Time series modeling of cell cycle exit identifies Brd4 dependent regulation of cerebellar neurogenesis

Cerebellar neuronal progenitors undergo a series of divisions before irreversibly exiting the cell cycle and differentiating into neurons. Dysfunction of this process underlies many neurological diseases including ataxia and the most common pediatric brain tumor, medulloblastoma. To better define the pathways controlling the most abundant neuronal cells in the mammalian cerebellum, cerebellar granule cell progenitors (GCPs), we performed RNA-sequencing of GCPs exiting the cell cycle. Time-series modeling of GCP cell cycle exit identified downregulation of activity of the epigenetic reader protein Brd4. Brd4 binding to the Gli1 locus is controlled by Casein Kinase 1δ (CK1 δ)-dependent phosphorylation during GCP proliferation, and decreases during GCP cell cycle exit. Importantly, conditional deletion of Brd4 in vivo in the developing cerebellum induces cerebellar morphological deficits and ataxia. These studies define an essential role for Brd4 in cerebellar granule cell neurogenesis and are critical for designing clinical trials utilizing Brd4 inhibitors in neurological indications

Drug and disease signature integration identifies synergistic combinations in glioblastoma

Dataset for the paper "Drug and disease signature integration identifies synergistic combinations in glioblastoma

CB-14 * GENOMIC APPROACHES TO IDENTIFY CODING AND NONCODING RNA TARGETS IN MEDULLOBLASTOMA

Medulloblastoma is the most common malignant pediatric brain tumor. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from this disease. Medulloblastoma includes four groups (SHH, WNT, Group 3 and Group 4), which show differences in karyotype, histology, and prognosis. Since some of these tumors originate from granule cell progenitors (GCPs) of the cerebellum a better understanding of the mechanisms controlling progenitor cycle exit and differentiation could unravel new promising targets for medulloblastoma. To gain insight into the mechanisms controlling GCP proliferation and differentiation, we performed RNA sequencing of GCPs at different stages of differentiation. These cells originate in the external germinal layer (EGL) of the cerebellum, undergo predominantly symmetric divisions during early postnatal EGL development, and exit the cell cycle within a narrow time frame. We studied GCP cell cycle exit and obtained several differentially expressed lncRNAs governing neuronal differentiation. We demonstrate that some of these lncRNAs are involved in GCP cell cycle exit and are potentially dysregulated in mouse models of medulloblastoma. Further, we demonstrate that the Anaphase Promoting Complex/cyclosome (APC/C) is also potentially dysregulated in medulloblastoma, thus leading to uncontrolled cell proliferation via lncRNA expression. These studies underscore a previously unappreciated role for APC/C in controlling epigenetic pathways in medulloblastoma

GE-32 * AN INTERGRADED BIOINFORMATICS APPROACH FOR IDENTIFYING NOVEL GENE NETWORKS IN GLIOBLASTOMA

Glioblastoma (GBM) is the most common and aggressive malignant brain tumor. Despite treatment advances, the median survival time is still below 2 years since recurrence is nearly universal. Therefore, the discovery of novel and specific molecular targets is needed. However, the identification of such targets is difficult given the high degree of variability among patient samples and individual sequencing analysis is needed for patient specific therapies. Identifying differentially expressed (DE) genes based on small sample sizes is yet another challenge since there is high variability among the different analysis algorithms. To circumvent this problem, we implemented a bioinformatics pipeline, which utilizes the large number of samples in TCGA as a reference to identify DE genes in an individual patient's tumor. By using this algorithm, we produced enriched single patient RNAseq DE gene lists and subsequently calculated a hypergeometric probability and correlation coefficient for every gene pair on these lists. Furthermore, by using the most significant of these pairs, we generated gene association networks. Importantly, our networks were validated utilizing protein-protein interaction studies and therefore could be used to identify patient specific combination therapies for GBM

EG-04 * DEVELOPMENT OF HIGHLY POTENT, SELECTIVE BET BROMODOMAIN INHIBITORS THAT ARE CNS PENETRANT AND EFFECTIVE IN RODENT MODELS OF BRAIN CANCER

BRD2, BRD3, and BRD4 are members of the BET family of bromodomain inhibitors that have received intense current interest as novel treatments for cancer. The BET proteins function as epigenetic modulators that recognize specifically marked regions of histones and thereby influence gene transcription. Numerous highly potent, highly selective BET inhibitors have emerged and some (e.g. IBET-762) have advanced to clinical trials. We aimed to develop BET inhibitors as drug for untreatable forms of brain cancer including GBM (glioblastoma multiforme) and metastatic brain cancer. Unfortunately, we found that they are poorly suited as drugs for any indications that require high CNS drug exposure because they have high susceptibility to efflux transporters and low passive cellular permeability. To improve CNS penetration, we employed a structure-based design approach that involved (1) disrupting key transporter pharmacophore points and (2) altering the physical properties to improve cellular permeability. In this manner we have identified EP11313 which has strong potency (BRD4 IC(50) 7 nM), low efflux (ER <2), high passive cellular permeability (Papp 13.3 × 10(−6) cm/s), moderate oral bioavailability in mouse (59%) and high CNS exposure. EP11313 (after daily drug administration for 3 weeks) shows antiproliferative effects in TMZ-resistant cancer patient stem cell lines and dose-dependent tumor reduction in nu/nu mice that were centrally transplanted with luciferase-expressing GBM cell xenografts

Time series modeling of cell cycle exit identifies Brd4 dependent regulation of cerebellar neurogenesis

Cerebellar neuronal progenitors undergo a series of divisions before irreversibly exiting the cell cycle and differentiating into neurons. Dysfunction of this process underlies many neurological diseases including ataxia and the most common pediatric brain tumor, medulloblastoma. To better define the pathways controlling the most abundant neuronal cells in the mammalian cerebellum, cerebellar granule cell progenitors (GCPs), we performed RNA-sequencing of GCPs exiting the cell cycle. Time-series modeling of GCP cell cycle exit identified downregulation of activity of the epigenetic reader protein Brd4. Brd4 binding to the Gli1 locus is controlled by Casein Kinase 1δ (CK1 δ)-dependent phosphorylation during GCP proliferation, and decreases during GCP cell cycle exit. Importantly, conditional deletion of Brd4 in vivo in the developing cerebellum induces cerebellar morphological deficits and ataxia. These studies define an essential role for Brd4 in cerebellar granule cell neurogenesis and are critical for designing clinical trials utilizing Brd4 inhibitors in neurological indications

A proteogenomic portrait of lung squamous cell carcinoma

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC