SOD1 is a synthetic lethal target in PPM1D-mutant leukemia cells

The DNA damage response is critical for maintaining genome integrity and is commonly disrupted in the development of cancer. PPM1D (protein phosphatase, Mg2+/Mn2+ dependent 1D) is a master negative regulator of the response; gain-of-function mutations and amplifications of PPM1D are found across several human cancers making it a relevant pharmacologic target. Here, we used CRISPR/Cas9 screening to identify synthetic-lethal dependencies of PPM1D, uncovering superoxide dismutase-1 (SOD1) as a potential target for PPM1D-mutant cells. We revealed a dysregulated redox landscape characterized by elevated levels of reactive oxygen species and a compromised response to oxidative stress in PPM1D-mutant cells. Altogether, our results demonstrate the protective role of SOD1 against oxidative stress in PPM1D-mutant leukemia cells and highlight a new potential therapeutic strategy against PPM1D-mutant cancers.

MYC regulates CSF1 expression via microRNA 17/20a to modulate tumor-associated macrophages in osteosarcoma

Osteosarcoma (OS) is the most common primary bone tumor of childhood. Approximately 20%-30% of OSs carry amplification of chromosome 8q24, which harbors the oncogene c-MYC and correlates with a poor prognosis. To understand the mechanisms that underlie the ability of MYC to alter both the tumor and its surrounding tumor microenvironment (TME), we generated and molecularly characterized an osteoblast-specific Cre-Lox-Stop-Lox-c-MycT58A p53fl/+ knockin genetically engineered mouse model (GEMM). Phenotypically, the Myc-knockin GEMM had rapid tumor development with a high incidence of metastasis. MYC-dependent gene signatures in our murine model demonstrated significant homology to the human hyperactivated MYC OS. We established that hyperactivation of MYC led to an immune-depleted TME in OS demonstrated by the reduced number of leukocytes, particularly macrophages. MYC hyperactivation led to the downregulation of macrophage colony-stimulating factor 1, through increased microRNA 17/20a expression, causing a reduction of macrophage population in the TME of OS. Furthermore, we developed cell lines from the GEMM tumors, including a degradation tag-MYC model system, which validated our MYC-dependent findings both in vitro and in vivo. Our studies utilized innovative and clinically relevant models to identify a potentially novel molecular mechanism through which MYC regulates the profile and function of the OS immune landscape.

Functional genomic analysis of non-canonical DNA regulatory elements of the aryl hydrocarbon receptor

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that binds DNA and regulates genes in response to halogenated and polycyclic aromatic hydrocarbons. AHR also regulates the development and function of the liver and the immune system. In the canonical pathway, AHR binds a consensus DNA sequence, termed the xenobiotic response element (XRE), recruits protein coregulators, and regulates target gene expression. Emerging evidence suggests that AHR may regulate gene expression via an additional pathway, by binding to a non-consensus DNA sequence termed the non-consensus XRE (NC-XRE). The prevalence of NC-XRE motifs in the genome is not known. Studies using chromatin immunoprecipitation and reporter genes provide indirect evidence of AHR-NC-XRE interactions, but direct evidence for an AHR-NCXRE interaction that regulates transcription in a natural genomic context is lacking. Here, we analyzed AHR binding to NC-XRE DNA on a genome-wide scale in mouse liver. We integrated ChIP-seq and RNA-seq data and identified putative AHR target genes with NC-XRE motifs in regulatory regions. We also performed functional genomics at a single locus, the mouse Serpine1 gene. Deleting NC-XRE motifs from the Serpine1 promoter reduced the upregulation of Serpine1 by TCDD, an AHR ligand. We conclude that AHR upregulates Serpine1 via NC-XRE DNA. NC-XRE motifs are prevalent throughout regions of the genome where AHR binds. Taken together, our results suggest that AHR regulates genes via NC-XRE motifs. Our results will also improve our ability to identify AHR target genes and their physiologic relevance.

