Fernández-Zapico, Martín E.

e16185 Background: Comprehensive sequencing efforts have identified fibroblast growth factor receptor (FGFR) translocations in numerous cancers. FGFR2 fusions were recently identified as an actionable therapeutic target in ̃17% of cholangiocarcinoma patients, predominantly found in patients with intrahepatic cholangiocarcinoma. Genomic partners for FGFR fusions are variable. In addition, obtaining high yield tissue biopsies for CCA remains challenging and tumor tissue available for molecular analyses is scarce. When combined, these two factors make detection of FGFR fusions in CCA challenging. An accurate molecular assay to detect FGFR fusions in CCA could improve utilization of FGFR-targeted therapies. Methods: The objective of our study was to develop an approach for targeted RNA analysis to improve sensitivity for FGFR fusion detection from limited tumor material. We adapted the sensitive targeted digital sequencing (TARDIS) approach recently developed in our lab for analysis of RNA. This approach utilizes a combination of open-ended targeted amplification followed by ligation, enabling detection of tyrosine kinase fusions without prior knowledge of the precise sequence of the fusion breakpoint or identity of the fusion partner. For evaluation of analytical performance, we analyzed RNA from a CCA organoid model with a known FGFR2 fusion, and Seraseq Fusion RNA Mix v3 Reference Material with two known FGFR3 fusions. Results: Without prior knowledge the partner or coordinates of the fusion breakpoint, we detected an FGFR2-KIF5C fusion in RNA from a CCA organoid model. The fusion breakpoint coordinates predicted by TARDIS-RNA were validated by comparison with RNA-Seq. To assess sensitivity and quantitative performance of the assay, we analyzed a serial dilution of the reference RNA sample from Seraseq with concentration of RNA molecules representing candidate fusions verified by digital PCR. Using TARDIS-RNA to analyze replicates with 5 ng RNA input, we were able to detect candidate fusions represented by as few as 2.7 fusion molecules on average. Concentrations of fusion molecules measured using the two methods were highly correlated (R = 0.96). Conclusions: These results demonstrate sensitivity and quantitative performance of a targeted RNA sequencing assay to detect and quantify FGFR fusions in tumor specimen from intrahepatic cholangiocarcinoma. On-going work is focused on further evaluating assay performance and characterizing FGFR fusions using additional tissue specimen.

Introduction: Truncating mutations in Additional Sex Combs-Like 1 (ASXL1) are associated with a high-risk disease phenotype in myeloid malignancies. In chronic myelomonocytic leukemia (CMML), truncating ASXL1 mutations are known to increase transcriptional activity of leukemic driver genes and have been associated with gene body hypermethylation. We interrogated the transcriptome and methylome of patients with ASXL1-mutant (MT) and -wildtype (WT) CMML using a multi-omics approach to test the hypothesis that gene expression is mediated through gene body methylation. Methods: Bone marrow mononuclear cells from patients with ASXL1 WT (n=8) and MT (n=8) CMML were subjected to targeted NGS of DNA, whole transcriptome shotgun sequencing (RNA-seq), and immunoprecipitation of DNA methyl residues (DIP-seq). After quality control all samples were sequenced on an Illumina HiSeq 4000 before further processing and data analysis. Differential gene expression analysis was performed to identify genes up-regulated in MT CMML. The samples in the two groups were treated as biological replicates and subjected to a consensus peak calling strategy requiring an overlap of at least 30% between samples and an adjusted p-value < 5x10-5 for a methylation peak to be considered statistically significant. For validation purposes methylation analysis was performed on 3 ASXL1 MT and 3 WT CMML patients using Illumina Infinium MethylationEPIC microarrays and differentially methylated regions were identified using a bump hunting strategy. Gene body methylation was defined as methylation in gene bodies (outside the promoter region, i.e. transcription start site ±2kb). Gene body methylation was compared between WT and MT CMML for the up-regulated genes and correlated with expression of all genes in MT CMML. Results: Sixteen WHO-defined CMML patients were included, median age 69 years (48-77), 63% male, 50% had truncating ASXL1 frame shift mutations. Abnormal karyotypes were observed in the same number of patients and the burden of co-mutations was similar between the two groups (median number per group 3 vs. 3, p=0.508). This included several modulators of DNA methylation including TET2, DNMT3A, and IDH2 (median number per group 1 vs. 1, p=0.699). There was a predominant up-regulation of gene expression in MT CMML: 707 genes up- and 124 down-regulated (FDR<0.050) without evidence of differential methylation in promoter regions of the differentially expressed genes. There was no difference in the number of genes with consensus methylation peaks in the gene body or the extent of gene body methylation (area under the consensus peaks) between MT and WT CMML for the differentially expressed genes (Figure 1a). We further validated these results using methylation microarrays (Figure 1b). Among the MT CMML patients, there was a curvilinear relationship between gene body methylation and gene expression across all genes with intermediate gene body methylation being associated with the highest gene expression (Figure 1c). As an alternative unbiased approach, we identified 1595 differentially methylated regions (DMR, regions with FDR<0.05) in the validation data set. We mapped all hypermethylated regions to gene bodies requiring that there was no concurrent hypermethylation of the promoter region of the same gene. With this approach we identified one of the 707 up-regulated genes (0.14%) with evidence of isolated gene body hypermethylation (HBZ, log2-fold change in gene expression 4.25, FDR=0.0008, DMR area=1.61, DMR FDR=0.018). Representative examples of up-regulated mitotic kinases without evidence of differential gene body methylation are shown in Figure 1d (pie charts represent the mean β-values of microarray probes, p-values represent the comparisons of mean β-values between MT and WT CMML per gene). Conclusions: Gene body methylation was positively associated with gene expression in MT CMML. However, the lack of differential gene body methylation between WT and MT CMML for the up-regulated genes make it an unlikely explanation for the observed increase in transcriptional activity among patients with MT CMML. Figure 1 Disclosures Ordog: Millipore Sigma: Patents & Royalties.

Introduction: Additional Sex Combs-Like 1 (ASXL1) is a chromatin modifier frequently affected by truncating mutations in myeloid malignancies. In chronic myelomonocytic leukemia (CMML), truncating ASXL1 mutations are associated with the overexpression of leukemogenic driver genes, however the molecular mechanisms underlying this transcriptional activation remain controversial. We performed single-cell chromatin accessibility studies of ASXL1-mutant (MT) and -wildtype (WT) CMML to identify cis-regulatory elements (CREs) such as distal enhancer elements that may explain the observed transcriptional activity in MT CMML. Methods: Bone marrow mononuclear cells from a patient with WT and a patient with MT CMML were subjected to single-cell DNA transposase accessibility studies (scATAC-seq). The cryopreserved cells were thawed and resuspended and approximately 100000 viable mononuclear cells per sample were subjected to transposase assays before proceeding to single-cell partitioning into gel beads in emulsion, barcoding, library construction, and sequencing following an established 10X Genomics workflow. The target cell recovery was approximately 2000 cells per sample. Genomic libraries were sequenced on an Illumina HiSeq 4000 before demultiplexing, alignment to the reference genome, and post-alignment quality control. The 10X Genomics Cell Ranger ATAC software was used for demultiplexing, alignment of the reads to the GRCh38 reference genome, filtering and quality control, counting of barcodes and unique molecular identifiers, identification of transposase cut sites, detection of accessible chromatin peaks, count matrix generation for peaks and transcription factors, clustering, and differential accessibility analysis. The two-sample Kolmogorov-Smirnov test for equality of distribution functions was used to compare the distributions of single-cell entropies. Single-cell cis-co-accessibility scores were estimated using Cicero. Results: To mitigate potential effects on the analysis introduced by unequal cell recovery due to experimental conditions, we randomly sampled 1500 single cells from each genotype. Visualizing the first two principal components of the chromatin accessibility data revealed the differences in chromatin conformation between genotypes and also the increased heterogeneity within the MT sample (Figure 1a). To quantify this increase in intratumoral heterogeneity of chromatin accessibility in MT CMML, we calculated the single-cell entropies for both genotypes. There was an increase in the dispersion of single-cell entropy values (mean 0.793±0.026 versus 0.811±0.012, p=6.19x10-151) in MT compared to WT disease (Figure 1b). To leverage the power of the single-cell chromatin accessibility data, we estimated cis-co-accessibility scores (two-way chromatin interactions). There were 631 genes involved in two-way chromatin interactions that were either specific to MT CMML or were shared between MT and WT CMML and showed an increase in co-accessibility in MT CMML. Co-accessibility was higher in MT compared to WT CMML, regardless whether the chromatin interaction was MT-specific or shared between the genotypes (Figure 1c). Gene ontology analysis revealed increased chromatin accessibility in genes involved in the regulation of cell cycle, nuclear division, chromosome organization, cell cycle phase transition, DNA conformation change, and DNA replication (FDR<1.00x10-5). The construction of cis-co-accessibility networks demonstrated a remodeling of the chromatin landscape with MT-specific chromatin interactions involving key mitotic kinases such as MAP2K3 (Figure 1d). Conclusions: MT CMML is characterized by an increase in intratumoral heterogeneity and increased chromatin accessibility. The increased chromatin co-accessibility involved key mitotic kinases and may serve as a plausible explanation for the increased transcriptional activity observed in MT CMML. Figure 1 Disclosures Ordog: Millipore Sigma: Patents & Royalties.

