Cell of origin epigenetic priming determines susceptibility to Tet2 mutation

Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.

Gene expression alterations in salivary gland epithelia of Sjögren's syndrome patients are associated with clinical and histopathological manifestations

Sjögren's syndrome (SS) is a complex autoimmune disease associated with lymphocytic infiltration and secretory dysfunction of salivary and lacrimal glands. Although the etiology of SS remains unclear, evidence suggests that epithelial damage of the glands elicits immune and fibrotic responses in SS. To define molecular changes underlying epithelial tissue damage in SS, we laser capture microdissected (LCM) labial salivary gland epithelia from 8 SS and 8 non-SS controls for analysis by RNA sequencing (RNAseq). Computational interrogation of gene expression signatures revealed that, in addition to a division of SS and non-SS samples, there was a potential intermediate state overlapping clustering of SS and non-SS samples. Differential expression analysis uncovered signaling events likely associated with distinct SS pathogenesis. Notable signals included the enrichment of IFN-γ and JAK/STAT-regulated genes, and the induction of genes encoding secreted factors, such as LTF, BMP3, and MMP7, implicated in immune responses, matrix remodeling and tissue destruction. Identification of gene expression signatures of salivary epithelia associated with mixed clinical and histopathological characteristics suggests that SS pathology may be defined by distinct molecular subtypes. We conclude that gene expression changes arising in the damaged salivary epithelia may offer novel insights into the signals contributing to SS development and progression.

Abstract 2442: Identification of a novel role for the β-catenin/CBP signaling in epigenetic regulation of the N-glycosylation gene, DPAGT1, in head and neck cancer

Aberrant activation of the DPAGT1 gene, encoding an essential enzyme in the metabolic pathway of protein N-glycosylation, has been shown to be associated with head and neck squamous cell carcinoma (HNSCC). We have shown that DPAGT1 inhibits intercellular adhesion and functions in a positive feedback loop with Wnt/β-catenin signaling, and that the nuclear β-catenin/CBP signaling underlies the progression of HNSCC to advanced disease. However, the tumor promoting effects of DPAGT1 and its molecular links to the nuclear β-catenin/CBP axis are not well defined. We carried out genomic and functional analyses of DPAGT1 perturbation in indolent (CAL27) and metastatic (HSC-3) HNSCC cells, and in orthotopic HSC-3-derived xenografts in mice. We further generated and annotated DPAGT1 inhibition signature in HSC-3 cells and interrogated it in TCGA HNSCC. We then examined the effects of inhibition of β-catenin-CBP interaction with E7386 on DPAGT1 expression using ChIP-seq and computational approaches. E7386, a novel β-catenin/CBP modulator displays activity profile that closely overlaps with that of ICG-001, but exhibits ~50 - 100-fold lower EC50 values. Ectopic expression of DPAGT1 in indolent CAL27 cells induced epithelial-to-mesenchymal transition (EMT) which coincided with increased abundance of active β-catenin. Partial knockdown of DPAGT1 with siRNA in metastatic HSC-3 cells inhibited EMT, diminished cell migration and enhanced intercellular adhesion. Inhibition of the DPAGT1 enzyme activity using tunicamycin interfered with orthotopic tongue tumor growth and metastasis. DPAGT1 knockdown in HSC-3 cells defined DPAGT1-activated gene signature as enriched in pro-tumorigenic signaling pathways, including stem cell-like genes. Integrative analysis of the DPAGT1-activated genes in TCGA validated the association of DPAGT1 activity with the EMT transcription factors, ZEB1, Twist1/2 and Slug. ChIP-seq analyses without and with the E7386 treatment revealed reduced occupancy of H3K4me3 at two DPAGT1 transcription start sites following the E7386 treatment. In conclusion, our studies align aberrant activation of DPAGT1 with the induction of EMT and stem cell associated genes and suggest a novel role of β-catenin/CBP/MLL1 in the epigenetic regulation DPAGT1 and protein N-glycosylation in HNSCC.

