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XLSX file - 134K, Table S8. Most effective genotype-selective combinations.

PDF file - 1.1MB, Figure S1. Single agent concentration-effect curves, related to Figure 1; Figure S2. Drug class and concentration choices for combinatorial drug screening, related to Figure 2; Figure S3, Mutant BRAF and mutant RAS selective drug pairs, related to Figure 3; Figure S4. Analysis of drug combinations by target class, related to Figure 4D; Figure S5. Sensitization of mutant BRAF lines with lapatinib and MK-2206, related to Figure 5; Figure S6. Immunoblot analyses of vemurafenib-resistant lines after drug treatments, related to Figure 5; Figure S7. Signaling and biological effects of simvastatin and flavopiridol in vitro and in vivo, related to Figure 6

PDF file - 169K, Table S1. Agents used in single-agent HTS; Table S2. Melanoma cell lines and mutation status; Table S3. Concentrations required to inhibit 50% of cell growth (GI50) in single-agent screens; Table S4. Single agents with significant genotype-selective efficacy; Table S5. Agents and concentrations chosen for cHTS; Table S6. Partial list of drug pairs showing genotype selectivity; Table S7. Genotype-selective combinations with simvastatin; Table S9. Combination index (CI) values for select drug combinations

PDF file - 84K

Supplemental Figure 2. VEGFR TKIs inhibit the migration of NSCLC cells with KDR CNGs.

Purpose: VEGF pathway inhibitors have been investigated as therapeutic agents in the treatment of non–small cell lung cancer (NSCLC) because of its central role in angiogenesis. These agents have improved survival in patients with advanced NSCLC, but the effects have been modest. Although VEGFR2/KDR is typically localized to the vasculature, amplification of KDR has reported to occur in 9% to 30% of the DNA from different lung cancers. We investigated the signaling pathways activated downstream of KDR and whether KDR amplification is associated with benefit in patients with NSCLC treated with the VEGFR inhibitor vandetanib.Methods: NSCLC cell lines with or without KDR amplification were studied for the effects of VEGFR tyrosine kinase inhibitors (TKI) on cell viability and migration. Archival tumor samples collected from patients with platinum-refractory NSCLC in the phase III ZODIAC study of vandetanib plus docetaxel or placebo plus docetaxel (N = 294) were screened for KDR amplification by FISH.Results: KDR amplification was associated with VEGF-induced activation of mTOR, p38, and invasiveness in NSCLC cell lines. However, VEGFR TKIs did not inhibit proliferation of NSCLC cell lines with KDR amplification. VEGFR inhibition decreased cell motility as well as expression of HIF1α in KDR-amplified NSCLC cells. In the ZODIAC study, KDR amplification was observed in 15% of patients and was not associated with improved progression-free survival, overall survival, or objective response rate for the vandetanib arm.Conclusions: Preclinical studies suggest KDR activates invasion but not survival pathways in KDR-amplified NSCLC models. Patients with NSCLC whose tumor had KDR amplification were not associated with clinical benefit for vandetanib in combination with docetaxel. Clin Cancer Res; 22(8); 1940–50. ©2015 AACR.

Supplemental Figure 1. (A) Calu-1 cells were treated with VEGF (50 ng/ml) for 15 minutes and phospho-p38 levels were evaluated by Western blotting. VEGF treatment resulted in activation of p38, and this was blocked with the addition of VEGFR TKIs axitinib or sorafenib. (B) A549, H23, and Calu-1 cells express minimal levels of VEGFR1 as determined by ELISA assay. SKNAS neuroblastoma cells serve as a positive control.

In the TCGA NSCLC dataset there was a significantly greater prevalence of p53 mutations in patients with KDR CNG compared to KDR CNG negative patients (p = 0.001).

