CRISPR and transposon in vivo screens for cancer drivers and therapeutic targets

Funder: Wellcome Trust; doi: http://dx.doi.org/10.13039/100004440Funder: National Institute for Health Research; doi: http://dx.doi.org/10.13039/501100000272Funder: prostate cancer research councilAbstract: Human cancers harbor substantial genetic, epigenetic, and transcriptional changes, only some of which drive oncogenesis at certain times during cancer evolution. Identifying the cancer-driver alterations amongst the vast swathes of “passenger” changes still remains a major challenge. Transposon and CRISPR screens in vivo provide complementary methods for achieving this, and each platform has its own advantages. Here, we review recent major technological breakthroughs made with these two approaches and highlight future directions. We discuss how each genetic screening platform can provide unique insight into cancer evolution, including intra-tumoral heterogeneity, metastasis, and immune evasion, presenting transformative opportunities for targeted therapeutic intervention

Comparison of first-time microvascular decompression with percutaneous surgery for trigeminal neuralgia: long-term outcomes and prognostic factors.

OBJECTIVE: Common surgical treatments for trigeminal neuralgia (TN) include microvascular decompression (MVD) and percutaneous procedures (glycerol rhizolysis; thermocoagulation; and balloon compression). Although the efficacy of each procedure has been documented, direct comparisons of their relative efficacies for TN are lacking. We aimed to directly compare long-term outcomes after first-time MVD with percutaneous surgery in primary (idiopathic and classical) TN and identify predictors of outcome. METHODS: We conducted a retrospective analysis of prospectively collected data on 185 patients undergoing MVD and 129 undergoing percutaneous surgery. Procedures were performed by one of two neurosurgeons in a single centre; an independent observer collected long-term follow-up data by interviews, using the same outcome measures for all procedures. RESULTS: MVD patients were younger than those undergoing percutaneous surgery (P <.001). MVD provided superior initial pain relief (P <.001): 87.0% had Barrow Neurological Institute class I or II pain scores after MVD compared with 67.2% after percutaneous surgery. The complication rate for percutaneous procedures was 35.7% and for MVDs was 24.9% (P =.04), including minor and transient complications. Kaplan-Meier analysis demonstrated that MVD provided longer pain relief than percutaneous procedures (P <.001); 25% of patients had recurrence at 96 months following MVD compared with 12 months after percutaneous surgery. Subgroup analysis showed that balloon compression provided more durable relief amongst percutaneous procedures. Multivariate analysis revealed that post-operative numbness and age were prognostic factors for percutaneous procedures (P =.03 and .01, respectively). CONCLUSIONS: MVD provides better initial pain relief and longer durability of relief than percutaneous surgery, although carrying a small risk of major complications. Amongst percutaneous procedures, balloon compression gave the most durable relief from pain. Older age and post-operative numbness were predictors of good outcome from percutaneous surgery. These results can help clinicians to counsel patients with primary TN on neurosurgical treatment selection for pain relief

Correction to: PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas

An amendment to this paper has been published and can be accessed via the original article

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.

Anaplastic meningioma is a rare and aggressive brain tumor characterised by intractable recurrences and dismal outcomes. Here, we present an integrated analysis of the whole genome, transcriptome and methylation profiles of primary and recurrent anaplastic meningioma. A key finding was the delineation of distinct molecular subgroups that were associated with diametrically opposed survival outcomes. Relative to lower grade meningiomas, anaplastic tumors harbored frequent driver mutations in SWI/SNF complex genes, which were confined to the poor prognosis subgroup. Aggressive disease was further characterised by transcriptional evidence of increased PRC2 activity, stemness and epithelial-to-mesenchymal transition. Our analyses discern biologically distinct variants of anaplastic meningioma with prognostic and therapeutic significance

Correction to: PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas.

An amendment to this paper has been published and can be accessed via the original article

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

Anaplastic meningioma is a rare and aggressive brain tumor characterised by intractable recurrences and dismal outcomes. Here, we present an integrated analysis of the whole genome, transcriptome and methylation profiles of primary and recurrent anaplastic meningioma. A key finding was the delineation of distinct molecular subgroups that were associated with diametrically opposed survival outcomes. Relative to lower grade meningiomas, anaplastic tumors harbored frequent driver mutations in SWI/SNF complex genes, which were confined to the poor prognosis subgroup. Aggressive disease was further characterised by transcriptional evidence of increased PRC2 activity, stemness and epithelial-to-mesenchymal transition. Our analyses discern biologically distinct variants of anaplastic meningioma with prognostic and therapeutic significance

Genetically Engineered Mouse Models of Gliomas: Technological Developments for Translational Discoveries