Modeling Ewing Sarcoma Lung Metastasis

Ewing Sarcoma (EwS) is the second most common malignant bone tumor in adolescents and young adults. The single-most powerful predictor of outcome in EwS is presence of metastatic burden at the time of diagnosis. Patients with metastatic Ewing Sarcoma have an abysmal 5-year survival rate of 10%-25%, which has not changed over the past 30-40 years. Thus, unraveling underlying mechanisms of EwS metastasis are imperative for developing effective therapeutic measures. Investigations towards this goal are limited by the lack of reliable genetically engineered mouse models and specialized metastatic models. Using two established cell lines, A673 and TC71, we generated lung specific metastatic cell lines by serial orthotopic intra-tibial injection followed by isolation of cells from lung metastases. The lung metastatic lines generated exhibit distinct differential molecular signatures from the parental cells when analyzed using a multi-omics approach. These signatures overlapped with EwS patient primary bone and metastatic lung specimens supporting the clinical relevance of these preclinical models of EwS. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Intra-Tibial injection in NSG mice Basic Protocol 2: Development and characterization of lung metastatic cell line.

MYCN-driven fatty acid uptake is a metabolic vulnerability in neuroblastoma

Neuroblastoma (NB) is a childhood cancer arising from sympatho-adrenal neural crest cells. MYCN amplification is found in half of high-risk NB patients; however, no available therapies directly target MYCN. Using multi-dimensional metabolic profiling in MYCN expression systems and primary patient tumors, we comprehensively characterized the metabolic landscape driven by MYCN in NB. MYCN amplification leads to glycerolipid accumulation by promoting fatty acid (FA) uptake and biosynthesis. We found that cells expressing amplified MYCN depend highly on FA uptake for survival. Mechanistically, MYCN directly upregulates FA transport protein 2 (FATP2), encoded by SLC27A2. Genetic depletion of SLC27A2 impairs NB survival, and pharmacological SLC27A2 inhibition selectively suppresses tumor growth, prolongs animal survival, and exerts synergistic anti-tumor effects when combined with conventional chemotherapies in multiple preclinical NB models. This study identifies FA uptake as a critical metabolic dependency for MYCN-amplified tumors. Inhibiting FA uptake is an effective approach for improving current treatment regimens.

Abstract 6047: Identification of a 13 gene signature to predict survival in localized osteosarcoma

Osteosarcoma (OS) is the most prevalent bone tumor in pediatric patients. Regimens of neoadjuvant chemotherapy have improved survival of OS patients greatly, however the 5-year survival rate for localized OS is 75% with a 30-50% recurrence rate. We sought to identify genes which could predict chemo-response and survival in localized OS. The TARGET OS RNA-seq dataset was utilized to identify genes and pathways associated with localized patient relapse and survival. We identified 478 differentially expressed genes with a 1.5 FC and FDR < 0.05 common to overall survival and relapse We further performed string analysis to generate a protein-protein interaction network followed by hub analysis with Cytohubba using betweenness centrality and radiality measures. Combining the top 10 hub genes from these two methods resulted in a total of 13 genes: MYOM2, VEGFA, VCAM1, EGFR, MUC1, IHH, GLI1, GPC3, IGF2, GRIA1, GNG12, GNGT1 and C3. These 13 genes were used to stratify localized patients in the TARGET dataset into high-risk and low-risk tertiles. The low-risk group had 100% overall survival while the high-risk group had 44% 5-year survival (p=2e-4). We also found a significant correlation between the 13 genes and time to death in localized patients (p=0.04). Additionally, there was a significant difference in expression of the 13 genes between alive and deceased patients (p=2e-5) and patients who relapsed (p=1.5e-4). Overall, these data suggest that these 13 genes could predict relapse and overall survival in OS patients with localized disease in the TARGET cohort. We performed Weighted Gene Correlation Network Analysis (WGCNA) on the 478 overlapping genes and identified five modules, with our 13 genes split across these modules. All modules were also significantly correlated with vital status suggesting that the genes in our signature represent distinct sub-groups with possibly separate mechanisms. Over-representation analysis was performed for each module and while each module did have distinct pathways, there were 65 pathways which overlapped between 3 of the modules. Of particular interest was Hedgehog signaling, with 2 of our 13 genes, IHH and GLI1, key to Hedgehog signaling, and a Hedgehog pathway inhibitor, Gant-58, scored high in reversing the 478 gene signature as determined using Connectivity Map (Broad Institute). We tested Gant-58 against two PDX OS models. Gant-58 did not inhibit a non-relapsed, chemo sensitive localized PDX-derived cell line, but showed potent activity towards a recurrent localized PDX with elevated IHH and GLI1 expression (p<0.0001). In summary, we identified 13 genes that predict overall survival and relapse in localized OS patients. The 13 genes represent distinct modules of co-expressing genes that significantly correlate with survival. Furthermore, preliminary data indicate Hedgehog pathway has a key role in survival and recurrence of localized OS patients.