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Background: Mechanical thrombectomy (MT) has significantly improved clinical outcomes in acute ischemic stroke. We used single-cell RNA sequencing (scRNA-seq) to describe the landscape of human clots at single cell resolution seeking to provide greater mechanistic insight into stroke pathophysiology and to uncover an association with stroke origin. Methods: scRNA-seq was performed on 14 clots retrieved from 14 patients undergoing MT between October 2020-July 2022. We followed standard molecular biology and bioinformatics workflows for sample processing and data to characterize differences in cellular composition between clots of different stroke origin (atrial fibrillation (AF) and carotid atherosclerosis (CA)). Results: Clots revealed a significant heterogeneity of immune cells with major constituents including cells of the mononuclear phagocyte system (MPS) and neutrophils. The cellular populations most enriched in CA clots were B-cells and CD4+ T-cells. The cellular population most enriched in AF clots was red blood cells. When looking at cellular subpopulations of the MPS component, we found that CD16+ monocytes (intermediate and non-classical) were significantly more abundant than CD14+CD16- (classical) monocytes in all clots. Moreover, the proportions of CD16+ monocytes varied with stroke origin: the proportion of non-classical (CD14-CD16+) monocytes was higher in CA clots (p=0.05) whereas the proportion of intermediate monocytes (CD14+CD16+) was higher in FA clots (p=0.03). AF clots had upregulated biomarkers and pathways involved with AF or contractile dysfunction (IFI30, FABP4, PPAR, HOTAIR, ILK, Integrin). CA clots had upregulated biomarkers and pathways associated with cardiovascular diseases and atherogenesis (RNSE1, POLR2J3.1, PLTP, Sirtuin, FAK). (Figure) Conclusions: These results reveal a significant heterogeneity of immune cells and point to important differences in cellular composition associated with stroke etiology.

Introduction: Conventional MRI (cMRI) is not routinely available post-mechanical thrombectomy (MT), which can preclude accurate infarction assessment. Our objective was to evaluate the use of low-field portable MRI (pMRI) for bedside evaluation post-MT, including its use as a post-procedural baseline monitor. Methods: Low-field pMRI was used to obtain bedside imaging in post-MT patients between December 2021 to August 2022 at Yale-New Haven Hospital. All pMRI exams were conducted in the standard ferromagnetic environment of the IR suite. Volumetric analyses were performed by a neuroradiologist using 3D Slicer software. If cMRI was not available for comparison, a CT was used. Patients’ charts were reviewed for pre-revascularization MAP and occurrences of MAP dropping by 10% and 20% from individual baselines between the time of pMRI and delayed imaging. Results: A total of 25 patients (64% females, median age 77 years-old [IQR 69.5-84.5]) underwent bedside pMRIs in the IR suite post-MT. The median time from last known normal to access was 6 hours [IQR 4-17]. The median pMRI examination time was 30 minutes [IQR 17-32]. Of the 24 patients with available delayed imaging, 7 (29.2%) had infarct progression compared to immediate post-MT pMRI, while 15 patients (62.5%) had stable/decreased stroke volume. Two patients (8.3%) had parenchymal hemorrhage type 2 and were excluded from further analysis. There was no statistically significant difference between the proportions of favorable TICI scores (85.7% in the infarct progression group vs. 92.3% in the stable/decreased infarct group, p=1.00). Patients with infarct progression had comparable pre-revascularization MAP compared to those with stable/decreased delayed infarct volume (mean of 100.3±4.6 vs. 101.9±15.9 respectively, p=0.727) but had more occurrences of MAP dropping by 10% and 20% of their baseline between the time of pMRI and delayed imaging (mean of 35.0±23.3 vs. 14.7±11.3 occurrences, p=0.011; and mean of 21.7±16.5 vs. 8.5±9.5 occurrences, p=0.026, respectively). Conclusions: The use of low-field MRI in the post-MT setting can facilitate benchmark brain monitoring and serial examinations to evaluate the impact of potential physiological perturbations that may impact ongoing brain injury.

OBJECTIVE The Hospital Frailty Risk Score (HFRS) is a metric used to assess patient frailty risk in large national datasets using International Classification of Diseases, Tenth Revision (ICD-10) codes. While previous studies have assessed the association between frailty risk and postoperative outcomes in spine oncology, there is a paucity of data on the relationship between frailty risk and outcomes in patients undergoing surgery for spinal meningiomas. The goal of this study was to investigate the association between HFRS and hospital length of stay (LOS), discharge disposition, and cost of admission in patients undergoing surgery for spinal meningiomas. METHODS A retrospective cohort study was performed using the National Inpatient Sample Database from 2016 to 2019. Adult patients with benign or malignant spine meningiomas, identified using ICD-10 diagnostic and procedural coding, were stratified by HFRS: Low (HFRS 77.4%) were female and of the 2,815 Low risk patients, 2,185 (77.6%) were female. The Intermediate-High cohort was significantly older (Low: 60.94±14.63 years vs Intermediate-High: 66.93±14.23 years, p Low: 32.5% vs Intermediate-High: 74.5%, p Low: 7.1% vs Intermediate-High: 14.2, p = 0.018). Intermediate-High patients had longer mean LOS (Low: 4.02±2.30 days vs Intermediate-High: 7.14±6.03 days, p Low: $24,344±$16,743 vs Intermediate-High: $37,013±$27,547, p Low: 27.9% vs Intermediate-High: 55.7%, p

BackgroundTo evaluate the cost-effectiveness of endovascular thrombectomy (EVT) to treat large vessel occlusion (LVO) in patients with acute, minor stroke (National Institute of Health Stroke Scale (NIHSS) MethodsA Markov decision-analytic model was constructed accounting for both costs and outcomes from a societal perspective. Two different management strategies were evaluated: EVT and medical management. Base case analysis was done for three different sites of occlusion: proximal M1, distal M1 and M2 occlusions. One-way, two-way and probabilistic sensitivity analyses were performed.ResultsBase-case calculation showed EVT to be the dominant strategy in 65-year-old patients with proximal M1 occlusion and NIHSS ConclusionsEVT is cost-effective in patients with minor stroke and LVO in the long term (lifetime horizon), considering the poor outcomes and significant disability associated with non-reperfusion. Our study emphasizes the need for caution in interpreting previous observational studies which concluded similar results in EVT versus medical management in patients with minor stroke due to a high proportion of patients with M2 occlusions in the two strategies.

The future of cancer treatment is promising. Although marred by years of plateau in outcomes, new avenues have been identified that are poised to change how we treat cancer. Molecular targeted therapy or targeted therapy is one of these methods. Molecular targeted therapy involves identifying specific pathways or markers that allow cancer cells to flourish. Once identified, specific molecules can be used to block proliferative pathways, thereby negatively impacting tumor growth. Targeting specific pathways that prolong the survival of the cancer cell can lead to a decreased cancer burden, and improved patient outcomes. This article reviews the tenets of molecular targeted therapy, common pathways, target acquisition for drug development, and the pathways that have been elucidated in musculoskeletal tumors.

Purpose: VEGF pathway inhibitors have been investigated as therapeutic agents in the treatment of non–small cell lung cancer (NSCLC) because of its central role in angiogenesis. These agents have improved survival in patients with advanced NSCLC, but the effects have been modest. Although VEGFR2/KDR is typically localized to the vasculature, amplification of KDR has reported to occur in 9% to 30% of the DNA from different lung cancers. We investigated the signaling pathways activated downstream of KDR and whether KDR amplification is associated with benefit in patients with NSCLC treated with the VEGFR inhibitor vandetanib. Methods: NSCLC cell lines with or without KDR amplification were studied for the effects of VEGFR tyrosine kinase inhibitors (TKI) on cell viability and migration. Archival tumor samples collected from patients with platinum-refractory NSCLC in the phase III ZODIAC study of vandetanib plus docetaxel or placebo plus docetaxel (N = 294) were screened for KDR amplification by FISH. Results: KDR amplification was associated with VEGF-induced activation of mTOR, p38, and invasiveness in NSCLC cell lines. However, VEGFR TKIs did not inhibit proliferation of NSCLC cell lines with KDR amplification. VEGFR inhibition decreased cell motility as well as expression of HIF1α in KDR-amplified NSCLC cells. In the ZODIAC study, KDR amplification was observed in 15% of patients and was not associated with improved progression-free survival, overall survival, or objective response rate for the vandetanib arm. Conclusions: Preclinical studies suggest KDR activates invasion but not survival pathways in KDR-amplified NSCLC models. Patients with NSCLC whose tumor had KDR amplification were not associated with clinical benefit for vandetanib in combination with docetaxel. Clin Cancer Res; 22(8); 1940–50. ©2015 AACR.

The endothelial glycocalyx, a glycosaminoglycan layer located on the apical surface of vascular endothelial cells, has been shown to be important for several endothelial functions. Previous studies have documented that the glycocalyx is highly abundant in the mouse common carotid region, where the endothelium is exposed to laminar shear stress, and it is resistant to atherosclerosis. In contrast, the glycocalyx is scarce or absent in the mouse internal carotid sinus region, an area exposed to nonlaminar shear stress and highly susceptible to atherosclerosis. On the basis of these observations, we hypothesized that the expression of components of the endothelial glycocalyx is differentially regulated by distinct hemodynamic environments. To test this hypothesis, human endothelial cells were exposed to shear stress waveforms characteristic of atherosclerosis-resistant or atherosclerosis-susceptible regions of the human carotid, and the expression of several components of the glycocalyx was assessed. These experiments revealed that expression of several components of the endothelial glycocalyx is differentially regulated by distinct shear stress waveforms. Interestingly, we found that heparan sulfate expression is increased and evenly distributed on the apical surface of endothelial cells exposed to the atheroprotective waveform and is irregularly present in cells exposed to the atheroprone waveform. Furthermore, expression of a heparan sulfate proteoglycan, syndecan-1, is also differentially regulated by the two waveforms, and its suppression mutes the atheroprotective flow-induced cell surface expression of heparan sulfate. Collectively, these data link distinct hemodynamic environments to the differential expression of critical components of the endothelial glycocalyx.

Blood oxygenators provide crucial life support for patients suffering from respiratory failure, but their use is severely limited by the complex nature of the blood circuit and by complications including bleeding and clotting. We have fabricated and tested a multilayer microfluidic blood oxygenation prototype designed to have a lower blood prime volume and improved blood circulation relative to current hollow fiber cartridge oxygenators. Here we address processes for scaling the device toward clinically relevant oxygen transfer rates while maintaining a low prime volume of blood in the device, which is required for clinical applications in cardiopulmonary support and ultimately for chronic use. Approaches for scaling the device toward clinically relevant gas transfer rates, both by expanding the active surface area of the network of blood microchannels in a planar layer and by increasing the number of microfluidic layers stacked together in a three-dimensional device are addressed. In addition to reducing prime volume and enhancing gas transfer efficiency, the geometric properties of the microchannel networks are designed to increase device safety by providing a biomimetic and physiologically realistic flow path for the blood. Safety and hemocompatibility are also influenced by blood-surface interactions within the device. In order to further enhance device safety and hemocompatibility, we have demonstrated successful coating of the blood flow pathways with human endothelial cells, in order to confer the ability of the endothelium to inhibit coagulation and thrombus formation. Blood testing results provide confirmation of fibrin clot formation in non-endothelialized devices, while negligible clot formation was documented in cell-coated devices. Gas transfer testing demonstrates that the endothelial lining does not reduce the transfer efficiency relative to acellular devices. This process of scaling the microfluidic architecture and utilizing autologous cells to line the channels and mitigate coagulation represents a promising avenue for therapy for patients suffering from a range of acute and chronic lung diseases.

The Kruppel-like factor 2 (KLF2) and Kruppel-like factor 4 (KLF4) transcription factors have recently been shown to act as critical regulators of endothelial homeostasis. While several insights have been made into the signaling mechanisms orchestrating endothelial KLF2 expression, those governing the expression of KLF4 in the vascular endothelium remain largely unknown. Here, we show that diverse vasoprotective stimuli including an atheroprotective shear stress waveform, simvastatin, and resveratrol induce the expression of KLF4 in cultured human endothelial cells. We further demonstrate that the induction of KLF4 by resveratrol and atheroprotective shear stress occurs via a MEK5/MEF2-dependent signaling pathway. Since MEK5 activation is also critical for the expression of KLF2, we assessed the individual contribution of KLF4 and KLF2 to the global transcriptional activity triggered by MEK5 activation. Genome-wide transcriptional profiling of endothelial cells overexpressing KLF4, KLF2, or constitutively active MEK5 revealed that 59.2% of the genes regulated by the activation of MEK5 were similarly controlled by either KLF2 or KLF4. Collectively, our data identify a significant degree of mechanistic and functional conservation between KLF2 and KLF4, and importantly, provide further insights into the complex regulatory networks governing endothelial vasoprotection.

Waters impacted by fecal pollution can exact high risks to human health and can result in financial losses due to closures of water systems used for recreation and for harvesting seafood. Identifying the sources of fecal pollution in water is paramount in assessing the potential human health risks involved as well as in assessing necessary remedial action. Recently, various researchers have used the ribotyping method to identify sources of bacterial indicators ( Escherichia coli and enterococci) in environmental waters. While these studies have identified genotypic differences between human- and animal-derived indicators that are capable of differentiating organisms isolated from humans and various animal hosts, most have focused on organisms collected from a confined geographic area and have not addressed the question of whether these ribotype profiles are watershed specific or if they can be applied universally to organisms from other geographic locations. In this study, E. coli isolates were obtained from humans, beef cattle, dairy cattle, swine, and poultry from locations in northern, central, and southern Florida and were subjected to ribotyping analysis. The intent was to determine (i) if ribotype profiles are capable of discriminating the source of E. coli at the host species level and (ii) if the resulting fingerprints are uniform over an extended geographic area or if they can be applied only to a specific watershed. Our research indicated that, using a single restriction enzyme ( Hin dIII), the ribotyping procedure is not capable of differentiating E. coli isolates from the different animal species sampled in this study. Results indicate, however, that this procedure can still be used effectively to differentiate E. coli as being either human or animal derived when applied to organisms isolated from a large geographic region.

Nitric oxide (NO) produced by vascular endothelial cells is a potent vasodilator and an antiinflammatory mediator. Regulating production of endothelial-derived NO is a complex undertaking, involving multiple signaling and genetic pathways that are activated by diverse humoral and biomechanical stimuli. To gain a thorough understanding of the rich diversity of responses observed experimentally, it is necessary to account for an ensemble of these pathways acting simultaneously. In this article, we have assembled four quantitative molecular pathways previously proposed for shear-stress-induced NO production. In these pathways, endothelial NO synthase is activated 1), via calcium release, 2), via phosphorylation reactions, and 3), via enhanced protein expression. To these activation pathways, we have added a fourth, a pathway describing actual NO production from endothelial NO synthase and its various protein partners. These pathways were combined and simulated using CytoSolve, a computational environment for combining independent pathway calculations. The integrated model is able to describe the experimentally observed change in NO production with time after the application of fluid shear stress. This model can also be used to predict the specific effects on the system after interventional pharmacological or genetic changes. Importantly, this model reflects the up-to-date understanding of the NO system, providing a platform upon which information can be aggregated in an additive way., National Institutes of Health (U.S.) (Grant R01HL090856), Singapore-MIT Alliance Computational and Systems Biology Program

The efficacy levels of different physical and chemical washing treatments in the reduction of viral and bacterial pathogens from inoculated strawberries were evaluated. Escherichia coli O157:H7, Salmonella Montevideo, poliovirus 1, and the bacteriophages PRD1, phiX174, and MS2 were used as model and surrogate organisms. Chemicals readily available to producers and/or consumers were evaluated as antimicrobial additives for the production of washes. The gentle agitation of contaminated strawberries in water for 2 min led to reductions in microbial populations ranging from 41 to 79% and from 62 to 90% at water temperatures of 22 and 43 degrees C, respectively. Significant reductions (98%) in numbers of bacteria and viruses were obtained with sodium hypochlorite (50 to 300 ppm of free chlorine), Oxine or Carnebon (200 ppm of product generating "stabilized chlorine dioxide"), Tsunami (100 ppm of peroxyacetic acid), and Alcide (100 or 200 ppm of acidified sodium chlorite) washes. Overall, 200 ppm of acidified sodium chlorite produced the greatest reductions of microorganisms. Hydrogen peroxide (0.5%) was slightly less effective than free chlorine in a strawberry wash and caused slight fruit discoloration. Cetylpyridinium chloride (0.1%) was effective in the reduction of bacterial species, while trisodium phosphate (1%) was effective against viruses. The consumer-oriented produce wash Fit was very effective (99%) in reducing the numbers of bacteria but not in reducing the numbers of viruses. Another wash, Healthy Harvest, was significantly less effective than Fit in reducing bacterial pathogens but more effective for viruses. The performance of automatic dishwashing detergent was similar to that of Healthy Harvest and significantly better than that of liquid dishwashing detergent. Solutions containing table salt (2% NaCl) or vinegar (10%) reduced the numbers of bacteria by about 90%, whereas only the vinegar wash reduced the numbers of viruses significantly (ca. 95%).