Citation Format: Khalid A. Alamoud, Vinay Kartha, Huamei Yang, Andrew Tilston-Lunel, Anthony Federico, Manish Bais, Takachi Owa, Kenichi Nomoto, Xalarabos Varelas, Stefano Monti, Maria A. Kukuruzinska. Identification of a novel role for the β-catenin/CBP signaling in epigenetic regulation of the N-glycosylation gene, DPAGT1, in head and neck cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2442.

Abstract 2453: Inhibition of β-catenin/CBP signaling with E7386 targets epigenetic changes associated with cancer stem cells in head and neck cancer

Head and neck squamous cell carcinoma (HNSCC) is a pernicious malignancy that arises from populations of cancer stem cells (CSCs). We and others have shown that the Wnt/β-catenin signaling pathway drives CSC gene expression mediated, in part, by epigenetic alterations directed by interactions between nuclear β-catenin and the cAMP-responsive element binding (CREB)-binding protein (CBP). In HNSCC, the β-catenin/CBP complex recruits the histone methyltransferase, MLL1, to drive trimethylation of H3K4me3 to induce an open chromatin structure and expression of CSC genes. Further, β-catenin/CBP signaling is highly correlated with the activity of the paralogous transcriptional regulators YAP and TAZ (YAP/TAZ), which are pro-tumorigenic factors in HNSCC. We reported that a small molecule inhibitor of the β-catenin-CBP interaction, ICG-001, blocks oncogenic phenotypes in cellular, zebrafish, and murine models of HNSCC, concomitant with the reduction of CSC traits. Recently, a novel β-catenin/CBP modulator, E7386, has been shown to be effective against a number of neoplasms in preclinical studies. Here, we compared anti-cancer properties of E7386 with ICG-001 to define its molecular mechanisms and validate the β-catenin/CBP axis as a bona fide therapeutic target in HNSCC.

Anti-HNSCC activity of E7386 was evaluated in four human HNSCC cell lines using genomic, molecular, biochemical and functional approaches, including global ChIP-seq for H3K4me3. The set of transcripts significantly down-regulated by E7386 in HNSCC cells was projected onto a TCGA RNA-seq data (n=318) using ASSIGN, where samples were scored based on the coordinated expression of the gene signature which, in turn, reflected the level of E7386 inhibition per sample. The E7386 inhibition score was then tested for its association with survival by stratifying TCGA patients (n=318) into high- and low-score groups. Results showed that E7386 had highly overlapping activity signatures with ICG-001 (R = 0.997) with ~50 - 100-fold lower EC50. Similar to ICG-001, treatment with E7386 blocked association between β-catenin and CBP with a concomitant reduction in CBP and MLL1 abundance and global H3K4 trimethylation. E7386 repressed an oncogenic gene expression signature regulated by YAP1/TAZ and impeded HNSCC cell proliferation, promoting E-cadherin adhesion and junctional localization of β-catenin. Importantly, E7386 inhibition-associated transcriptional signatures tracked with tumor grade and poor human HNSCC patient survival. In conclusion, inhibiting β-catenin/CBP activity with E7386 represents a novel approach aimed at targeting epigenetically driven changes in the chromatin structure in HNSCC.

Citation Format: Huamei Yang, Vinay Kartha, Khalid A. Alamoud, Anthony Federico, Andrew Tilston-Lunel, Bach-Cuc Nguyen, Takashi Owa, Kenichi Nomoto, Xaralabos Varelas, Stefano Monti, Maria A. Kukuruzinska. Inhibition of β-catenin/CBP signaling with E7386 targets epigenetic changes associated with cancer stem cells in head and neck cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2453.

