Systematic determination of genetic network architecture

Technologies to measure whole-genome mRNA abundances and methods to organize and display such data are emerging as valuable tools for systems-level exploration of transcriptional regulatory networks. For instance, it has been shown that mRNA data from 118 genes, measured at several time points in the developing hindbrain of mice, can be hierarchically clustered into various patterns (or 'waves') whose members tend to participate in common processes. We have previously shown that hierarchical clustering can group together genes whose cis-regulatory elements are bound by the same proteins in vivo. Hierarchical clustering has also been used to organize genes into hierarchical dendograms on the basis of their expression across multiple growth conditions. The application of Fourier analysis to synchronized yeast mRNA expression data has identified cell-cycle periodic genes, many of which have expected cis-regulatory elements. Here we apply a systematic set of statistical algorithms, based on whole-genome mRNA data, partitional clustering and motif discovery, to identify transcriptional regulatory sub-networks in yeast-without any a priori knowledge of their structure or any assumptions about their dynamics. This approach uncovered new regulons (sets of co-regulated genes) and their putative cis-regulatory elements. We used statistical characterization of known regulons and motifs to derive criteria by which we infer the biological significance of newly discovered regulons and motifs. Our approach holds promise for the rapid elucidation of genetic network architecture in sequenced organisms in which little biology is known.

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

AlignACE is a Gibbs sampling algorithm for identifying motifs that are over-represented in a set of DNA sequences. When used to search upstream of apparently coregulated genes, AlignACE finds motifs that often correspond to the DNA binding preferences of transcription factors. We previously used AlignACE to analyze whole genome mRNA expression data. Here, we present a more detailed study of its effectiveness as applied to a variety of groups of genes in the Saccharomyces cerevisiae genome. Published functional catalogs of genes and sets of genes grouped by common name provided 248 groups, resulting in 3311 motifs. In conjunction with this analysis, we present measures for gauging the tendency of a motif to target a given set of genes relative to all other genes in the genome and for gauging the degree to which a motif is preferentially located in a certain distance range upstream of translational start sites. We demonstrate improved methods for comparing and clustering sequence motifs. Many previously identified cis-regulatory elements were found. We also describe previously unidentified motifs, one of which has been verified by experiments in our laboratory. An extensive set of AlignACE runs on randomly selected sets of genes and on sets of genes whose upstream regions contain known transcription factor binding sites serve as controls.

The Rac1-GEF Tiam1 couples the NMDA receptor to the activity-dependent development of dendritic arbors and spines

NMDA-type glutamate receptors play a critical role in the activity-dependent development and structural remodeling of dendritic arbors and spines. However, the molecular mechanisms that link NMDA receptor activation to changes in dendritic morphology remain unclear. We report that the Rac1-GEF Tiam1 is present in dendrites and spines and is required for their development. Tiam1 interacts with the NMDA receptor and is phosphorylated in a calcium-dependent manner in response to NMDA receptor stimulation. Blockade of Tiam1 function with RNAi and dominant interfering mutants of Tiam1 suggests that Tiam1 mediates effects of the NMDA receptor on dendritic development by inducing Rac1-dependent actin remodeling and protein synthesis. Taken together, these findings define a molecular mechanism by which NMDA receptor signaling controls the growth and morphology of dendritic arbors and spines.

Selection analyses of insertional mutants using subgenic-resolution arrays

We describe a method of genome-wide analysis of quantitative growth phenotypes using insertional mutagenesis and DNA microarrays. We applied the method to assess the fitness contributions of Escherichia coli gene domains under specific growth conditions. A transposon library was subjected to competitive growth selection in Luria-Bertani (LB) and in glucose minimal media. Transposon-containing genomic DNA fragments from the selected libraries were compared with the initial unselected transposon insertion library on DNA microarrays to identify insertions that affect fitness. Genes involved in the biosynthesis of nutrients not provided in the growth medium were found to be significantly enriched in the set of genes containing negatively selected insertions. The data also identify fitness contributions of several uncharacterized genes, including putative transcriptional regulators and enzymes. The applicability of this high-resolution array selection in other species is discussed.

Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli

A global methylation-based technique was used to identify, display, and quantitate the in vivo occupancy of numerous protein-binding sites within the Escherichia coli genome. The protein occupancy profiles of these sites showed variation across different growth conditions and genetic backgrounds. Of the 25 sites identified in this study, 24 occurred within 5' noncoding regions. Protein occupancy at 13 of these sites was supported by independent biochemical and genetic evidence. Most of the remaining 12 sites fell upstream of genes with no previously known function. A multivariate statistical analysis was utilized to group such uncharacterized genes with well-characterized ones, providing insights into their function based on a common pattern of transcriptional regulation.

Abstract 5863: RGX-202, a first-in-class small-molecule inhibitor of the creatine transporter SLC6a8, is a robust suppressor of cancer growth and metastatic progression

Background: Colorectal cancer (CRC) is one of the leading causes of cancer deaths worldwide with more than 140,000 patients diagnosed and nearly 50,000 deaths annually in the U.S. alone. Roughly 60% of patients present with locally advanced or distant metastatic disease, with the liver being a primary site of metastatic colonization. Creatine metabolism has been implicated in colon cancer progression and metastatic colonization of the liver. Metastatic colon cancer cells upregulate and release creatine kinase-B (CKB) into the extracellular space, where it phosphorylates creatine to generate the high-energy metabolite phosphocreatine. Phosphocreatine is imported via the creatine transporter SLC6a8. Intracellular phosphocreatine can be converted to ATP to fuel the survival of metastatic cancer cells within the hypoxic hepatic microenvironment. Consistent with this finding, genetic depletion of SLC6a8 in colon and pancreatic cancer cell lines significantly reduced liver colonization in mouse xenograft models.

Results: We herein demonstrate that the novel small molecule RGX-202 is a robust inhibitor of creatine uptake in cancer cells, both in vitro and in vivo. Oral administration of RGX-202 induced apoptosis of colon cancer cells in vivo, and significantly suppressed colon cancer liver metastatic colonization and primary tumor growth, both in KRAS wild-type and KRAS mutant colon cancer cell lines as well as in human PDX mouse models. Using genetic studies, these effects were found to be dependent on tumoral expression of SLC6a8. In addition, combination treatment of the CT26 syngeneic colon cancer mouse model with 5-FU resulted in synergistic antitumor activity, with complete tumor regressions observed in more than 40% of treated mice. Similarly, combination treatment of the KPC syngeneic mouse model with gemcitabine significantly reduced the growth of primary pancreatic tumors. Definitive 28-day GLP toxicology and pharmacokinetics studies of RGX-202 are currently ongoing. Preliminary observations suggest good tolerability in several animal species with a favorable pharmacokinetic profile, including bioavailability.

Conclusion: These results strongly support clinical development of RGX-202 in patients with gastrointestinal cancers, including colorectal and pancreatic cancer, both as monotherapy and in combination with standard-of-care treatment.

Citation Format: Isabel Kurth, Celia Andreu, Shugaku Takeda, Helen Tian, Foster Gonsalves, Katya Leites, Subhasree Sridhar, Jia Min Loo, Rob Busby, Sohail Tavazoie, Masoud Tavazoie. RGX-202, a first-in-class small-molecule inhibitor of the creatine transporter SLC6a8, is a robust suppressor of cancer growth and metastatic progression [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 5863.

