enhanced infiltration of peripheral blood immune cells (including cytotoxic T-cells, neutrophils, and macrophages). Additionally, this rescue phenotype is observed in a sex-biased manner: 65% of Yap1f/f;fSmoM2;GFAPcre males are rescued in contrast to 35% of females. These observations implicate Yap1 as a mediator of sex-biased brain-tumor formation, either through direct modulation of MB cells and/or through indirectly mediating the MB immune landscape. We are currently testing the role of sex-specific differences in the developing mouse brain to elucidate context-dependent function of Yap1 in MB genesis and maintenance.

MiR-584-5p potentiates vincristine and radiation response by inducing spindle defects and DNA damage in medulloblastoma

Despite improvements in overall survival, only a modest percentage of patients survives high-risk medulloblastoma. The devastating side effects of radiation and chemotherapy substantially reduce quality of life for surviving patients. Here, using genomic screens, we identified miR-584-5p as a potent therapeutic adjuvant that potentiates medulloblastoma to radiation and vincristine. MiR-584-5p inhibited medulloblastoma growth and prolonged survival of mice in pre-clinical tumor models. MiR-584-5p overexpression caused cell cycle arrest, DNA damage, and spindle defects in medulloblastoma cells. MiR-584-5p mediated its tumor suppressor and therapy-sensitizing effects by targeting HDAC1 and eIF4E3. MiR-584-5p overexpression or HDAC1/eIF4E3 silencing inhibited medulloblastoma stem cell self-renewal without affecting neural stem cell growth. In medulloblastoma patients, reduced expression of miR-584-5p correlated with increased levels of HDAC1/eIF4E3. These findings identify a previously undefined role for miR-584-5p/HDAC1/eIF4E3 in regulating DNA repair, microtubule dynamics, and stemness in medulloblastoma and set the stage for a new way to treat medulloblastoma using miR-584-5p.

Cross-talk among writers, readers, and erasers of m6A regulates cancer growth and progression

The importance of RNA methylation in biological processes is an emerging focus of investigation. We report that altering m⁶A levels by silencing either N ⁶-adenosine methyltransferase METTL14 (methyltransferase-like 14) or demethylase ALKBH5 (ALKB homolog 5) inhibits cancer growth and invasion. METTL14/ALKBH5 mediate their protumorigenic function by regulating m⁶A levels of key epithelial-mesenchymal transition and angiogenesis-associated transcripts, including transforming growth factor-β signaling pathway genes. Using MeRIP-seq (methylated RNA immunoprecipitation sequencing) analysis and functional studies, we find that these target genes are particularly sensitive to changes in m⁶A modifications, as altered m⁶A status leads to aberrant expression of these genes, resulting in inappropriate cell cycle progression and evasion of apoptosis. Our results reveal that METTL14 and ALKBH5 determine the m⁶A status of target genes by controlling each other's expression and by inhibiting m⁶A reader YTHDF3 (YTH N ⁶-methyladenosine RNA binding protein 3), which blocks RNA demethylase activity. Furthermore, we show that ALKBH5/METTL14 constitute a positive feedback loop with RNA stability factor HuR to regulate the stability of target transcripts. We discover that hypoxia alters the level/activity of writers, erasers, and readers, leading to decreased m⁶A and consequently increased expression of target transcripts in cancer cells. This study unveils a previously undefined role for m⁶A in cancer and shows that the collaboration among writers-erasers-readers sets up the m⁶A threshold to ensure the stability of progrowth/proliferation-specific genes, and protumorigenic stimulus, such as hypoxia, perturbs that m⁶A threshold, leading to uncontrolled expression/activity of those genes, resulting in tumor growth, angiogenesis, and progression.

Abstract 4146: N6Methyladenosine RNA demethylase ALKBH5 as a novel therapeutic target for osteosarcoma