Abstract PR08: Leveraging single-cell epigenomics to uncover regulatory programs in lung adenocarcinoma

A hallmark of cancer development is the loss of cellular identity due to the dysregulation of regulatory networks that maintain functional, differentiated states. Chromatin state has been linked to this control of cellular identity and developmental processes; however, the mechanisms by which these regulatory landscapes are disrupted during cancer progression are not well understood. To this end, we leveraged an optimized single-cell ATAC-sequencing (scATAC-seq) strategy using a combinatorial indexing-based technology to assess chromatin state changes that occur in a mouse model of lung adenocarcinoma (LUAD). We utilized a well-established LUAD mouse model in which mice conditionally express the KrasG12D mutation and lose p53 expression in alveolar type II cells following Cre-mediated recombination, termed the KP model. In this model, KP tumors progress from early-stage hyperplasias to metastatic, advanced adenocarcinomas without acquiring additional somatic mutations, suggesting that these phenotypic transitions may be driven in part by epigenetic mechanisms. Using scATAC-seq, we profiled 16,044 normal lung, primary KP tumor, and metastatic cells to assess chromatin state changes across LUAD progression. We found that LUAD tumor evolution was characterized by a heterogeneous epigenomic continuum that was associated with loss of alveolar identity and progression to metastasis. Interestingly, we identified a reproducible metastatic state that was homogeneous, suggesting that cancer cells funnel towards a stable epigenetic state. In addition, we utilized novel computational tools to assess combinatorial transcription factor (TF)-driven programs that delineate stages of cancer progression in the KP model. From these analyses, we identified a clear transition point that corresponded to progressive gain of RUNX2 transcription factor activity. Using CRISPR activation and knockout strategies, we found that RUNX2 regulated the chromatin accessibility of several regulatory programs involved in extracellular matrix remodeling, suggesting that RUNX2 signaling is a critical event in LUAD progression and metastasis. In addition, gene signatures derived from this RUNX-activated state were highly predictive of survival in human LUAD. Together, these results demonstrated the power of single-cell epigenomics to identify TF-driven regulatory programs as key biomarkers of tumor progression.

This abstract is also being presented as Poster A40.

Citation Format: Lindsay M. LaFave, Vinay Kartha, Sai Ma, Kevin Meli, Isabella Del Priore, Caleb Lareau, Venkat Sanker, Santiago Naranjo, Peter Westcott, Zachary Chiang, Alison Brack, Travis Law, Aviv Regev, Jason D Buenrostro, Tyler Jacks. Leveraging single-cell epigenomics to uncover regulatory programs in lung adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR08.

Abstract 2633: Deciphering the role of protein glycosylation in oral cancer: insights into tumor biology and treatment

Head and neck cancer is a debilitating malignancy, with the majority of cases arising in the oral cavity as oral squamous cell carcinoma (OSCC). A major driver of OSCC is the epidermal growth factor receptor (EGFR), whose activity is aberrantly upregulated in >80% of tumors. EGFR is highly modified with N-linked glycans; fucosylation of N-glycans interferes with EGFR dimerization and activation. Thus, post-transcriptional changes may govern EGFR activity. In OSCC, EGFR signaling converges on Wnt/β-catenin activity, known to play pivotal roles in the pathobiology of this malignancy through the interaction of nuclear β-catenin with the histone acetyltransferase CREB-binding protein (CBP). We have shown that a small molecule inhibitor of β-catenin-CBP interaction, ICG-001, interferes with OSCC proliferation and aggressive features in cellular, zebrafish and murine models. Also, OSCC-cell line derived mouse tumor xenografts exhibit reduced EGFR abundance, and genomic analyses show a positive correlation between ICG-001 and EGFR inhibition. Given that modification of EGFR with N-glycans impacts its cell-surface localization and signaling, we hypothesized that ICG-001 affects EGFR N-glycosylation. To determine the effect of inhibition of β-catenin/CBP activity on cellular N-glycosylation programs, N-glycans from CAL27 and HSC3 cells treated with ICG-001 or vehicle control were released, permethylated, and analyzed via MALDI-TOF MS. Next, EGFR glycopeptides from CAL27 and HSC3 cells treated with ICG-001 or vehicle control, were analyzed with an Orbitrap Fusion™ Lumos™ Tribrid™ mass spectrometer (Thermo Scientific) using EThcD. In CAL27 cells, we observed higher levels of high mannose (less processed) N-glycans and complex fucosylated N-glycans, whereas in HSC3 cells we observed complex, afucosylated N-glycans. After ICG-001 treatment, HSC3 cells displayed higher levels of fucosylated N-glycans, suggesting that ICG-001, via inhibition of β-catenin/CBP signaling, promotes a more indolent-like glycan profile. Similarly, EGFR from CAL27 cells had highly fucosylated N-glycans, while EGFR from HSC3 cells displayed N-glycans with a paucity of fucose. Treatment of HSC3 cells with ICG-001 led to higher fucosylation, potentially inhibiting EGFR signaling. Parallel analyses of gene expression signatures in response to ICG-001 treatment in HSC-3 cells showed increased transcriptional expression of fucosyltransferases, FUT2 and FUT3. Our studies suggest that the β-catenin/CBP axis promotes EGFR signaling through downregulation of FUT2 and FUT3 expression and activity. Thus, inhibition of β-catenin/CBP signaling with ICG-001 may serve as a therapeutic approach to downregulate EGFR pro-tumorigenic activity in OSCC. Supported by NIH grants P41 GM104603 (CEC), F32 CA196157 (KBC), and by the Evans Center for Interdisciplinary Biomedical Research ARC #9950000118 (MAK).

