Recapitulation of tumor heterogeneity and molecular signatures in a 3D brain cancer model with decreased sensitivity to histone deacetylase inhibition

INTRODUCTION Physiologically relevant pre-clinical ex vivo models recapitulating CNS tumor micro-environmental complexity will aid development of biologically-targeted agents. We present comprehensive characterization of tumor aggregates generated using the 3D Rotary Cell Culture System (RCCS). METHODS CNS cancer cell lines were grown in conventional 2D cultures and the RCCS and comparison with a cohort of 53 pediatric high grade gliomas conducted by genome wide gene expression and microRNA arrays, coupled with immunohistochemistry, ex vivo magnetic resonance spectroscopy and drug sensitivity evaluation using the histone deacetylase inhibitor, Vorinostat. RESULTS Macroscopic RCCS aggregates recapitulated the heterogeneous morphology of brain tumors with a distinct proliferating rim, necrotic core and oxygen tension gradient. Gene expression and microRNA analyses revealed significant differences with 3D expression intermediate to 2D cultures and primary brain tumors. Metabolic profiling revealed differential profiles, with an increase in tumor specific metabolites in 3D. To evaluate the potential of the RCCS as a drug testing tool, we determined the efficacy of Vorinostat against aggregates of U87 and KNS42 glioblastoma cells. Both lines demonstrated markedly reduced sensitivity when assaying in 3D culture conditions compared to classical 2D drug screen approaches. CONCLUSIONS Our comprehensive characterization demonstrates that 3D RCCS culture of high grade brain tumor cells has profound effects on the genetic, epigenetic and metabolic profiles of cultured cells, with these cells residing as an intermediate phenotype between that of 2D cultures and primary tumors. There is a discrepancy between 2D culture and tumor molecular profiles, and RCCS partially re-capitulates tissue specific features, allowing drug testing in a more relevant ex vivo system

TSUGI : a framework for building PHP-based learning tools

Innovation on ICT-based learning depends on the ability of researchers, developers and services (and content) providers to push new kinds of tools and services in real life contexts. This implies that new developments need to be interoperable with the current LMS that are running almost everywhere. Thus, either new developments have to be custom built for every LMS or there is a real need for an interoperability standard Over the last 8 years IMS Global Learning Consortium has pushed the IMS Learning tools interoperability as the missing standard. IMS LTI has been developed in collaboration with the major LMS and tools authors in a long process where reference implementations and automated compliance tests have been created, and IMS LTI is supported for all the major commercial and open source LMS. But despite the collaborative open process there are different versions of the standard (Simple LTI, Basic LTI, LTI 1.0, LTI 1.1 and soon LTI 2.0) and there are subtle differences in the implementation of LTI provided by each LMS, which defeats the whole purpose of having an interoperability standard. For this reason the TSUGI project has been created: to provide a framework that makes as simple as possible to develop and deploy LTI applications.Peer ReviewedPostprint (published version

TSUGI : a framework for building PHP-based learning tools

Innovation on ICT-based learning depends on the ability of researchers, developers and services (and content) providers to push new kinds of tools and services in real life contexts. This implies that new developments need to be interoperable with the current LMS that are running almost everywhere. Thus, either new developments have to be custom built for every LMS or there is a real need for an interoperability standard Over the last 8 years IMS Global Learning Consortium has pushed the IMS Learning tools interoperability as the missing standard. IMS LTI has been developed in collaboration with the major LMS and tools authors in a long process where reference implementations and automated compliance tests have been created, and IMS LTI is supported for all the major commercial and open source LMS. But despite the collaborative open process there are different versions of the standard (Simple LTI, Basic LTI, LTI 1.0, LTI 1.1 and soon LTI 2.0) and there are subtle differences in the implementation of LTI provided by each LMS, which defeats the whole purpose of having an interoperability standard. For this reason the TSUGI project has been created: to provide a framework that makes as simple as possible to develop and deploy LTI applications.Peer Reviewe

The medical necessity of advanced molecular testing in the diagnosis and treatment of brain tumor patients

Accurate pathologic diagnoses and molecularly informed treatment decisions for a wide variety of cancers depend on robust clinical molecular testing that uses genomic, epigenomic, and transcriptomic-based tools. Nowhere is this more essential than in the workup of brain tumors, as emphasized by the incorporation of molecular criteria into the 2016 World Health Organization classification of central nervous system tumors and the updated official guidelines of the National Comprehensive Cancer Network. Despite the medical necessity of molecular testing in brain tumors, access to and utilization of molecular diagnostics is still highly variable across institutions, and a lack of reimbursement for such testing remains a significant obstacle. The objectives of this review are (i) to identify barriers to adoption of molecular testing in brain tumors, (ii) to describe the current molecular tools recommended for the clinical evaluation of brain tumors, and (iii) to summarize how molecular data are interpreted to guide clinical care, so as to improve understanding and justification for their coverage in the routine workup of adult and pediatric brain tumor cases