Osteosarcoma (OS) is the most prevalent primary bone malignancy that affects children and young adults. Despite several years of research, survival outcome of OS patients has not improved in last three decades. OS is treated with multi-modal chemotherapy, which is highly toxic and does not work well for metastatic and chemo-resistant tumors. Currently there is no FDA approved drug that can serve as an alternative to chemotherapy, warranting an urgent need to find more efficacious and targeted therapeutics for OS. Here, we report that RNA demethylase AlkB Homolog 5 (ALKBH5) may serve as a novel therapeutic adjuvant for treating OS. N6 Methyladenosine (m6 A) is the most common internal mRNA modification, which is modulated by the multi-component RNA methyltransferase complex, RNA demethylase (ALKBH5) and m6A readers . We show that ALKBH5 is amplified in sarcomas and its expression is highly elevated in osteosarcoma patients. We demonstrate that silencing of ALKBH5 inhibits the OS growth and migration without affecting the viability of normal human fetal osteoblast cells. Our results reveal that ALKBH5 depletion impairs the cell cycle progression and induces apoptosis in OS cells. Interestingly, we demonstrate that reduction in ALKBH5 levels suppresses the DNA damage repair capacity of osteosarcoma cells rendering them sensitive to DNA damaging agent like Doxorubicin. Using DR-GFP reporter-based homologous recombination (HR) assay, we show that ALKBH5 depletion leads to reduced HR-mediated DNA repair capacity of osteosarcoma cells. Supporting this, we observed significantly reduced expression of several genes that are known to play critical roles in cell cycle progression and DNA damage repair. In summary, this study shows that ALKBH5 is a critical regulator of OS growth and chemosensitivity. Approaches aimed at silencing ALKBH5 can be potentially used to inhibit osteosarcoma growth and progression as well as sensitize osteosarcoma cells to DNA damaging agents.

Citation Format: Pooja Yadav, Panneerdoss Subbarayalu, Nourhan Abdelfattah, Vijay K. Eedunuri, Yidong Chen, Manjeet K. Rao. N6Methyladenosine RNA demethylase ALKBH5 as a novel therapeutic target for osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4146.

Abstract P6-06-04: Targeting replication stress in triple negative breast cancer treatment regimen: An emerging approach

Triple-negative breast cancers (TNBCs) represent aggressive heterogeneous subtype of breast cancer with poor clinical outcome. TNBCs have been reported to have high levels of replication stress due to i) various oncogene activations (C-myc or EGFR) ii) germline BRCA mutations iii) “BRCAness” in the absence of BRCA mutations in sporadic TNBCs. Replication stress is known to cause genomic instability, promote tumorigenesis and plays a critical role in therapy resistance in TNBCs. Therefore, targeting replication stress has emerged as an effective approach for better TNBC treatment through further downregulation of the remaining checkpoints to induce catastrophic failure of TNBC cells proliferation. Herein, we evaluated the anticancer efficacy of Carbazole Blue (CB), a synthetic analogue of Carbazole, on TNBC cells growth and progression. Our results demonstrated that CB inhibits short and long term viability of TNBC (MDA-MB-231, MDA-MB-468 and BT549) cells in a dose dependent manner without affecting normal mammary epithelial (MCF-10A) cells. In addition, CB treatment significantly reduced proliferation of TNBC cells, as evidenced by the BrdU proliferation assay. Consistent with this, our results further demonstrated that CB treatment induced G1/S cell cycle arrest and apoptosis in TNBCs. Importantly, systemic delivery of CB using nanoparticle-based delivery approach suppressed breast cancer growth without inducing toxicity, in preclinical orthotopic xenograft and PDX mouse models of TNBC. Furthermore, our gene microarray analysis revealed that CB treatment modulates the expression and activity of several genes known to be involved in DNA replication (CDC6, CDT1, MCMs, Claspin, POLE and PCNA) and associated DNA repair machinery such as (XRCC3, Exo1 and RAD51), which play pivotal roles in replication stress. Our results for the first time highlight the potential use of CB as a novel and potent therapeutic agent for treating TNBCs. As exploiting replication stress to treat cancer is gaining major interest, compound/s that may induce replication stress and inhibit DNA repair ability of cancer cells, has immense translational potential.

Citation Format: Rajamanickam S, Park JH, Bates K, Timilsina S, Eedunuri VK, Onyeagucha B, Subbarayalu P, Abdelfattah N, Jung KH, Favours E, Mohammad TA, Chen H-IH, Vadlamudi RK, Chen Y, Kaipparettu BA, Arbiser JL, Rao MK. Targeting replication stress in triple negative breast cancer treatment regimen: An emerging approach [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-06-04.

