TAMI-76. INTEGRATED MULTI-OMICS REVEAL INTRATUMOUR HETEROGENEITY AND NOVEL THERAPEUTIC TARGETS IN PAEDIATRIC EPENDYMOMA

Abstract Ependymoma (EPN) is the second most common malignant paediatric brain tumour with a five-year survival rate of only 25% following relapse. While molecular heterogeneity between EPN tumours is well understood, little is known concerning spatially-distinct intratumour heterogeneity within patients. In this context, we present a multi-omics integration of expression data at transcriptomic and metabolomic levels revealing intratumour heterogeneity and novel therapeutic targets. Surgically resected ependymoma tissue from two epigenetic subgroups, posterior fossa-A (PF-A) and supratentorial RELA, were first homogenised and polar metabolites, lipids and RNA simultaneously extracted from the same cellular population. Using liquid chromatography-mass spectrometry (LC-MS) and RNAseq 115 metabolites and 1580 upregulated genes were identified between the two subgroups, therefore validating previously reported genetic clustering of these two subtypes. Sampling of anatomically distinct regions was performed between eight PF-A EPN patients and multi-omic data was compared across 28 intratumour regions, with at least 3 different regions per patient. Integration of genes and metabolites revealed 124 dysregulated metabolic pathways, encompassing 156 genes and 49 metabolites. A large number of interactions occur in the gluconeogenesis and glycine pathways in 6 out of 8 patients, putatively representing therapeutically relevant ubiquitous metabolic pathways critical for EPN survival. Each anatomical region also presented at least one unique gene-metabolite interaction demonstrating heterogeneity within and across PF-A EPN tumours. A subset of the eight most prevalent genes across patients (GAD1, NT5C, FBP1, FMO3, HK3, TALDO1, NT5E, ALDH3A1) were selected for in vitro metabolic assays using 10 repurposed cytotoxic agents against PF-A EPN cell lines derived from intratumour regions of the same patient. 5/8 genes map within the gluconeogenesis metabolic pathway, further highlighting its significance within PF-A EPN. This is the first instance where multi-omic data integration and intratumour heterogeneity has been investigated for paediatric EPN revealing novel potential targets in the context of gene-metabolite correlations.

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Targeting the NAD Salvage Synthesis Pathway as a Novel Therapeutic Strategy for Osteosarcomas with Low NAPRT Expression

International Journal of Molecular Sciences ◽

10.3390/ijms22126273 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6273

Author(s):

Natasja Franceschini ◽

Jan Oosting ◽

Maud Tamsma ◽

Bertine Niessen ◽

Inge Briaire-de Bruijn ◽

...

Keyword(s):

Cell Lines ◽

Metabolic Pathways ◽

Therapeutic Strategy ◽

Rna Expression ◽

Primary Tumors ◽

Nicotinamide Phosphoribosyltransferase ◽

Nad Synthesis ◽

Vitro Model ◽

Novel Therapeutic

For osteosarcoma (OS), the most common primary malignant bone tumor, overall survival has hardly improved over the last four decades. Especially for metastatic OS, novel therapeutic targets are urgently needed. A hallmark of cancer is aberrant metabolism, which justifies targeting metabolic pathways as a promising therapeutic strategy. One of these metabolic pathways, the NAD+ synthesis pathway, can be considered as a potential target for OS treatment. Nicotinamide phosphoribosyltransferase (NAMPT) is the rate-limiting enzyme in the classical salvage pathway for NAD+ synthesis, and NAMPT is overexpressed in OS. In this study, five OS cell lines were treated with the NAMPT inhibitor FK866, which was shown to decrease nuclei count in a 2D in vitro model without inducing caspase-driven apoptosis. The reduction in cell viability by FK866 was confirmed in a 3D model of OS cell lines (n = 3). Interestingly, only OS cells with low nicotinic acid phosphoribosyltransferase domain containing 1 (NAPRT1) RNA expression were sensitive to NAMPT inhibition. Using a publicly available (Therapeutically Applicable Research to Generate Effective Treatments (TARGET)) and a previously published dataset, it was shown that in OS cell lines and primary tumors, low NAPRT1 RNA expression correlated with NAPRT1 methylation around the transcription start site. These results suggest that targeting NAMPT in osteosarcoma could be considered as a novel therapeutic strategy, where low NAPRT expression can serve as a biomarker for the selection of eligible patients.

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Targeting the Oncogene eIF4E with Ribavirin: A Novel Therapeutic Avenue in Acute Myeloid Leukemia.

Blood ◽

10.1182/blood.v114.22.2085.2085 ◽

2009 ◽

Vol 114 (22) ◽

pp. 2085-2085

Author(s):

Sarit E. Assouline ◽

Eftihia Cocolakis ◽

Caroline Rousseau ◽

Biljana Culjkovic ◽

Nathalie Beslu ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Acquired Resistance ◽

Colony Growth ◽

Cytotoxic Agents ◽

Acute Myelocytic Leukemia ◽

Molecular Response ◽

Acute Myeloid ◽

Novel Therapeutic

Abstract Abstract 2085 Poster Board II-62 Over the past 10 years, the incidence of acute myeloid leukemia (AML) has increased significantly with approximately 15 000 new cases annually. Standard induction chemotherapy consisting of cytarabine (Ara-C) and an anthracycline induces remission rates between 50% and 85%. Unfortunately, the majority of patients who achieve remission will relapse and die from their disease within 2 years, highlighting the need for novel therapeutic targets. The eukaryotic translation factor (eIF4E) is overexpressed in many human malignancies, including AML, and is associated with poor prognosis as well as clinical progression. Ribavirin, an anti-viral molecule, is classically used in the treatment of hepatitis C (with interferon), SARS, RSV, Lassa fever and influenza. Its structure physically mimics the m(7)G cap of mRNA, thus inhibiting eIF4E-induced export and translation of sensitive transcripts. We are carrying out the first clinical trial targeting eIF4E with ribavirin in AML patients. Clinical and molecular efficacy has been evaluated in 13 patients to date. The treatment was well tolerated by all patients with no marked toxicity observed. Importantly, no patients developed hemolytic anemia. We demonstrated that ribavirin effectively induces the relocalization of nuclear eIF4E to the cytoplasm and the reduction of eIF4E as well as its target proteins, including suppression of Akt activation. This led to dramatic clinical improvement, including one complete remission, two partial remissions, two blast responses and four patients with stable disease. Final response data will be presented along with translational correlates. Notably, lack of response or relapse after remission was associated with lack of molecular response in leukemic blasts. Despite the encouraging responses of patient on ribavirin, all patients acquired resistance to therapy and eventually relapsed. Hence, we sought novel therapies to combine with ribavirin in order to overcome resistance and maintain remissions. Using a cell line that overexpresses eIF4E, we screened a library of 5000 known drugs and searched for compounds that synergize with ribavirin to suppress tumor growth. We identified nearly 50 lead compounds, many of which are structurally related, with similar biological activity, and are currently used medically for indications other than cancer. Early clinical observations suggest that combinations of cytotoxic agents lead to substantially better clinical outcomes relative to monotherapies. Furthermore, various drugs that suppress the PI3/Akt pathway were found to sensitize leukemia cells to Ara-C. Thus, we combined Ara-C with ribavirin in vitro, and observed an improved reduction in colony growth of AML specimens. Combination therapy with ribavirin and Ara-C in patients with acute myelocytic leukemia is currently ongoing. Preliminary results will be presented. Disclosures: Borden: Translational Therapeutics: Equity Ownership.

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277 Identification of Novel Therapeutic Targets Through an Integrated in Vitro and in Vivo Whole Genome ShRNA Screen in Glioma Stem Cells

European Journal of Cancer ◽

10.1016/s0959-8049(12)70972-3 ◽

2012 ◽

Vol 48 ◽

pp. S67-S68

Author(s):

M. Sanzey ◽

A. Golebiewska ◽

D. Stieber ◽

P. Nazarov ◽

A. Muller ◽

...

Keyword(s):

Stem Cells ◽

Therapeutic Targets ◽

Glioma Stem Cells ◽

Whole Genome ◽

Shrna Screen ◽

Novel Therapeutic

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Identification and Validation of Novel Therapeutic Targets for Multiple Myeloma

Journal of Clinical Oncology ◽

10.1200/jco.2005.05.024 ◽

2005 ◽

Vol 23 (26) ◽

pp. 6345-6350 ◽

Cited By ~ 56

Author(s):

Teru Hideshima ◽

Dharminder Chauhan ◽

Paul Richardson ◽

Kenneth C. Anderson

Keyword(s):

Multiple Myeloma ◽

Drug Resistance ◽

Tumor Cell ◽

Therapeutic Targets ◽

Novel Therapies ◽

Combination Therapies ◽

And Migration ◽

Novel Therapeutic

In vitro and in vivo models have been developed that have allowed for delineation of mechanisms of multiple myeloma (MM) cell homing to bone marrow (BM); tumor cell adhesion to extracellular matrix proteins and BM stromal cells; and cytokine-mediated growth, survival, drug resistance, and migration within the BM milieu. Delineation of the signaling cascades mediating these sequelae has identified multiple novel therapeutic targets in the tumor cell and its BM microenvironment. Importantly, novel therapies targeting the tumor cell and the BM, as well as those targeting the tumor cell or BM alone, can overcome the growth, survival, conventional drug resistance, and migration of MM cells bound to BM using both in vitro and in vivo severe combined immunodeficiency mouse models of human MM. These studies have translated rapidly from the bench to the bedside in derived clinical trials, and have already led to the United States Food and Drug Administration approval of the novel proteasome inhibitor bortezomib for treatment of relapsed/refractory MM. Novel agents will need to be combined to enhance cytotoxicity, avoid development of drug resistance, and allow for use of lower doses in combination therapies. Genomics, proteomics, and cell signaling studies have helped to identify in vivo mechanisms of sensitivity versus resistance to novel therapies, as well as aiding in the rational application of combination therapies. These studies have therefore provided the framework for a new treatment paradigm targeting the MM cell in its BM milieu to overcome drug resistance and improve patient outcome in MM.

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