The most common brain tumours, gliomas, have significant morbidity. Detailed biological and genetic understanding of these tumours is needed in order to devise effective, rational therapies. In an era generating unprecedented quantities of genomic sequencing data from human cancers, complementary methods of deciphering the underlying functional cancer genes and mechanisms are becoming even more important. Genetically engineered mouse models of gliomas have provided a platform for investigating the molecular underpinning of this complex disease, and new tools for such models are emerging that are enabling us to answer the most important questions in the field. Here, I discuss improvements to genome engineering technologies that have led to more faithful mouse models resembling human gliomas, including new cre/LoxP transgenic lines that allow more accurate cell targeting of genetic recombination, Sleeping Beauty and piggyBac transposons for the integration of transgenes and genetic screens, and CRISPR-cas9 for generating genetic knockout and functional screens. Applications of these technologies are providing novel insights into the functional genetic drivers of gliomagenesis, how these genes cooperate with one another, and the potential cells-of-origin of gliomas, knowledge of which is critical to the development of targeted treatments for patients in the clinic

Genetic dissection of EGFRvIII brain and spinal mouse gliomas through whole-exome sequencing and in vivo piggyBac mutagenesis forward genetic screening

Glioma is the commonest intrinsic brain tumor, and its high-grade form has a devastating prognosis. These tumors also arise in the spinal cord, carrying significant morbidity in children; however the genetics of these spinal gliomas is poorly understood. EGFRvIII is a common driver mutation in brain gliomas; it is unclear when this is acquired during glioma evolution and what its cooperative genetic drivers are. Here, we show that EGFRvIII initiates gliomagenesis in vivo; EGFRvIII leads to glioma precursors in the subventricular zone and brain surface, and later glioma formation in the brain and spinal cord. The long latency for tumor formation implies the need for additional mutations to drive gliomagenesis. In these tumors, we detected further genetic alterations including amplification of EGFRvIII, mutations of Trp53 and Tead2, and Cdkn2a deletion, through whole-exome sequencing. To shed further light on EGFR-cooperative genes for glioma progression, we conducted a genome-wide piggyBac transposon mutagenesis screen in vivo, which identified known glioma drivers (including Cdkn2a, Pten and Nf1) and novel putative partners, including genes that regulate neuronal differentiation such as Sox6 and Tcf12, and a novel regulator of the Ras pathway Spred1. RNA-sequencing confirmed the presence of fusion transcripts (transposon mediated effects) for these genes. We demonstrate the clinical relevance of these cooperative genes through comparison with large human glioma databases, demonstrating recurrent genetic alterations of these genes are in patient tumors implicating them as putative drivers, and we highlight that expression levels of Sox6 and Tcf12 correlate with patient prognosis. We show that there are shared and distinct mutated genes in brain and spinal gliomas. Although Pten is a well-known tumor suppressor for brain gliomas, it was not previously known whether Pten drives spinal gliomagenesis. Given recurrent transposon insertions in Pten were found in both brain and spinal gliomas, we generated conditional mice with EGFRvIII and Pten loss, demonstrating Pten accelerates spinal glioma formation. Our work elucidates the genetic evolutionary processes behind EGFRvIII-driven gliomas, provides a detailed genomic comparison between brain and spinal gliomas, and provides functional genomic datasets to help decipher complex human glioma genomes.Wellcome Trus

CRISPR and transposon in vivo screens for cancer drivers and therapeutic targets.

Human cancers harbor substantial genetic, epigenetic, and transcriptional changes, only some of which drive oncogenesis at certain times during cancer evolution. Identifying the cancer-driver alterations amongst the vast swathes of "passenger" changes still remains a major challenge. Transposon and CRISPR screens in vivo provide complementary methods for achieving this, and each platform has its own advantages. Here, we review recent major technological breakthroughs made with these two approaches and highlight future directions. We discuss how each genetic screening platform can provide unique insight into cancer evolution, including intra-tumoral heterogeneity, metastasis, and immune evasion, presenting transformative opportunities for targeted therapeutic intervention

Surgical Management of Incidental Gliomas

Detailed brain imaging studies discover gliomas incidentally before clinical symptoms or signs show. These tumors represent an early stage in the natural history of gliomas. Left untreated, they are likely to progress to a symptomatic stage and transform to malignant gliomas. A greater extent of resection delays the onset of malignant transformation and prolongs patient survival. Because incidental gliomas are typically smaller and less likely to be in eloquent brain locations, there is a strong case for early surgical intervention to maximize resection and improve outcomes. This article discusses developments in the surgical management of low-grade gliomas