Novel post-transcriptional and post-translational regulation of pro-apoptotic protein BOK and anti-apoptotic protein Mcl-1 determine the fate of breast cancer cells to survive or die

Deregulation of apoptosis is central to cancer progression and a major obstacle to effective treatment. The Bcl-2 gene family members play important roles in the regulation of apoptosis and are frequently altered in cancers. One such member is pro-apoptotic protein Bcl-2-related Ovarian Killer (BOK). Despite its critical role in apoptosis, the regulation of BOK expression is poorly understood in cancers. Here, we discovered that miR-296-5p regulates BOK expression by binding to its 3'-UTR in breast cancers. Interestingly, miR-296-5p also regulates the expression of anti-apoptotic protein myeloid cell leukemia 1 (Mcl-1), which is highly expressed in breast cancers. Our results reveal that Mcl-1 and BOK constitute a regulatory feedback loop as ectopic BOK expression induces Mcl-1, whereas silencing of Mcl-1 results in reduced BOK levels in breast cancer cells. In addition, we show that silencing of Mcl-1 but not BOK reduced the long-term growth of breast cancer cells. Silencing of both Mcl-1 and BOK rescued the effect of Mcl-1 silencing on breast cancer cell growth, suggesting that BOK is important for attenuating cell growth in the absence of Mcl-1. Depletion of BOK suppressed caspase-3 activation in the presence of paclitaxel and in turn protected cells from paclitaxel-induced apoptosis. Furthermore, we demonstrate that glycogen synthase kinase (GSK3) α/β interacts with BOK and regulates its level post-translationally in breast cancer cells. Taken together, our results suggest that fine tuning of the levels of pro-apoptotic protein BOK and anti-apoptotic protein Mcl-1 may decide the fate of cancer cells to either undergo apoptosis or proliferation.

Abstract 1116: Targeting replication stress by carbazole blue- A novel strategy to treat triple negative breast cancers

Background: Triple-negative breast cancers (TNBC) are the most aggressive forms of breast cancer and almost 60% of patients with TNBCs develop chemo-resistance, leading to recurrence, poor prognosis and poor survival. TNBCs have been reported to have high levels of replication stress, which plays pivotal role in genomic instability, and therapy resistance. Targeting replication stress is an emerging approach for better TNBC treatment. Here, we evaluated the anticancer efficacy of carbazole blue (CB), a synthetic analogue of carbazole that we recently synthesized on TNBC cells growth and progression.

Experimental Design: The effect of CB on breast cancer growth was assessed in vitro as well as in orthotopic mouse xenograft and PDX-models of breast cancer. In addition, the therapeutic efficacy and safety of CB was determined in long term toxicity studies in mice and also in ex-vivo explants from breast cancer patients. The mechanism of action of CB was evaluated by performing gene expression, cell cycle, apoptosis and DNA repair studies as well as proteins involved in the above mentioned mechanisms.

Results: Our results demonstrated that CB inhibits short and long term viability of TNBC cells in a dose dependent manner without affecting normal mammary epithelial cells. We show that the systemic delivery of CB using nanoparticle-based delivery approach suppressed breast cancer growth without inducing toxicity in preclinical and PDX mouse models of triple negative breast cancer. Our long term toxicity studies reveled that CB treatment did not induce any toxicity in Balb/c mice. Using ex-vivo explants from breast cancer patients, we demonstrated that CB modulated breast cancer growth. Consistent with that, our results revealed that CB treatment induced G1/S cell cycle arrest and apoptosis in TNBCs. Interestingly, our gene expression analysis revealed that CB modulates expression and activity of several genes known to be involved in DNA replication and DNA repair machinery.

Conclusions: Our results for the first time showed the CB can serve as a novel and potent therapeutic agent for treating breast cancer in general and TNBC in particular. These findings highlight the potential of CB to be applied as a safe regimen for treating breast cancer patients. As exploiting replication stress to treat cancer is gaining major interest, compound/s that may induce replication stress and inhibit DNA repair ability of cancer cells, has immense translational potential.

Citation Format: Subapriya Rajamanickam, Kaitlyn Bates, Santosh Timilsina, JunHyoung Park, Benjamin Onyeagucha, Panneerdoss Subbarayalu, Nourhan Abdelfattah, Kwang Hwa Jung, Edward Favours, Tabrez A. Mohammad, Hung-I Harry Chen, Benny A. Kaipparettu, Yidong Chen, Jack L. Arbiser, Manjeet K Rao. Targeting replication stress by carbazole blue- A novel strategy to treat triple negative breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1116. doi:10.1158/1538-7445.AM2017-1116

Abstract 5440: miRNAs as novel therapeutic adjuvants for improving the efficacy of vincristine and radiation therapy in treating medulloblastoma

Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Despite recent improvements in the overall survival, only a modest percentage of patients survive Myc-driven high-risk MB. The quality of life for surviving patients is substantially reduced due to the devastating and often irreversible side effects of radiation and chemotherapy. Recently, in a large unbiased genomic screen, we uncovered a group of microRNAs (miRNAs) capable of meditating drug sensitivity in c-myc amplified high-risk MB. Our functional screen of ~1900 miRNAs identified miR-584-5p as a potent candidate that uniquely sensitizes high-risk MB to radiation as well as vincristine (VCR) (20 to 25-fold dose reduction), an anti-mitotic agent routinely administered alongside radiation and in combination with other chemotherapeutic drugs to treat medulloblastoma patients. Our studies revealed that miR-584 might act as a potent tumor suppressor as it inhibited MB growth in vivo as well as migration and invasion of c-myc amplified MB. We show that miR-584 overexpression results in defective mitosis leading to mitotic catastrophe, apoptosis, DNA damage and G2-M cell-cycle arrest in high-risk MB cells without affecting normal neural stem cell growth. Notably, we discovered that miR-584 directly regulates the expression and activity of genes including histone deacetylase 1 (HDAC1), and eukaryotic translation initiation factor 4e family member 3 (EIF4E3) that are known to play important roles in microtubule dynamics, metaphase-anaphase transition and radio-resistance. Moreover, silencing either of these two target genes resulted in significant inhibition of MB growth and enhanced sensitivity to VCR and ionizing radiation. Overexpressing miR-584 or silencing either HDAC1 or EIF4E3 also inhibited the MB stem cell proliferation and self-renewal. We report that while miR-584-5p is predominantly expressed in normal brain and cerebellum, its expression is significantly reduced in MB patient derived xenografts (PDXs). In contrast to miR-584, EIF4E3 and HDAC1 were found to be overexpressed in medulloblastoma patients. These findings are highly significant, unexpected and innovative as this miRNA and its target genes are the first to be shown to affect the therapeutic efficacy of VCR and radiation in c-myc amplified high-risk medulloblastoma.

Citation Format: Nourhan Abdelfattah, Subapriya Rajamanickam, Panneerdoss Subbarayalu, Santosh Timilsina, Benjamin Onyeagucha, Yidong Chen, Manjeet Rao. miRNAs as novel therapeutic adjuvants for improving the efficacy of vincristine and radiation therapy in treating medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5440. doi:10.1158/1538-7445.AM2017-5440

Abstract B01: MicroRNAs as novel therapeutic adjuvants to treat high-risk medulloblastoma

Medulloblastoma is the most common malignant brain tumor in children, accounting for 18% of newly diagnosed brain tumors and 10% of all children cancer-related deaths. Despite improvement in the 5-year survival rate of medulloblastoma in recent years, only a small percentage of patients survive high-risk metastatic disease. The quality of life for those who do survive is often substantially reduced due to the toxicity associated with radiation and chemotherapy. Vincristine is a microtubule-destabilizing antimitotic drug, which is routinely administered in higher dosages to both high and average risk medulloblastoma patients. As a result, these patients suffer from devastating neurotoxic effects that include but not limited to: sensorimotor and autonomic neuropathy, hearing loss, mononeuropathy, and seizures. Using high-throughput microRNA mimic library screens, we identified a group of microRNAs that may improve the efficacy of vincristine against c-MYC amplified medulloblastoma as well as re-sensitize vincristine-resistant medulloblastoma. Our findings revealed that these microRNAs may act as tumor suppressors since their overexpression inhibited colony formation, migration and invasion ability of medulloblastoma cells. Furthermore, these microRNAs suppressed stem cell renewal/proliferation of c-MYC amplified medulloblastoma cells. Expression analysis, gene enrichment analysis and target prediction algorithms revealed that these microRNAs exert their vincristine sensitizing and tumor suppressor effect by targeting genes involved in microtubule organization, cell cycle regulation, DNA damage repair and mRNA translation. One of our most interesting targets is EIF4E3, which is a translation initiation factor. Our preliminary findings indicate that EIF4E3 may regulate medulloblastoma cell growth, progression and vincristine sensitivity by modulating c-MYC translation. Further experiments are underway to test the potential of candidate miRNA and EIF4E3 as vincristine sensitizer in vivo. In conclusion, this study may identify novel factors that have potential not only to decrease the current therapeutic dose of vincristine and therefore eliminate its side effects, but also have potential to multiply the efficacy of lower doses in order to overcome hard to treat high-risk tumors.

Citation Format: Nourhan Abdelfattah, Panneerdoss Subbarayalu, Benjamin Onyeagucha, Subapriya Rajamanickam, Hung-I Harry Chen, Manjeet Rao. MicroRNAs as novel therapeutic adjuvants to treat high-risk medulloblastoma.. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B01.