Targeted therapies designed to inhibit the vascular endothelial growth factor (VEGF) pathway have been extensively evaluated in the treatment of malignancies including Non-Small Cell Lung Cancer (NSCLC). VEGF pathway inhibitors such as bevacizumab, or the multitargeted receptor tyrosine kinase inhibitors (TKIs) vandetanib and sorafenib, have been shown to prolong progression-free survival (PFS) and/or overall survival (OS). These benefits, however, have been modest, seen only in subsets of patients. Thus, predictive markers for identifying which patients are likely to benefit are critically needed. Although expression of VEGF receptor-2 (VEGFR-2, also known as KDR) was initially thought to primarily occur in endothelial cells, VEGFR-2 has been detected on malignant cells, including lung cancer cells, and in NSCLC, overexpression of VEGFR-2 on tumor cells is associated with a poor clinical outcome. Amplification of KDR has been detected in lung cancer specimens at a relatively high frequency (9% and 32%). The consequences of KDR copy number gains (CNGs) are not yet understood. Recently, we have shown that NSCLC cell lines with KDR copy number gains (CNGs) were associated with in vitro resistance to platinum chemotherapy, and KDR CNG predicted worse overall survival in patients who received platinum adjuvant therapy but not in untreated patients. We investigated the hypothesis that NSCLC tumor cells with KDR CNG display increased sensitivity to VEGFR TKIs compared to tumor cells without KDR CNG. In tumor cell lines with KDR CNG, treatment with exogenous VEGF ligand enhanced cell motility and this was inhibited by VEGFR blockade with TKIs. Multiple receptor tyrosine kinases have been shown to drive HIF-1α levels, and NSCLC cells with KDR CNG express elevated levels of HIF-1α in normoxic conditions compared to NSCLC cell lines without KDR CNG. Here, we show that in NSCLC cell lines with KDR CNG, VEGFR TKIs decreased protein levels of HIF-1α and HIF-1α- regulated proteins. Furthermore, we report a clinical case in which a NSCLC patient with KDR CNG as determined by SNP array had a partial response to VEGFR inhibition with sorafenib. Citation Format: Monique B. Nilsson, Tina Cascone, Jayanthi Gudikote, Emily Roarty, Lixia Diao, Andrew Koo, Sumankalai Ramachandran, Erick Riquelme, Hai Tran, Ignacio Wistuba, David P. Carbone, John Heymach. KDR amplification in NSCLC is associated with sensitivity to VEGFR tyrosine kinase inhibitors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 374. doi:10.1158/1538-7445.AM2013-374

The local hemodynamic shear stress waveforms present in an artery dictate the endothelial cell phenotype. The observed decrease of the apical glycocalyx layer on the endothelium in atheroprone regions of the circulation suggests that the glycocalyx may have a central role in determining atherosclerotic plaque formation. However, the kinetics for the cells’ ability to adapt its glycocalyx to the environment have not been quantitatively resolved. Here we report that the heparan sulfate component of the glycocalyx of HUVECs increases by 1.4-fold following the onset of high shear stress, compared to static cultured cells, with a time constant of 19 h. Cell morphology experiments show that 12 h are required for the cells to elongate, but only after 36 h have the cells reached maximal alignment to the flow vector. Our findings demonstrate that following enzymatic degradation, heparan sulfate is restored to the cell surface within 12 h under flow whereas the time required is 20 h under static conditions. We also propose a model describing the contribution of endocytosis and exocytosis to apical heparan sulfate expression. The change in HS regrowth kinetics from static to high-shear EC phenotype implies a differential in the rate of endocytic and exocytic membrane turnover., National Heart, Lung, and Blood Institute (Grant HL090856-01), Singapore-MIT Alliance