The dynamics of signaling as a pharmacological target.

Highly networked signaling hubs are often associated with disease, but targeting them pharmacologically has largely been unsuccessful in the clinic because of their functional pleiotropy. Motivated by the hypothesis that a dynamic signaling code confers functional specificity, we investigated whether dynamic features may be targeted pharmacologically to achieve therapeutic specificity. With a virtual screen, we identified combinations of signaling hub topologies and dynamic signal profiles that are amenable to selective inhibition. Mathematical analysis revealed principles that may guide stimulus-specific inhibition of signaling hubs, even in the absence of detailed mathematical models. Using the NFκB signaling module as a test bed, we identified perturbations that selectively affect the response to cytokines or pathogen components. Together, our results demonstrate that the dynamics of signaling may serve as a pharmacological target, and we reveal principles that delineate the opportunities and constraints of developing stimulus-specific therapeutic agents aimed at pleiotropic signaling hubs.

Hepatitis C virus direct-acting antiviral nonadherence: Relationship to sustained virologic response and identification of at-risk patients.

OBJECTIVES: There is a dearth of literature on effects of nonadherence to hepatitis C virus (HCV) direct-acting antiviral (DAA) regimens; thus, the objective of our study was to assess the impact of adherence on sustained virologic response (SVR) and evaluate factors associated with nonadherence, such as race, psychiatric comorbidities, and therapy length. METHODS: We conducted a retrospective cohort study of patients completing DAA treatment between January 2014 and May 2016 within an interdisciplinary hepatology clinic. Adherence was defined a priori as 95% or greater of DAA doses taken within the prescribed treatment period. Post hoc analyses were done with adherence thresholds ≥ 90%, ≥ 85%, and ≥ 80% and adherence as a continuous percentage. Patients lost to follow-up before completing therapy or that discontinued therapy early were excluded from analyses. The association between adherence and SVR rates was assessed using Fisher exact test (for adherence thresholds) and the Wilcoxon rank-sum test (for continuous adherence). Factors associated with adherence were assessed similarly using Fisher exact and Wilcoxon rank-sum tests and multivariable logistic regression. RESULTS: Overall adherence was high, with an average of 97.8% of DAA doses taken within the prescribed treatment period. Achievement of SVR was not significantly different in adherent and nonadherent patients, at an adherence threshold of 95% or greater (93.4% vs. 88.5%; P = 0.246) or any of the post hoc adherence thresholds (≥ 90% [93.3% vs. 84.0%; P = 0.098], ≥ 85% [92.8% vs. 91.7%; P = 0.601], ≥ 80% [92.9% vs. 80.0%; P = 0.315], or as a continuous percentage [P = 0.328]). Black patients were significantly more likely to be nonadherent to DAAs than non-black patients at each adherence threshold (P < 0.05). No other factors evaluated were associated with nonadherence. CONCLUSION: A numerically higher but not statistically significant SVR failure rate was noted in nonadherent patients, although the gold standard definition for adherence remains to be established. Black patients may require additional adherence support.

The Prp19 complex and the Usp4Sart3 deubiquitinating enzyme control reversible ubiquitination at the spliceosome.

The spliceosome, a dynamic assembly of proteins and RNAs, catalyzes the excision of intron sequences from nascent mRNAs. Recent work has suggested that the activity and composition of the spliceosome are regulated by ubiquitination, but the underlying mechanisms have not been elucidated. Here, we report that the spliceosomal Prp19 complex modifies Prp3, a component of the U4 snRNP, with nonproteolytic K63-linked ubiquitin chains. The K63-linked chains increase the affinity of Prp3 for the U5 snRNP component Prp8, thereby allowing for the stabilization of the U4/U6.U5 snRNP. Prp3 is deubiquitinated by Usp4 and its substrate targeting factor, the U4/U6 recycling protein Sart3, which likely facilitates ejection of U4 proteins from the spliceosome during maturation of its active site. Loss of Usp4 in cells interferes with the accumulation of correctly spliced mRNAs, including those for alpha-tubulin and Bub1, and impairs cell cycle progression. We propose that the reversible ubiquitination of spliceosomal proteins, such as Prp3, guides rearrangements in the composition of the spliceosome at distinct steps of the splicing reaction.

PTEN loss in circulating tumour cells correlates with PTEN loss in fresh tumour tissue from castration-resistant prostate cancer patients.

BACKGROUND: PTEN gene loss occurs frequently in castration-resistant prostate cancer (CRPC) and may drive progression through activation of the PI3K/AKT pathway. Here, we developed a novel CTC-based assay to determine PTEN status and examined the correlation between PTEN status in CTCs and matched tumour tissue samples. METHODS: PTEN gene status in CTCs was evaluated on an enrichment-free platform (Epic Sciences) by fluorescence in situ hybridisation (FISH). PTEN status in archival and fresh tumour tissue was evaluated by FISH and immunohistochemistry. RESULTS: Peripheral blood was collected from 76 patients. Matched archival and fresh cancer tissue was available for 48 patients. PTEN gene status detected in CTCs was concordant with PTEN status in matched fresh tissues and archival tissue in 32 of 38 patients (84%) and 24 of 39 patients (62%), respectively. CTC counts were prognostic (continuous, P=0.001). PTEN loss in CTCs associated with worse survival in univariate analysis (HR 2.05; 95% CI 1.17-3.62; P=0.01) and with high lactate dehydrogenase (LDH) in metastatic CRPC patients. CONCLUSIONS: Our results illustrate the potential use of CTCs as a non-invasive, real-time liquid biopsy to determine PTEN gene status. The prognostic and predictive value of PTEN in CTCs warrants investigation in CRPC clinical trials of PI3K/AKT-targeted therapies.

Rapid and step-wise eye growth in molting diving beetle larvae.

However complex a visual system is, the size (and growth rate) of all its components-lens, retina and nervous system-must be precisely tuned to each other for the system to be functional. As organisms grow, their eyes must be able to achieve and maintain emmetropia, a state in which photoreceptors receive sharp images of objects that are at infinity. While there has been ample research into how vertebrates coordinate eyes growth, this has never been addressed in arthropods with camera eyes, which tend to grow dramatically and typically in a step-wise manner with each molt (ecdysis). Here, we used histological and optical methods to measure how the larval eyes of Sunburst Diving Beetles (Thermonectus marmoratus, Coleoptera, Dytiscidae) grow, and how well optical and morphological parameters match, during the dramatic growth that occurs between two consecutive larval stages. We find that the eye tubes of the principal eyes of T. marmoratus grow substantially around molt, with the vitreous-like crystalline cone contributing the most to the overall growth. Lenses also reform relatively quickly, undergoing a period of dysfunction and then regaining the ability to project sharp images onto the retina around 8 h post-molt.

Use of an Innovative Pharmaceutical Class Scoring Tool for Prioritized Annual Formulary Review.

Background: Though The Joint Commission requires health systems perform annual formulary review, guidance for how to perform this review is lacking. Published methods include comprehensive review of all pharmaceutical classes; however, this approach may not be the most efficient or effective option for a health system with a large formulary. Objective: To create a prioritization system for annual formulary review through development of a pharmaceutical class scoring tool. Methods: Drug information pharmacists developed the scoring tool, which used external and internal data to score pharmaceutical classes in 4 categories: safety, efficacy, cost, and utilization. The primary outcome, number of formulary changes resulting from pharmaceutical class review, was compared between the highest-scoring and lowest-scoring class to assess the tool's ability to prioritize high-yield class reviews. Results: The tool calculated scores for 91 pharmaceutical classes, altogether containing 962 medications. After review of the highest-scoring class, corticosteroids, 2 formulary changes were made: one dosage form was removed from formulary, and one medication was restricted to outpatient use only. Zero formulary changes resulted from review of the lowest-scoring class, pharmaceutical adjuvants. Conclusions: The tool described in this study prioritized annual formulary review efforts by identifying a pharmaceutical class with meaningful formulary optimization opportunities as the highest-scoring class, while correctly identifying a class with no optimization opportunities as the lowest-scoring class.

IkappaBepsilon provides negative feedback to control NF-kappaB oscillations, signaling dynamics, and inflammatory gene expression.

