The CRISPR-Cas9 system has revolutionized gene editing both on single genes and in multiplexed loss-of-function screens, enabling precise genome-scale identification of genes essential to proliferation and survival of cancer cells1,2. However, previous studies reported that a gene-independent anti-proliferative effect of Cas9-mediated DNA cleavage confounds such measurement of genetic dependency, leading to false positive results in copy number amplified regions3,4. We developed CERES, a computational method to estimate gene dependency levels from CRISPR-Cas9 essentiality screens while accounting for the copy-number-specific effect. As part of our efforts to define a cancer dependency map, we performed genome-scale CRISPR-Cas9 essentiality screens across 342 cancer cell lines and applied CERES to this dataset. We found that CERES reduced false positive results and estimated sgRNA activity for both this dataset and previously published screens performed with different sgRNA libraries. Here, we demonstrate the utility of this collection of screens, upon CERES correction, in revealing cancer-type-specific vulnerabilities.

Major efforts using loss-of-function genetic screens to systematically identify genes essential to the proliferation and survival of cancer cells have been reported [1][2][3][4][5][6][7][8][9] . Genes identified by these approaches may represent specific genetic vulnerabilities of cancer cells, suggesting treatment strategies and directing the development of novel therapeutics. The CRISPR-Cas9 genome editing system has proven to be a powerful tool to interrogate gene essentiality in cancer cell lines. Its relative ease of application, high rates of target validation, and increased specificity compared to RNA interference technology make it an ideal instrument for use in high-throughput functional genomic screening 10 .However, we and others have recently observed that measurements of genetic dependency in genome-scale CRISPR-Cas9 loss-of-function screens are influenced by the genomic copy number (CN) of the region targeted by the sgRNA-Cas9 complex [1][2][3][4] . Targeting Cas9 to DNA sequences within regions of high CN gain creates multiple DNA double-strand breaks (DSBs), inducing a gene-independent DNA damage response and a G2 cell-cycle arrest phenotype 2 .This systematic, sequence-independent effect due to DNA cleavage (copy-number effect)confounds the measurement of the consequences of gene deletion on cell viability (geneknockout effect) and is detectable even among low-level CN amplifications and deletions. In particular, this phenomenon hinders interpretation of CRISPR-Cas9 experiments in cancer cell

The word "biocompatibility," is inconsistent with the observations of healing for so-called biocompatible biomaterials. The vast majority of the millions of medical implants in humans today, presumably "biocompatible," are walled off by a dense, avascular, crosslinked collagen capsule, hardly suggestive of life or compatibility. In contrast, one is now seeing examples of implant biomaterials that lead to a vascularized reconstruction of localized tissue, a biological reaction different from traditional biocompatible materials that generate a foreign body capsule. Both the encapsulated biomaterials and the reconstructive biomaterials qualify as "biocompatible" by present day measurements of biocompatibility. Yet, this new generation of materials would seem to heal "compatibly" with the living organism, where older biomaterials are isolated from the living organism by the dense capsule. This review/perspective article will explore this biocompatibility etymological conundrum by reviewing the history of the concepts around biocompatibility, today's standard methods for assessing biocompatibility, a contemporary view of the foreign body reaction and finally, a compendium of new biomaterials that heal without the foreign body capsule. A new definition of biocompatibility is offered here to address advances in biomaterials design leading to biomaterials that heal into the body in a facile manner.

Diffuse midline gliomas are uniformly fatal pediatric central nervous system cancers, refractory to standard of care therapeutic modalities. The primary genetic drivers are a set of recurrent amino acid substitutions in genes encoding histone H3 (H3K27M), which are currently undruggable. These H3K27M oncohistones perturb normal chromatin architecture, resulting in an aberrant epigenetic landscape. To interrogate for epigenetic dependencies, we performed a CRISPR screen and show that patient-derived H3K27M-glioma neurospheres are dependent on core components of the mammalian BAF (SWI/SNF) chromatin remodeling complex. The BAF complex maintains glioma stem cells in a cycling, oligodendrocyte precursor cell (OPC)-like state, where genetic perturbation of the BAF catalytic subunit SMARCA4 (BRG1), as well as pharmacological suppression opposes proliferation, promotes progression of differentiation along the astrocytic lineage, and improves overall survival of patient-derived xenograft models. In summary, we demonstrate that therapeutic inhibition of BAF complex has translational potential for children with H3K27M-gliomas.