Citation Format: Tajhal D. Patel, Kshiti Dholakia, Tanmay R. Gandhi, Rupa S. Kanchi, Sandra L. Grimm, Chenlian Fu, Jason T. Yustein, Cristian Coarfa. Identification of a 13 gene signature to predict survival in localized osteosarcoma [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 6047.

Integrative metabolomics and transcriptomics analysis reveals novel therapeutic vulnerabilities in lung cancer

BACKGROUND

Non-small cell lung cancer (NSCLC) comprises the majority (~85%) of all lung tumors, with lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) being the most frequently diagnosed histological subtypes. Multi-modal omics profiling has been carried out in NSCLC, but no studies have yet reported a unique metabolite-related gene signature and altered metabolic pathways associated with LUAD and LUSC.

METHODS

We integrated transcriptomics and metabolomics to analyze 30 human lung tumors and adjacent noncancerous tissues. Differential co-expression was used to identify modules of metabolites that were altered between normal and tumor.

RESULTS

We identified unique metabolite-related gene signatures specific for LUAD and LUSC and key pathways aberrantly regulated at both transcriptional and metabolic levels. Differential co-expression analysis revealed that loss of coherence between metabolites in tumors is a major characteristic in both LUAD and LUSC. We identified one metabolic onco-module gained in LUAD, characterized by nine metabolites and 57 metabolic genes. Multi-omics integrative analysis revealed a 28 metabolic gene signature associated with poor survival in LUAD, with six metabolite-related genes as individual prognostic markers.

CONCLUSIONS

We demonstrated the clinical utility of this integrated metabolic gene signature in LUAD by using it to guide repurposing of AZD-6482, a PI3Kβ inhibitor which significantly inhibited three genes from the 28-gene signature. Overall, we have integrated metabolomics and transcriptomics analyses to show that LUAD and LUSC have distinct profiles, inferred gene signatures with prognostic value for patient survival, and identified therapeutic targets and repurposed drugs for potential use in NSCLC treatment.

K-Ras and p53 mouse model with molecular characteristics of human rhabdomyosarcoma and translational applications

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, with overall long-term survival rates of ∼65-70%. Thus, additional molecular insights and representative models are critical for identifying and evaluating new treatment modalities. Using MyoD-Cre-mediated introduction of mutant K-RasG12D and perturbations in p53, we developed a novel genetically engineered mouse model (GEMM) for RMS. The anatomic sites of primary RMS development recapitulated human disease, including tumors in the head, neck, extremities and abdomen. We confirmed RMS histology and diagnosis through Hematoxylin and Eosin staining, and positive immunohistochemical staining for desmin, myogenin, and phosphotungstic acid-Hematoxylin. Cell lines from GEMM tumors were established with the ability to engraft in immunocompetent mice with comparable histological and staining features as the primary tumors. Tail vein injection of cell lines had high metastatic potential to the lungs. Transcriptomic analyses of p53R172H/K-RasG12D GEMM-derived tumors showed evidence of high molecular homology with human RMS. Finally, pre-clinical use of these murine RMS lines showed similar therapeutic responsiveness to chemotherapy and targeted therapies as human RMS cell lines.

Development of sensory neurons in the absence of NGF/TrkA signaling in vivo

The neurotrophin survival dependence of peripheral neurons in vitro is regulated by the proapoptotic BCL-2 homolog BAX. To study peripheral neuron development in the absence of neurotrophin signaling, we have generated mice that are double null for BAX and nerve growth factor (NGF), and BAX and the NGF receptor TrkA. All dorsal root ganglion (DRG) neurons that normally die in the absence of NGF/TrkA signaling survive if BAX is also eliminated. These neurons extend axons through the dorsal roots and collateral branches into the dorsal horn. In contrast, superficial cutaneous innervation is absent. Furthermore, rescued sensory neurons fail to express biochemical markers characteristic of the nociceptive phenotype. These findings establish that NGF/TrkA signaling regulates peripheral target field innervation and is required for the full phenotypic differentiation of sensory neurons.

Production and characterization of an anti-serotonin 1A receptor antibody which detects functional 5-HT1A binding sites

We describe the production and characterization of a specific anti-5-HT1A receptor antibody made against a fusion protein consisting of glutathione-S-transferase (GST) coupled to a 75-amino acid sequence from the middle portion of the third intracellular loop (5-HT1A-m3i, serine253-arginine327) of the rat 5-HT1A receptor protein. This region was chosen to avoid putative phosphorylation and glycosylation sites and regions of known homology with other 5-HT receptors. Western blot analysis indicated that the polyclonal anti-5-HT1A-m3i antibody accurately recognized the fusion protein expressed in bacteria and labeled a prominent 67 kDa protein band in the hippocampus, cortex, brainstem, cerebellum and kidney with a density profile corresponding to the relative abundance of the 5-HT1A receptor in these tissues. No protein was detected in liver or muscle tissue preparations, and no protein bands were labeled in any of the above tissues following preabsorption of the antibody with the 5-HT1A-m3i fusion protein. Immunohistochemistry revealed prominent labeling in limbic structures including the hippocampus, amygdala, entorhinal cortex, and septum as well as in raphe nuclei. In the hippocampus, 5-HT1A-m3i labeling revealed a characteristic laminar pattern that coincided with that seen by autoradiographic binding of the 5-HT1A agonist [3H]-8-OH-DPAT in all strata of the hippocampal formation. In the dorsal and medial raphe nuclei, anti-5-HT1A-m3i antibodies labeled the somatodendritic membranes of 5-HT neurons, consistent with its role as an autoreceptor. The detailed matching of the anti-5-HT1A-m3i antibody with [3H]-8-OH-DPAT binding suggests that the antibody recognizes a functionally active form of the 5-HT1A receptor protein capable of binding 5-HT1A agonist ligands. These anti-5-HT1A antibodies may therefore be useful tools in localizing functional 5-HT1A receptors in specific regions of the brain as well as in studying the plasticity and ontogeny of the 5-HT1A receptor at the cellular and subcellular level.

Additive reduction of alcohol drinking by 5-HT1A antagonist WAY 100635 and serotonin uptake blocker fluoxetine in alcohol-preferring P rats

We found previously that alcohol-preferring (P) rats have fewer serotonin (5-HT) neurons and fibers in key brain regions than alcohol-nonpreferring (NP) rats. Because 5-HT uptake blockers increase synaptic 5-HT content and 5-HT1A receptor antagonists increase 5-HT release by disinhibiting 5-HT autoinnervation, in the present study, our intent was to determine whether increased synaptic 5-HT content and/or 5-HT release in P rats would effectively reduce alcohol consumption. In experiment 1, the 5-HT antagonist WAY 100635 (WAY) was tested on adult female P rats maintained on 24-hr free-choice access to ethanol (10% v/v) and water. Twice daily doses of WAY (0.05, 0.1, 0.5, and 1.0 mg/kg, subcutaneously) were administered to each rat in a counterbalanced order. Baseline ethanol intake, derived from the mean ethanol intakes of the three previous non-drug days, was approximately 8 g/kg/day. Results indicated that 0.05, 0.1, and 0.5 mg/kg doses of WAY reduced 24-hr ethanol drinking by 25-30% (p < 0.01) without affecting 24-hr water intake or body weight. In the second experiment, the effects of WAY (0.5 mg/kg), fluoxetine (1.0 mg/kg), or a combination of both were tested in another group of female P rats. WAY and fluoxetine, each alone, reduced ethanol drinking by around 20% and, when combined, decreased ethanol intake by 50%, whereas the body weight and the total fluid intake were not significantly affected. Taken together, these results indicate that both fluoxetine and WAY preferentially reduce ethanol drinking in the P line of rats and, when administered together, reduce ethanol intake in an additive manner. It is proposed that coadministration of these two compounds with distinct mechanisms of action may be a new strategy for reducing alcohol intake.

Genetic mapping of 20 novel expressed sequence tags from midgestation mouse embryos suggests chromosomal clustering

Current knowledge of genes that regulate pattern formation and differentiation processes during mammalian embryonic development is limited. In an effort to isolate developmentally relevant genes, 20 novel, end-sequenced cDNAs selected from a Day 10.5 postcoitum mouse embryo library were genetically mapped in intersubspecific backcross mice. Eleven of 20 cDNA clones mapped to three mouse autosomes (Chr 5, 11, and 14), a result that was unlikely (P < 0.03) if the distribution of genes expressed in embryos is random within the mouse genome. Several clones were candidates for mouse developmental mutations by virtue of genetic colocalization and concordance of embryonic expression patterns with the distribution of defects in mutant mice: Estm11 was a candidate for the mouse mutation wabbler-lethal (wl), since Estm11 mapped in the vicinity of wl on mouse Chr 14 and was expressed in those regions of embryonic brain that exhibit axonal degeneration in wl. End-sequence analysis, genetic mapping, and in situ hybridization appeared to be an effective combination of methods for identification and characterization of genes with potential regulatory functions during mammalian embryogenesis.

Increased 5-HT1A receptor immunoreactivity in the rat hippocampus following 5,7-dihydroxytryptamine lesions in the cingulum bundle and fimbria-fornix

Serotonin (5-HT) projections from the ascending raphe nuclei reach the dorsal hippocampus via the cingulum bundle (CB) and fimbria-fornix (FF). Microinjection of the serotonergic neurotoxin 5,7-dihydroxytryptamine (5,7-DHT) into the CB and FF produces a significant decrease in the density of 5-HT immunoreactive fibers in the hippocampus as early as 3 days postlesion (Zhou, F.C. and Azmitia, E.C. (1983) Brain Res. Bull., 373, 337-348). In the present study we used an anti-peptide antibody against the second extracellular loop of the 5-HT1A receptor and employed immunocytochemistry to examine changes in the expression and distribution of the 5-HT1A receptor in the hippocampus 14 days following administration of 5,7-DHT into the CB and FF. The density of 5-HT immunoreactive fibers was greatly reduced 14 days following the lesions. 5-HT1A immunoreactivity (IR) was localized to the proximal axon near the axon hillock of cells in the pyramidal cell layer of the cornu Ammonus and in the granule cell layer of the dentate gyrus. The intensity of 5-HT1A-IR was increased in the CA1 and dentate gyrus following 5,7-DHT lesions. Intensity in the CA3 also increased but not to a significant level. These findings demonstrate that 5-HT denervation in the hippocampus is followed by increased expression of the 5-HT1A receptor protein. These changes in receptor expression 14 days postlesion may represent adaptive changes by postsynaptic cells following reduced 5-HT innervation and may be the molecular basis for 5-HT1A receptor supersensitivity.