Dual targeting of the epigenome via FACT complex and histone deacetylase is a potent treatment strategy for DIPG

Diffuse intrinsic pontine glioma (DIPG) is an aggressive and incurable childhood brain tumor for which new treatments are needed. CBL0137 is an anti-cancer compound developed from quinacrine that targets facilitates chromatin transcription (FACT), a chromatin remodeling complex involved in transcription, replication, and DNA repair. We show that CBL0137 displays profound cytotoxic activity against a panel of patient-derived DIPG cultures by restoring tumor suppressor TP53 and Rb activity. Moreover, in an orthotopic model of DIPG, treatment with CBL0137 significantly extends animal survival. The FACT subunit SPT16 is found to directly interact with H3.3K27M, and treatment with CBL0137 restores both histone H3 acetylation and trimethylation. Combined treatment of CBL0137 with the histone deacetylase inhibitor panobinostat leads to inhibition of the Rb/E2F1 pathway and induction of apoptosis. The combination of CBL0137 and panobinostat significantly prolongs the survival of mice bearing DIPG orthografts, suggesting a potential treatment strategy for DIPG.

DIPG-27. TARGETING FACILITATES CHROMATIN TRANSCRIPTION (FACT) AS A NOVEL STRATEGY FOR DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG) THAT ENHANCES RESPONSE TO HISTONE DEACETYLASE (HDAC) INHIBITION

Diffuse intrinsic pontine glioma (DIPG) is an aggressive and incurable childhood brain tumour for which new treatments are needed. A high throughput drug screen of 3500 pharmaceutical compounds identified anti-malarials, including quinacrine as having potent activity against DIPG neurospheres. CBL0137, a compound modelled on quinacrine, is an anti-cancer compound which targets Facilitates Chromatin Transcription (FACT), a chromatin remodelling complex involved in transcription, replication, and DNA repair. CBL0137 effectively crosses the blood-brain barrier and is currently in Phase I trials in adult cancer. CBL0137 induced apoptosis in DIPG neurospheres in vitro and had profound cytotoxic activity against a panel of DIPG cultures. In a DIPG orthotopic model, treatment with CBL0137 significantly improved survival. We found that treatment with CBL0137 up-regulated TP53 and increased histone H3.3 acetylation and tri-methylation in DIPG cells. We therefore examined the interaction between CBL0137 and the HDAC inhibitor, panobinostat. In vitro experiments showed that the two agents had profound synergistic activity against DIPG neurospheres in clonogenic assays and enhanced apoptosis. Transcriptomic analysis and immunoblotting indicated that combination treatment activated signalling pathways controlled by Retinoblastoma (RB)/E2F1 and subsequently increased phosphorylation and enzymatic activity of enhancer of zeste homolog 2 (EZH2). Consistent with the in vitro results, the combination of CBL0137 and panobinostat significantly prolonged the survival of two orthotopic models of DIPG, while histological analysis showed increased H3K27me3 and decreased Ki67 positive cells. Given these promising results, a paediatric trial of CBL0137 is planned to open through the Children’s Oncology Group with an expansion cohort for DIPG patients.

A simple, accurate and universal method for quantification of PCR

Background

Research into gene expression enables scientists to decipher the complex regulatory networks that control fundamental biological processes. Quantitative real-time PCR (qPCR) is a powerful and ubiquitous method for interrogation of gene expression. Accurate quantification is essential for correct interpretation of qPCR data. However, conventional relative and absolute quantification methodologies often give erroneous results or are laborious to perform.

To overcome these failings, we developed an accurate, simple to use, universal calibrator, AccuCal.

Results

Herein, we show that AccuCal quantification can be used with either dye- or probe-based detection methods and is accurate over a dynamic range of ≥10⁵ copies, for amplicons up to 500 base pairs (bp). By providing absolute quantification of all genes of interest, AccuCal exposes, and circumvents, the well-known biases of qPCR, thus allowing objective experimental conclusions to be drawn.

Conclusion

We propose that AccuCal supersedes the traditional quantification methods of PCR.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0256-y) contains supplementary material, which is available to authorized users.

Expression of doublecortin (DCX) and doublecortin-like kinase (DCLK) within the developing chick brain

Doublecortin (DCX) is a microtubule-associated protein widely expressed in the developing mammalian nervous system and important for neuronal migration. DCX is known to belong to a novel protein family defined by sequence homology and the presence of a conserved microtubule-binding domain, but the functions of other members of this family are still undefined. In this study, we describe the cloning of the chick ortholog of doublecortin-like kinase (DCLK), a member of this family, and assess the expression of DCX and DCLK in the layered regions of the developing chick brain. DCX and DCLK are widely expressed in pallial and subpallial structures, including the telencephalon, optic tectum, and cerebellum, in similar distribution patterns. In addition to their expression in migrating cells, both proteins were also detected in the ventricular zone and in postmigratory Purkinje cells. Finally, DCX and DCLK were found to be coexpressed in all areas examined. In postmigratory Purkinje cells, DCX and DCLK both colocalized to the cell membrane, although DCLK was also distributed more generally throughout the cell soma. These data are consistent with multiple roles for DCX and DCLK in the developing chicken brain and suggest that the chick cerebellum will be an intriguing system to explore the effects of DCX and DCLK on postmigratory neuronal function.