Polycystic kidney disease (PKD) has been linked to abnormal structure/function of ciliary proteins, leading to renal dysfunction. Recently, attention has been focused in the significant vascular abnormalities associated with PKD, but the mechanisms underlying this phenomenon remain elusive. Here, we seek to define the molecular events regulating the angiogenic imbalance observed in PKD. Using micro computed tomography (n=7) and protein expression analysis (n=5), we assessed the vascular density and the angiogenic profile of noncystic organs in a well-established PKD rat model (Polycystic Kidney-PCK rat). Heart and lungs of PCK rats have reduced vascular density and decreased expression of angiogenic factors compared with wild type. Similarly, PCK-vascular smooth muscle cells (VSMCs; n=4) exhibited lower levels of vascular markers. Then, using small interfering RNA (n=4), we determined the role of the ciliary protein fibrocystin in wild type-VSMCs, a critical component/regulator of vascular structure and function. Reduction of fibrocystin in wild type-VSMCs (n=4) led to an abnormal angiogenic potential similar to that observed in PCK-VSMCs. Furthermore, we investigated the involvement of the hedgehog signaling, a pathway closely linked to the primary cilium and associated with vascular development, in PKD. Mechanistically, we demonstrated that impairment of the hedgehog signaling mediates, in part, this abnormal angiogenic phenotype. Lastly, overexpression of Gli1 in PCK-VSMCs (n=4) restored the expression levels of proangiogenic molecules. Our data support a critical role of fibrocystin in the abnormal vascular phenotype of PKD and indicate that a dysregulation of hedgehog may be responsible, at least in part, for these vascular deficiencies.

Abstract Adenosquamous cancer of the pancreas (ASCP) is a subtype of pancreatic cancer that has a worse prognosis and greater metastatic potential than the more common pancreatic ductal adenocarcinoma (PDAC) subtype. To distinguish the genomic landscape of ASCP and identify actionable targets for this lethal cancer, we applied DNA content flow cytometry to a series of 15 tumor samples including five patient-derived xenografts (PDX). We interrogated purified sorted tumor fractions from these samples with whole-genome copy-number variant (CNV), whole-exome sequencing, and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analyses. These identified a variety of somatic genomic lesions targeting chromatin regulators in ASCP genomes that were superimposed on well-characterized genomic lesions including mutations in TP53 (87%) and KRAS (73%), amplification of MYC (47%), and homozygous deletion of CDKN2A (40%) that are common in PDACs. Furthermore, a comparison of ATAC-seq profiles of three ASCP and three PDAC genomes using flow-sorted PDX models identified genes with accessible chromatin unique to the ASCP genomes, including the lysine methyltransferase SMYD2 and the pancreatic cancer stem cell regulator RORC in all three ASCPs, and a FGFR1-ERLIN2 fusion associated with focal CNVs in both genes in a single ASCP. Finally, we demonstrate significant activity of a pan FGFR inhibitor against organoids derived from the FGFR1-ERLIN2 fusion–positive ASCP PDX model. Our results suggest that the genomic and epigenomic landscape of ASCP provide new strategies for targeting this aggressive subtype of pancreatic cancer. Significance: These data provide a unique description of the ASCP genomic and epigenomic landscape and identify candidate therapeutic targets for this dismal cancer.

Abstract Introduction: D/L-alpha-metyrosine (SM-88, racemetyrosine) is a clinical stage chemically modified racemic amino acid therapy with broad anticancer activity in patients across 15 different indications. While amino acid metabolism has been leveraged in oncology imaging for decades, SM-88 offers a novel therapeutic approach to selectively disrupt cancer cells. This study explored phenotypic and mechanistic effects of exposing cancer cells to D/L-alpha-metyrosine as well as potential immunomodulation of the in vivo tumor microenvironment related to tyrosine hydroxylase inhibition and catecholamine depletion. Methods: In vitro experiments were conducted in a range of human and mouse cancer cell lines, including MCF-7, 4T1, HCT116, CAPAN2, PAN02, PANC01. The effect of SM-88 methyl-ester (SM-88 ME) alone on viability, apoptosis, migration/invasion, protein synthesis inhibition, autophagy, cell cycle arrest, and ROS generation was assessed. In vivo experiments included xenograph studies of HCT116 with monotherapy consisting of either IP injections up to 200 mg/kg/day of SM-88 ME, or orally administered SM-88 up to 324 mg/kg/day. Orthotopic xenographs of 4T1 and PAN02 models using monotherapy doses up to 200 mg/kg/day are ongoing. Ongoing immunohistochemistry and flow cytometry is focused on correlation with LAT1 expression and efficacy, alteration in macrophage polarization (M1/M2 ratio), Tregs, and various T cell populations in the tumor microenvironment. Results: Exposure to SM-88 ME exhibited a dose dependent increase in ROS, as well as decreases in caspase 3/7 activation. An increase in ROS following exposure to SM-88 ME was also observed in PAN02 cells. Similar decreases in caspase 3/7 activation were observed in CAPAN2, HCT116, and MCF7 cells. Interestingly, across a variety of cell lines including PAN02, PANC1, and 4T1 cell morphology changes suggested the formation of autophagic vacuoles. Viability across all cell lines was reduced in a dose and time dependent manner. In a mouse HCT116 SC xenograft model, mice receiving 324 mg/kg/day SM-88 ME showed significantly reduced tumor size compared to control mice. Additional in vitro and in vivo experiments are ongoing. Conclusions: The importance of amino acid metabolism in cancer has gained greater awareness over the past decade, however potential therapeutic approaches in this area remain limited. SM-88 has been dosed in over 180 cancer patients with encouraging efficacy and safety findings to date. Early data suggest increases in ROS generation and decreases in apoptosis may occur in certain cancer types (PAN02 pancreatic cancer), suggesting a shift away from apoptosis and towards autophagy. Potential immune modulatory effects of SM-88, including alterations in macrophage polarization related to tyrosine hydroxylase inhibition and subsequent reductions in catecholamine production are being examined. Citation Format: Alexander Vandell, Jonathan Eckard, Steve Hoffman, Giuseppe Del Priore, Martin Fernandez-Zapico. In vitro and in vivo anticancer effects of D/L-alpha-metyrosine (SM-88), a novel metabolism-based therapy [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 5998.

Abstract Introduction: TYME-18 is a combination of an ambiphilic steroid acid, tauroursodeoxycholic acid (TUDCA) and surfactants (N-methyl pyrrolidone, polidocanol, and linoleic acid) administered intratumorally to induce regression without injuring adjacent tissue. Methods: Balb/C mice were inoculated with CT-26 cancer (106 cells) until a tumor was established to approximately 100 mm3. An initial feasibility semi-quantitative assessment was performed with 10 animals (table 1). A larger confirmatory experiment testing the individual components of TYME-18 was also conducted (tables 2 & 3). Mice received intra-tumoral injections of TYME-18 with surfactants; or surfactants without TUDCA, or vehicle with measurements 3 times/wk. Intra-tumoral injections were administered 6 times at 3-day intervals over a total of 4 weeks. Animals were sacrificed when tumors reached 2000 mm3 or at the end of the study (16 weeks). Table 1.HISTOPATHOLOGIC FINDINGSFinal tumor sizes & intratumoral necrosis. TYME-18 vs Control. CT-26 model. (Fisher's Exact Test p=0.001)GroupAnimal IDTumor SizeIntratumoral NecrosisControlG1A-1>1 cmModerateG1A-2>1 cmMildG1B-2>1 cmMildG1B-3>1 cmModerateG1B-4>1 cmModerate-TreatedG2A-1<1 – 5 mmSevereG2A-3<1 – 5 mmSevereG2B-1<1 – 5 mmSevereG2B-3<1 – 5 mmSevereG2B-55 – 6 mmSevere- Table 2.Days Post Implementation average tumor volume mm3 (ANOVA P<0.0001)0369121520Vehicle83.1157.9263.4401.4613.9849.41368.9Surfactant Alone76.4131.1166.3209.6274.3345.7642.8TYME-1880.528.228.934.235.854.457.2- Table 3.Tumor Free Mice at Study End: Day 112 (Fisher's Exact Test p < 0.0001)Treatment# of Mice# Tumor Free Mice% Tumor Free MiceVehicle2000Surfactant Alone1218.33TYME-18121191.6 Results: TYME-18 demonstrated a significant difference between treated and untreated animals (see Tables 1, 2, 3). A minor reduction in tumor cell mass was observed in response to the surfactant, with the greatest response (ANOVA p=.001) observed in the TYME-18 (surfactant + TUDCA) (table 2). Discussion: The local administration of an ambiphilic steroid acid along with surfactants, impeded the ability of tumors to increase in size. Both the surfactants and the ambiphilc steroid acid contributed to this effect with an apparent synergistic effect. Aside from the physical chemical acid effect on tissue, ambiphilic steroid acids are now recognized as important regulators of energy metabolism. Their effects on FXR, LXR, PPAR-α, PPAR-γ are known to regulate important changes in energy metabolism including insulin utilization, the sensitivity of the insulin receptor, the transcription of the genes that mediate glucose and lipid metabolism as well as various immune effects; all of which could be useful in the treatment of cancer. Currently, TYME-18 is under investigation as a simple and nontoxic treatment for tumors for which systemic therapy is not indicated. Citation Format: John Rothman, Steve Hoffman, Allyson Ocean, Jonathan Eckard, Giuseppe Del Priore, Martin Fernandez-Zapico. In vivo mouse model data demonstrating reduction in tumor cell proliferation following intratumoral administration of TYME 18 [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 2764.