Citation Format: Kevin B. Chandler, Vanessa L. Stahl, Khalid Alamoud, Bach-Cuc Nguyen, Vinay Kartha, Khikmet Sadykov, Stefano Monti, Maria A. Kukuruzinska, Catherine E. Costello. Deciphering the role of protein glycosylation in oral cancer: insights into tumor biology and treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2633.

Abstract 803: Targeting β-catenin/CBP signaling in OSCC

Objectives: Oral squamous cell carcinoma (OSCC) is an aggressive malignancy characterized by molecular heterogeneity and locoregional spread associated with high morbidity. Aggressive cancers are thought to arise from populations of cancer initiating cells (CICs) that exhibit the properties of stem cells and drive tumor development, recurrence and resistance to therapy. The transcriptional regulator, β-catenin, has been implicated in OSCC CICs. Nuclear β-catenin has been shown to recruit the chromatin remodeling CREB binding protein (CBP) to drive expression of proliferation and survival genes, as well as genes that maintain stem-like phenotypes. We hypothesized that targeting β-catenin-CBP interaction will inhibit CICs in oral tumors and restore an epithelial phenotype.

Methods: To test tumor aggressive potential of OSCC CICs, we used zebrafish as a model system. We isolated CD44+CD24hiCD29hi cells fom aggressive HSC-3 OSCC cells by FACS and assayed their ability to drive tumor growth and metastases in zebrafish compared to unsorted and CD44+CD24lowCD29low cells. In addition, we examined the role of the β-catenin/CBP axis in the aggressive phenotype of these cells. We also assessed whether the β-catenin/CBP axis affected CICs in tumors from immune competent HPV+ mice.

Results: Zebrafish injected with subpopulation of cells co-expressing CD44+CD24hiCD2hi primitive cell surface markers drove rapid tumor growth and metastases, followed by unsorted and sorted CD44+CD24lowCD29low. Treatment of CD44+CD24hiCD29hi cells with a small molecule inhibitor of the β-catenin-CBP interaction, ICG-001, interfered with tumor growth and metastases in zebrafish. Further, ICG-001 inhibited tumor growth in immunocompetent HPV+ murine model. On a cellular level, ICG-001 promoted membrane localization of β-catenin, enhanced E-cadherin adhesion and restored epithelial phenotype. Significantly, ICG-001 gene signatures tracked with reduced overall patient survival in the cancer genome atlas, TCGA. Conclusion: Our studies indicate that the β-catenin/CBP axis promotes OSCC CICs and that ICG-001 may be an effective therapeutic agent for this malignancy.

Support: Evans Center for Interdisciplinary Biomedical Research ARC funding AU 5303015 8000000.

Citation Format: Khalid Alamoud, Khikmet Sadykov, Vinay Kartha, Stefano Monti, Anna Belkina, Jennifer Snyder-Cappione, Sara Pai, Maria Kukuruzinska. Targeting β-catenin/CBP signaling in OSCC [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 803. doi:10.1158/1538-7445.AM2017-803