Avian Purkinje neuronal cultures: extrinsic control of morphology by cell type and glutamate

An in vitro coculture system is described to study the avian Purkinje neuron and the interactions occurring with astrocytes and granule cells during development in the cerebellum. Astrocytes initially and granule cells later regulate Purkinje neuron morphology. The coculture system presented here provides an excellent system for investigating the morphological, immunocytochemical, and electrophysiological differentiation of Purkinje neurons under controlled conditions and for studying cell-cell interactions and extrinsic factors, e.g., glutamate in normal and neuropathological conditions.

CROC-4: a novel brain specific transcriptional activator of c-fos expressed from proliferation through to maturation of multiple neuronal cell types

A novel, brain-specific cDNA, denoted CROC-4, was cloned from human brain by a contingent replication of cDNA procedure capable of detecting transcriptional activators of the human c-fos proto-oncogene promoter. CROC-4 encoded an 18-kDa serine/threonine-rich polypeptide containing a P-loop motif and an SH3-binding region with phosphorylation sites for a variety of protein kinases (cdc2, CDK2, MAPK, CDK5, protein kinase C, Ca(2+)/calmodulin protein kinase 2, casein kinase 2) involved in cell proliferation and differentiation. Immunohistochemistry revealed that during early development, expression was associated with proliferating and migrating cells throughout the rodent brain, initially appearing in the proliferative ventricular zones. During late development and in adult human brain, CROC-4 was expressed in diverse brain regions including the thalamus, subthalamic nucleus, corpus callosum, substantia nigra, caudate nucleus, amygdala, and hippocampus. The association of CROC-4 expression with proliferating regions of developing brain and retention in regions of the adult brain, as well as the punctate nuclear location, suggest that CROC-4 participates in brain-specific c-fos signaling pathways involved in cellular remodeling of brain architecture.

Epigenetic factors controlling the development of avian Purkinje neurons

Using a unique protocol, we have developed an avian neuron culture system in which a high yield of Purkinje neurons is obtained more readily than with pre-existing methods. Purkinje neurons were identified in vitro using the specific antibodies calbindin and cyclic GMP-kinase. Survival of Purkinje neurons was dependent on astrocyte contact and enhanced by astrocytic factors supplied to the medium by a monolayer of astrocytes grown on coated membranes suspended in the culture wells but not in contact with the neurons. The age of the cerebellum from which astrocytes were obtained was shown to affect the morphological development of the Purkinje neurons suggesting the developmentally-regulated expression of growth factors. However, in the presence of the astrocytes, Purkinje neurons could only progress to a limited stage of development based on morphological criteria. The addition to the culture of cerebellar granule neurons at a time of Purkinje neuron development that they would expect to encounter them in vivo resulted in a shift of Purkinje neurons to a mature phenotype. This maturation effect was increased in response to increasing levels of granule neurons, but was independent of the granule neuron ages used. This system offers significant advantages over other Purkinje neuron culture systems and will be useful for studying the extrinsic factors involved in Purkinje neuron development and histogenesis.

Induction of neuron-specific tropomyosin mRNAs by nerve growth factor is dependent on morphological differentiation

We have examined the expression of brain-specific tropomyosins during neuronal differentiation. Both TmBr-1 and TmBr-3 were shown to be neuron specific. TmBr-1 and TmBr-3 mRNA levels increased during the most active phase of neurite outgrowth in the developing rat cerebellum. In PC12 cells stimulated by nerve growth factor (NGF) to differentiate to the neuronal phenotype, TmBr-1 and TmBr-3 levels increased with an increasing degree of morphological differentiation. Induction of TmBr-1 and TmBr-3 expression only occurred under conditions where PC12 cells were permitted to extend neurites. NGF was unable to maintain levels of TmBr-1 and TmBr-3 with the loss of neuronal phenotype by resuspension of differentiated PC12 cells. The unique cellular expression and regulation in vivo and in vitro of TmBr-1 and TmBr-3 strongly suggests a critical role of these tropomyosins in neuronal microfilament function. The findings reveal that the induction and maintenance of the neuronal tropomyosins is dependent on morphological differentiation and the maintenance of the neuronal phenotype.

Expression of actin and myosin genes during PC12 cell differentiation

We have measured the accumulation of transcripts for myosin and actin during NGF induced differentiation of PC12 cells. Beta (beta) and gamma (gamma) actin and myosin light chains (MLC) 2 and 3 show different patterns of expression, with transient elevations in gene expression one day after NGF addition. This elevation occurs earlier than that of neurite outgrowth, neurofilament protein (NF68) (16) and Thy-1 glycoprotein gene expression. These results suggest differing mechanisms of control of actin and myosin expression, together with a varying function and relationship between them during NGF-induced neurite differentiation.