Pancreatic cancer remains among the deadliest forms of cancer with a 5 year survival rate less than 10%. With increasing numbers being observed, there is an urgent need to elucidate the pathogenesis of pancreatic cancer. While both contribute to disease progression, neither genetic nor environmental factors completely explain susceptibility or pathogenesis. Defining the links between genetic and environmental events represents an opportunity to understand the pathogenesis of pancreatic cancer. Epigenetics, the study of mitotically heritable changes in genome function without a change in nucleotide sequence, is an emerging field of research in pancreatic cancer. The main epigenetic mechanisms include DNA methylation, histone modifications and RNA interference, all of which are altered by changes to the environment. Epigenetic mechanisms are being investigated to clarify the underlying pathogenesis of pancreatic cancer including an increasing number of studies examining the role as possible diagnostic and prognostic biomarkers. These mechanisms also provide targets for promising new therapeutic approaches for this devastating malignancy.

The Hedgehog-regulated transcription factors GLI1 and GLI2 play overlapping roles in development and disease; however, the mechanisms underlying their interplay remain elusive. We report for the first time that GLI1 and GLI2 physically and functionally interact in cancer cells. GLI1 and GLI2 were shown to co-immunoprecipitate in PANC1 pancreatic cancer cells and RMS13 rhabdomyosarcoma cells. Mapping analysis demonstrated that the zinc finger domains of both proteins are required for their heteromerization. RNAi knockdown of either GLI1 or GLI2 inhibited expression of many well-characterized GLI target genes (BCL2, MYCN, PTCH2, IL7 and CCND1) in PANC1 cells, whereas PTCH1 expression was only inhibited by GLI1 depletion. qPCR screening of a large set of putative canonical and non-canonical Hedgehog/GLI targets identified further genes (e.g. E2F1, BMP1, CDK2) strongly down-regulated by GLI1 and/or GLI2 depletion in PANC1 cells, and demonstrated that ANO1, AQP1 and SOCS1 are up-regulated by knockdown of either GLI1 or GLI2. Chromatin immunoprecipitation showed that GLI1 and GLI2 occupied the same regions at the BCL2, MYCN and CCND1 promoters. Furthermore, depletion of GLI1 inhibited GLI2 occupancy at these promoters, suggesting that GLI1/GLI2 interaction is required for the recruitment of GLI2 to these sites. Together, these findings indicate that GLI1 and GLI2 co-ordinately regulate the transcription of some genes, and provide mechanistic insight into the roles of GLI proteins in carcinogenesis.

Abstract Summary: In this issue, Hou and colleagues present their exciting work demonstrating that, through remodeling of the local tumor microenvironment (TME), pancreatic ductal adenocarcinoma forms a tumor-supportive niche capable of liberating cancer cells from dependence on oncogenic KRAS signaling. Through extensive experimentation both in vitro and in vivo, the authors reveal that the HDAC5–CCL2 axis drives the recruitment of tumor-associated macrophages to the TME to provide trophic signaling. See related article by Hou et al., p. 1058.