Abstract LB-277: Characterization of the anti-cancer and immunologic activity of RGX-019, a novel pre-clinical stage humanized monoclonal antibody targeting the MERTK receptor

MERTK, a receptor tyrosine kinase of the TYRO3/AXL/MERTK (TAM) family, is expressed in innate immune cells including macrophages, dendritic cells and NK cells and is overexpressed in a wide variety of cancers, including leukemia and many solid cancers. Activation of MERTK on cancer cells via ligand binding results in activation of several tumor-promoting signaling pathways, which stimulate proliferation, migration and angiogenesis, and decrease apoptosis and chemosensitivity. Furthermore, activation of MERTK on macrophages drives immune evasion through the promotion of an immune-suppressive M2 phenotype. Pre-clinical and

clinical studies have shown promising emerging evidence of anti-tumor efficacy upon modulation of TAM receptor signaling. Herein, we report the pre-clinical characterization of RGX-019, a humanized IgG1 antibody with high affinity and specificity for human MERTK.

Surface Plasmon Resonance, cell-based binding assays and competition ELISA demonstrate high affinity/avidity binding for RGX-019 to human MERTK. In contrast, binding to human AXL, human TYRO3, or murine MERTK was not detected. Binding of RGX-019 to the MERTK receptor triggered its rapid internalization and degradation from the surface of human cancer cells within 4 hours and prevented Gas6 induced phosphorylation of AKT, a downstream signal transduction pathway that promotes cell growth and survival. RGX-019 treatment of SKMel5 melanoma cells effectively inhibited colony formation. RGX-019-induced degradation of MERTK in in vitro differentiated human M2 macrophages reduced AKT activation and promoted a pro-inflammatory cytokine signature. Furthermore, a related surrogate murine MERTK antibody significantly inhibited growth of MDA-MB-231 breast cancer tumors, demonstrating single agent anti-tumor efficacy in vivo. These findings demonstrate that RGX-019 is a potent and selective inhibitor of MERTK signaling with a unique mechanism-of-action that potently disrupts MERTK signaling in both cancer cells and immune-suppressive macrophages via MERTK receptor degradation. This activity results in robust repression of cancer cell growth both in vitro and in vivo. Overall, these data support further development of RGX-019 as a cancer therapeutic.

Citation Format: Shugaku Takeda, Celia Andreu-Agullo, Subhasree Sridhar, Nils Halberg, Ivo C. Lorenz, Sohail Tavazoie, Isabel Kurth, Masoud Tavazoie. Characterization of the anti-cancer and immunologic activity of RGX-019, a novel pre-clinical stage humanized monoclonal antibody targeting the MERTK receptor [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 LB-277.

Abstract LB-133: Correlative analysis of pharmacokinetics and pharmacodynamics of RGX-104, a first-in-class Liver-X-Receptor (LXR) agonist, and clinical outcomes in patients with advanced solid tumors

RGX-104, a first-in-class small-molecule LXR agonist modulates innate immunity and cancer progression via transcriptional activation of ApoE. ApoE protein suppresses tumor cell invasion and angiogenesis, and also depletes circulating and tumoral myeloid derived suppressor cells (MDSC), leading to T cell activation.A multivariate approach was used to address pharmacokinetic (PK) and pharmacodynamic relationships of RGX-104 in a phase 1 dose escalation study in patients with relapsed/refractory solid tumors. The study entailed multiple escalation arms with RGX-104 as monotherapy and in combination with nivolumab, ipilimumab, or docetaxel. Various markers including intratumoral ApoE and its receptor LRP1 in biopsy specimens, gene expression of LXR-targets in whole blood, serum markers including cytokines and lipids, as well as immune cell types such as MDSC, CD8 T-cells, and neutrophils in peripheral blood from patients were monitored at several time points. PK metrics were tracked to assess dose response relationships. Clinical outcomes such as objective response, time to disease progression, and duration on therapy were used for exploratory correlative analyses. A generally dose dependent increase in steady state exposure to RGX-104 was observed among all cohorts; the lowest efficacious exposure among patients with partial response was ~14,000 ng*h/mL. Treatment with RGX-104 at doses ranging from 120 mg BID to 240 mg BID induced expression of LXR targets, ApoE [2.7X (p=0.008) to 7.1X (p=0.007)] and ABCA1 [ 6.3X (p=1.20E-03) to 7X (p=8.1E-04] over baseline in a generally dose-dependent manner as assessed in whole blood. Similarly, MDSC depletion, ranging from 70%-90% relative to baseline, was observed in patients treated with RGX-104 along with concomitant CD8 T-cell activation; similar effects were noted in patients in combination cohorts. A model to explore dose dependency of change in immune cell types suggested that baseline levels of MDSC were most predictive of the magnitude of MDSC reduction after treatment, and that favorable clinical outcomes correlate with the extent of MDSC reduction and T cell activation. Low baseline levels of tumoral ApoE were associated with greater clinical benefit, with almost all patients with stable disease or partial response exhibiting ApoE tumor positive score of ≤20%; these patients also exhibited low/negative PD-L1 (<1%) staining, revealing a target specific tumor biomarker and PD-L1 subset that could support prospective patient selection. These and additional markers will be tracked in expansion cohorts of RGX-104 in combination with pembrolizumab and carboplatin/pemetrexed for 1st line treatment of patients with metastatic non-small cell lung cancer (PD-L1 <1%) and in combination with docetaxel for 2nd line treatment of patients with small cell lung cancer.

Citation Format: Monica Mita, Alan Mita, Erika Hamilton, Gerald S. Falchook, Michael Postow, Bartosz Chmielowski, Russell J. Schilder, James Strauss, Emerson Lim, Shubham Pant, Angela Jain, Oliver Rixe, Rebecca Redman, Kevin B. Kim, Tomislav Dragovich, R. Donald Harvey, Igor Puzanov, Nimisha Schneider, Renee Deehan, Tobi Guennel, Joe Lin, Sohail Tavazoie, Roger Waltzman, Eric Rowinsky, Michael Szarek, Subhasree Sridhar, Robert Busby, Narayan Lebaka, Celia Andreu, Isabel Kurth, David Darst, Masoud Tavazoie, Syed Raza, Robert Wasserman, Foster C. Gonsalves. Correlative analysis of pharmacokinetics and pharmacodynamics of RGX-104, a first-in-class Liver-X-Receptor (LXR) agonist, and clinical outcomes in patients with advanced solid tumors [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 LB-133.

Abstract IA05: Small RNAs reveal nuclear hormone receptor targeting as a novel therapy for melanoma

In recent years, numerous genes that drive melanoma metastasis or progression of established metastatic melanoma have been identified. The identification of such genes and their associated pathways have revealed insights into the cellular processes involved in these clinically important events. Our laboratory has found that deregulated expression of microRNAs is a major mechanism by which such gene-expression states that enable metastatic progression are achieved in various solid cancers. In melanoma, we have identified 3 microRNAs (miR-1908, miR-199a5p, and miR-199a3p) to be over-expressed in metastatic sub-populations of human melanoma cells. The expression levels of these microRNAs predict metastatic relapse in primary cutaneous melanomas. These microRNAs convergently target the gene ApoE, which through genetic, molecular, pharmacological, and clinical association analyses, we have identified as a robust suppressor of melanoma metastasis and metastatic progression. We have demonstrated pre-clinical proof-of-concept for the therapeutic activation of ApoE through transcriptional engagement of the Liver-X nuclear hormone receptor (LXR). Oral administration of multiple LXR agonists suppressed the growth of primary and metastatic melanoma in mice. Genetic studies revealed that the effects of LXR agonists are mediated through LXRβ, which elicits these effects through ApoE induction in the stromal and tumoral compartments. LXRβ; agonism suppressed progression in immunocompetent, xenograft, patient-derived xenograft, and genetically initiated melanomas. Moreover, LXRβ agonism exhibited combinatorial efficacy with B-Raf inhibitors and anti-CTLA4 immunotherapy. We provide pre-clinical proof-of-concept for therapeutic activation of nuclear hormone receptors in melanoma.

Citation Format: Sohail Tavazoie. Small RNAs reveal nuclear hormone receptor targeting as a novel therapy for melanoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Melanoma: From Biology to Therapy; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(14 Suppl):Abstract nr IA05.