Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation

Targeted transcriptional regulation is a powerful tool to study genetic mediators of cellular behavior. Here, we show that catalytically dead Cas9 (dCas9) targeted to genomic regions upstream or downstream of the transcription start site allows for specific and sustainable gene-expression level alterations in tumor cells in vitro and in syngeneic immune-competent mouse models. We used this approach for a high-coverage pooled gene-activation screen in vivo and discovered previously unidentified modulators of tumor growth and therapeutic response. Moreover, by using dCas9 linked to an activation domain, we can either enhance or suppress target gene expression simply by changing the genetic location of dCas9 binding relative to the transcription start site. We demonstrate that these directed changes in gene-transcription levels occur with minimal off-target effects. Our findings highlight the use of dCas9-mediated transcriptional regulation as a versatile tool to reproducibly interrogate tumor phenotypes in vivo. Keywords: cancer genetics; cancer models; cancer therapeutic resistance; gene regulation; CRISPRNational Cancer Institute (U.S.) (Grant U54-CA112967-06)National Cancer Institute (U.S.) (Grant P30-CA14051

The effect of matrix metalloproteinase 2 and matrix metalloproteinase 2/9 deletion in experimental post-thrombotic vein wall remodeling

BackgroundVein wall fibrotic injury following deep venous thrombosis (VT) is associated with elevated matrix metalloproteinases (MMPs). Whether and by what mechanism MMP2 contributes to vein wall remodeling after VT is unknown.MethodsStasis VT was produced by ligation of the inferior vena cava and tissue was harvested at 2, 8, and 21 days in MMP2 -/- and genetic wild type (WT) mice. Tissue analysis by immunohistochemistry, enzyme-linked immunosorbent assay, real-time polymerase chain reaction, and zymography was performed.ResultsThrombus resolution was less at 8 days in MMP2 -/- compared with WT, evidenced by a 51% increase in VT size (P < .01), and threefold fewer von Willebrand's factor positive channels (P < .05). In MMP2 -/- mice, the main phenotypic fibrotic differences occurred at 8 days post-VT, with significantly less vein wall collagen content (P = .013), fourfold lower procollagen III gene expression (P < .01), but no difference in procollagen I compared with WT. Decreased inflammation in MMP2 -/- vein walls was suggested by ∼ threefold reduced TNFα and IL-1β at 2 days and 8 days post-VT (P < .05). A fourfold increase in vein wall monocytes (P = .03) with threefold decreased apoptosis (P < .05), but no difference in cellular proliferation at 8 days was found in MMP2 -/- compared with WT. As increased compensatory MMP9 activity was observed in the MMP2 -/-mice, MMP2/9 double null mice had thrombus induced with VT harvest at 8 days. Consistently, twofold larger VT, a threefold decrease in vein wall collagen, and a threefold increase in monocytes were found (all P < .05). Similar findings were observed in MMP9 -/- mice administered an exogenous MMP2 inhibitor.ConclusionsIn stasis VT, deletion of MMP2 was associated with less midterm vein wall fibrosis and inflammation, despite an increase in monocytes. Consideration that VT resolution was impaired with MMP2 (and MMP2/9) deletion suggests direct inhibition will likely also require anticoagulant therapy.Clinical RelevancePost-thrombotic syndrome has no direct therapies and causes significant morbidity. Anticoagulation limits thrombosis but does not clinically impact directly the vein wall response to injury as well as has bleeding risks. In this experimental study, we show that matrix metalloproteinase 2 genetic deletion lessens fibrotic injury and inflammation at the midterm timepoint, yet is also important for thrombus resolution. Future therapies that positively impact vein wall remodeling will need to account for how the thrombus responds as well

Additive Manufacturing of Transparent Fused Quartz

This paper investigates a filament-fed process for additive manufacturing (AM) of fused quartz. Glasses such as fused quartz have significant scientific and engineering applications, which include optics, communications, electronics, and hermetic seals. AM has several attractive benefits such as increased design freedom, faster prototyping, and lower processing costs for small production volumes. However, current research into glass AM has focused primarily on nonoptical applications. Fused quartz is studied here because of its desirability for use in high-quality optics due to its high transmissivity and thermal stability. Fused quartz filaments are fed into a CO2 laser-generated molten region, smoothly depositing material onto the workpiece. Spectroscopy and pyrometry are used to measure the thermal radiation incandescently emitted from the molten region. The effects of the laser power and scan speed are determined by measuring the morphology of single tracks. Thin walls are printed to study the effects of layer-to-layer height. This information is used to deposit solid pieces including a cylindrical-convex shape capable of focusing visible light. The transmittance and index homogeneity of the printed fused quartz are measured. These results show that the filament-fed process has the potential to print transmissive optics

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

While the catalog of mammalian transcripts and their expression levels in different cell types and disease states is rapidly expanding, our understanding of transcript function lags behind. We present a robust technology enabling systematic investigation of the cellular consequences of repressing or inducing individual transcripts. We identify rules for specific targeting of transcriptional repressors (CRISPRi), typically achieving 90%–99% knockdown with minimal off-target effects, and activators (CRISPRa) to endogenous genes via endonuclease-deficient Cas9. Together they enable modulation of gene expression over a ∼1,000-fold range. Using these rules, we construct genome-scale CRISPRi and CRISPRa libraries, each of which we validate with two pooled screens. Growth-based screens identify essential genes, tumor suppressors, and regulators of differentiation. Screens for sensitivity to a cholera-diphtheria toxin provide broad insights into the mechanisms of pathogen entry, retrotranslocation and toxicity. Our results establish CRISPRi and CRISPRa as powerful tools that provide rich and complementary information for mapping complex pathways

Coordination of sustainable financing for evidence-based youth mental health treatments: Protocol for development and evaluation of the fiscal mapping process

BACKGROUND: Sustained delivery of evidence-based treatments (EBTs) is essential to addressing the public health and economic impacts of youth mental health problems, but is complicated by the limited and fragmented funding available to youth mental health service agencies (hereafter, service agencies ). Strategic planning tools are needed that can guide these service agencies in their coordination of sustainable funding for EBTs. This protocol describes a mixed-methods research project designed to (1) develop and (2) evaluate our novel fiscal mapping process that guides strategic planning efforts to finance the sustainment of EBTs in youth mental health services. METHOD: Participants will be 48 expert stakeholder participants, including representatives from ten service agencies and their partners from funding agencies (various public and private sources) and intermediary organizations (which provide guidance and support on the delivery of specific EBTs). Aim 1 is to develop the fiscal mapping process: a multi-step, structured tool that guides service agencies in selecting the optimal combination of strategies for financing their EBT sustainment efforts. We will adapt the fiscal mapping process from an established intervention mapping process and will incorporate an existing compilation of 23 financing strategies. We will then engage participants in a modified Delphi exercise to achieve consensus on the fiscal mapping process steps and gather information that can inform the selection of strategies. Aim 2 is to evaluate preliminary impacts of the fiscal mapping process on service agencies\u27 EBT sustainment capacities (i.e., structures and processes that support sustainment) and outcomes (e.g., intentions to sustain). The ten agencies will pilot test the fiscal mapping process. We will evaluate how the fiscal mapping process impacts EBT sustainment capacities and outcomes using a comparative case study approach, incorporating data from focus groups and document review. After pilot testing, the stakeholder participants will conceptualize the process and outcomes of fiscal mapping in a participatory modeling exercise to help inform future use and evaluation of the tool. DISCUSSION: This project will generate the fiscal mapping process, which will facilitate the coordination of an array of financing strategies to sustain EBTs in community youth mental health services. This tool will promote the sustainment of youth-focused EBTs

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ∼100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses.National Human Genome Research Institute (U.S.) (Grant P50HG006193

Case Report Cardiac Gated Computed Tomography Used to Confirm Iatrogenic Aortic Valve Leaflet Perforation after Mitral Valve Replacement

Aortic insufficiency from iatrogenic valve perforation from nonaortic valve operations is rarely reported despite the prevalence of these procedures. Rapid diagnosis of these defects is essential to prevent deterioration of cardiac function. In this paper, we describe a young man who reported to our institution after two open cardiac surgeries with new aortic regurgitation found to be due to an iatrogenic perforation of his noncoronary aortic valve cusp. This defect was not appreciated by previous intraoperative transesophageal echocardiography and was inadequately visualized on follow-up transthoracic and transesophageal echocardiograms. In contrast, cardiac gated computed tomography clearly visualized the defect and its surrounding structures. This case highlights the utility of cardiac gated computed tomography for cases of suspected valvular perforation when echocardiography is not readily available or inadequate imaging is obtained

Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol.

While some of the variance observed in adiposity and weight change within populations can be accounted for by traditional risk factors, a new factor, the gut microbiota, has recently been associated with obesity. However, the causal mechanisms through which the gut microbiota and its metabolites, short chain fatty acids (SCFAs) influence obesity are unknown, as are the individual obesogenic effects of the individual SCFAs (butyrate, acetate and propionate). This study, METS-Microbiome, proposes to examine the influence of novel risk factors, the gut microbiota and SCFAs, on obesity, adiposity and weight change in an international established cohort spanning the epidemiologic transition. The parent study; Modeling the Epidemiologic Transition Study (METS) is a well-established and ongoing prospective cohort study designed to assess the association between body composition, physical activity, and relative weight, weight gain and cardiometabolic disease risk in five diverse population-based samples in 2500 people of African descent. The cohort has been prospectively followed since 2009. Annual measures of obesity risk factors, including body composition, objectively measured physical activity and dietary intake, components which vary across the spectrum of social and economic development. In our new study; METS-Microbiome, in addition to continuing yearly measures of obesity risk, we will also measure gut microbiota and stool SCFAs in all contactable participants, and follow participants for a further 3 years, thus providing one of the largest gut microbiota population-based studies to date. This new study capitalizes upon an existing, extensively well described cohort of adults of African-origin, with significant variability as a result of the widespread geographic distributions, and therefore variation in the environmental covariate exposures. The METS-Microbiome study will substantially advance the understanding of the role gut microbiota and SCFAs play in the development of obesity and provide novel obesity therapeutic targets targeting SCFAs producing features of the gut microbiota. Registered NCT03378765 Date first posted: December 20, 2017