NF-kappaB signaling is known to be critically regulated by the NF-kappaB-inducible inhibitor protein IkappaBalpha. The resulting negative feedback has been shown to produce a propensity for oscillations in NF-kappaB activity. We report integrated experimental and computational studies that demonstrate that another IkappaB isoform, IkappaBepsilon, also provides negative feedback on NF-kappaB activity, but with distinct functional consequences. Upon stimulation, NF-kappaB-induced transcription of IkappaBepsilon is delayed, relative to that of IkappaBalpha, rendering the two negative feedback loops to be in antiphase. As a result, IkappaBepsilon has a role in dampening IkappaBalpha-mediated oscillations during long-lasting NF-kappaB activity. Furthermore, we demonstrate the requirement of both of these distinct negative feedback regulators for the termination of NF-kappaB activity and NF-kappaB-mediated gene expression in response to transient stimulation. Our findings extend the capabilities of a computational model of IkappaB-NF-kappaB signaling and reveal a novel regulatory module of two antiphase negative feedback loops that allows for the fine-tuning of the dynamics of a mammalian signaling pathway.

Verifying the value of existing frameworks for formulary review at a large academic health system: assessing inter-rater reliability.

BACKGROUND: The value assessment framework (VAF) is one approach to assessing the evidence and value of medications. VAFs are a way to measure and communicate the value of medications and other health care technologies for decision-making purposes. Given the increasing number of high-cost medications, challenging formulary inquiries, and critiques of currently available tools, health systems need to explore a standardized way to incorporate value assessment into formulary decision making. OBJECTIVES: To (a) evaluate existing VAFs by measuring inter-rater reliability among typical clinicians completing formulary reviews and (b) explore general implications of applying these tools to formulary decision making for all medications at a large academic health system. METHODS: This was a retrospective, observational study at a single health system. A list of medications added, denied, and removed from the system formulary from September 1, 2013, through August 31, 2018, was collected. Published VAFs, such as the American Society of Clinical Oncology (ASCO) Value Framework, European Society of Medical Oncology (ESMO) Magnitude of Clinical Benefit Scale, National Comprehensive Cancer Network (NCCN) Evidence Blocks, American College of Cardiology/American Heart Association Value Framework, and the incremental cost-effectiveness ratio (ICER) calculation were applied by 3 different reviewer groups. The primary outcome was inter-rater reliability among the 3 different reviewers for a given framework. Cohen's weighted kappa and the intraclass correlation coefficient (ICC) were used to assess inter-rater reliability. RESULTS: The frameworks were applied to 94 medications. The VAFs with the highest ICCs between all 3 raters were NCCN (0.635; 95% CI = 0.387-0.823) and ASCO (0.634; 95% CI = 0.370-0.832), both indicating moderate inter-rater reliability. The VAFs with the lowest ICCs were ESMO (0.368; 95% CI = 0.126-0.611) and ICER (0.159; 95% = CI -0.018-0.365), with ICCs corresponding to poor reliability. CONCLUSIONS: Because high-cost medications are a challenge to health systems, VAFs may be beneficial to target formulary decision making in this setting. Applying VAFs proactively may improve interrater reliability and usability in formulary decision making. DISCLOSURES: No outside funding supported this study. The authors have nothing to disclose.

A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity.

Cellular signal transduction pathways are usually studied following administration of an external stimulus. However, disease-associated aberrant activity of the pathway is often due to misregulation of the equilibrium state. The transcription factor NF-kappaB is typically described as being held inactive in the cytoplasm by binding its inhibitor, IkappaB, until an external stimulus triggers IkappaB degradation through an IkappaB kinase-dependent degradation pathway. Combining genetic, biochemical, and computational tools, we investigate steady-state regulation of the NF-kappaB signaling module and its impact on stimulus responsiveness. We present newly measured in vivo degradation rate constants for NF-kappaB-bound and -unbound IkappaB proteins that are critical for accurate computational predictions of steady-state IkappaB protein levels and basal NF-kappaB activity. Simulations reveal a homeostatic NF-kappaB signaling module in which differential degradation rates of free and bound pools of IkappaB represent a novel cross-regulation mechanism that imparts functional robustness to the signaling module.

Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis.

Genomic instability is a hallmark of cancer often associated with poor patient outcome and resistance to targeted therapy. Assessment of genomic instability in bulk tumor or biopsy can be complicated due to sample availability, surrounding tissue contamination, or tumor heterogeneity. The Epic Sciences circulating tumor cell (CTC) platform utilizes a non-enrichment based approach for the detection and characterization of rare tumor cells in clinical blood samples. Genomic profiling of individual CTCs could provide a portrait of cancer heterogeneity, identify clonal and sub-clonal drivers, and monitor disease progression. To that end, we developed a single cell Copy Number Variation (CNV) Assay to evaluate genomic instability and CNVs in patient CTCs. For proof of concept, prostate cancer cell lines, LNCaP, PC3 and VCaP, were spiked into healthy donor blood to create mock patient-like samples for downstream single cell genomic analysis. In addition, samples from seven metastatic castration resistant prostate cancer (mCRPC) patients were included to evaluate clinical feasibility. CTCs were enumerated and characterized using the Epic Sciences CTC Platform. Identified single CTCs were recovered, whole genome amplified, and sequenced using an Illumina NextSeq 500. CTCs were then analyzed for genome-wide copy number variations, followed by genomic instability analyses. Large-scale state transitions (LSTs) were measured as surrogates of genomic instability. Genomic instability scores were determined reproducibly for LNCaP, PC3, and VCaP, and were higher than white blood cell (WBC) controls from healthy donors. A wide range of LST scores were observed within and among the seven mCRPC patient samples. On the gene level, loss of the PTEN tumor suppressor was observed in PC3 and 5/7 (71%) patients. Amplification of the androgen receptor (AR) gene was observed in VCaP cells and 5/7 (71%) mCRPC patients. Using an in silico down-sampling approach, we determined that DNA copy number and genomic instability can be detected with as few as 350K sequencing reads. The data shown here demonstrate the feasibility of detecting genomic instabilities at the single cell level using the Epic Sciences CTC Platform. Understanding CTC heterogeneity has great potential for patient stratification prior to treatment with targeted therapies and for monitoring disease evolution during treatment.

Analytical Validation and Capabilities of the Epic CTC Platform: Enrichment-Free Circulating Tumour Cell Detection and Characterization.

The Epic Platform was developed for the unbiased detection and molecular characterization of circulating tumour cells (CTCs). Here, we report assay performance data, including accuracy, linearity, specificity and intra/inter-assay precision of CTC enumeration in healthy donor (HD) blood samples spiked with varying concentrations of cancer cell line controls (CLCs). Additionally, we demonstrate clinical feasibility for CTC detection in a small cohort of metastatic castrate-resistant prostate cancer (mCRPC) patients. The Epic Platform demonstrated accuracy, linearity and sensitivity for the enumeration of all CLC concentrations tested. Furthermore, we established the precision between multiple operators and slide staining batches and assay specificity showing zero CTCs detected in 18 healthy donor samples. In a clinical feasibility study, at least one traditional CTC/mL (CK+, CD45-, and intact nuclei) was detected in 89 % of 44 mCRPC samples, whereas 100 % of samples had CTCs enumerated if additional CTC subpopulations (CK-/CD45- and CK+ apoptotic CTCs) were included in the analysis. In addition to presenting Epic Platform's performance with respect to CTC enumeration, we provide examples of its integrated downstream capabilities, including protein biomarker expression and downstream genomic analyses at single cell resolution.

Enhanced Targeting of the EGFR Network with MM-151, an Oligoclonal Anti-EGFR Antibody Therapeutic.

Although EGFR is a validated therapeutic target across multiple cancer indications, the often modest clinical responses to current anti-EGFR agents suggest the need for improved therapeutics. Here, we demonstrate that signal amplification driven by high-affinity EGFR ligands limits the capacity of monoclonal anti-EGFR antibodies to block pathway signaling and cell proliferation and that these ligands are commonly coexpressed with low-affinity EGFR ligands in epithelial tumors. To develop an improved antibody therapeutic capable of overcoming high-affinity ligand-mediated signal amplification, we used a network biology approach comprised of signaling studies and computational modeling of receptor-antagonist interactions. Model simulations suggested that an oligoclonal antibody combination may overcome signal amplification within the EGFR:ERK pathway driven by all EGFR ligands. Based on this, we designed MM-151, a combination of three fully human IgG1 monoclonal antibodies that can simultaneously engage distinct, nonoverlapping epitopes on EGFR with subnanomolar affinities. In signaling studies, MM-151 antagonized high-affinity EGFR ligands more effectively than cetuximab, leading to an approximately 65-fold greater decrease in signal amplification to ERK. In cell viability studies, MM-151 demonstrated antiproliferative activity against high-affinity EGFR ligands, either singly or in combination, while cetuximab activity was largely abrogated under these conditions. We confirmed this finding both in vitro and in vivo in a cell line model of autocrine high-affinity ligand expression. Together, these preclinical studies provide rationale for the clinical study of MM-151 and suggest that high-affinity EGFR ligand expression may be a predictive response marker that distinguishes MM-151 from other anti-EGFR therapeutics.

Encoding NF-kappaB temporal control in response to TNF: distinct roles for the negative regulators IkappaBalpha and A20.

TNF-induced NF-kappaB activity shows complex temporal regulation whose different phases lead to distinct gene expression programs. Combining experimental studies and mathematical modeling, we identify two temporal amplification steps-one determined by the obligate negative feedback regulator IkappaBalpha-that define the duration of the first phase of NF-kappaB activity. The second phase is defined by A20, whose inducible expression provides for a rheostat function by which other inflammatory stimuli can regulate TNF responses. Our results delineate the nonredundant functions implied by the knockout phenotypes of ikappabalpha and a20, and identify the latter as a signaling cross-talk mediator controlling inflammatory and developmental responses.

A fourth IkappaB protein within the NF-kappaB signaling module.

Inflammatory NF-kappaB/RelA activation is mediated by the three canonical inhibitors, IkappaBalpha, -beta, and -epsilon. We report here the characterization of a fourth inhibitor, nfkappab2/p100, that forms two distinct inhibitory complexes with RelA, one of which mediates developmental NF-kappaB activation. Our genetic evidence confirms that p100 is required and sufficient as a fourth IkappaB protein for noncanonical NF-kappaB signaling downstream of NIK and IKK1. We develop a mathematical model of the four-IkappaB-containing NF-kappaB signaling module to account for NF-kappaB/RelA:p50 activation in response to inflammatory and developmental stimuli and find signaling crosstalk between them that determines gene-expression programs. Further combined computational and experimental studies reveal that mutant cells with altered balances between canonical and noncanonical IkappaB proteins may exhibit inappropriate inflammatory gene expression in response to developmental signals. Our results have important implications for physiological and pathological scenarios in which inflammatory and developmental signals converge.

Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses.

Dynamic properties of signaling pathways control their behavior and function. We undertook an iterative computational and experimental investigation of the dynamic properties of tumor necrosis factor (TNF)alpha-mediated activation of the transcription factor NF-kappaB. Surprisingly, we found that the temporal profile of the NF-kappaB activity is invariant to the TNFalpha dose. We reverse engineered a computational model of the signaling pathway to identify mechanisms that impart this important response characteristic, thus predicting that the IKK activity profile must transiently peak at all TNFalpha doses to generate the observed NF-kappaB dynamics. Experimental confirmation of this prediction emphasizes the importance of mechanisms that rapidly down-regulate IKK following TNFalpha activation. A refined computational model further revealed signaling characteristics that ensure robust TNFalpha-mediated cell-cell communication over considerable distances, allowing for fidelity of cellular inflammatory responses in infected tissue.

Stimulus specificity of gene expression programs determined by temporal control of IKK activity.

A small number of mammalian signaling pathways mediate a myriad of distinct physiological responses to diverse cellular stimuli. Temporal control of the signaling module that contains IkappaB kinase (IKK), its substrate inhibitor of NF-kappaB (IkappaB), and the key inflammatory transcription factor NF-kappaB can allow for selective gene activation. We have demonstrated that different inflammatory stimuli induce distinct IKK profiles, and we examined the underlying molecular mechanisms. Although tumor necrosis factor-alpha (TNFalpha)-induced IKK activity was rapidly attenuated by negative feedback, lipopolysaccharide (LPS) signaling and LPS-specific gene expression programs were dependent on a cytokine-mediated positive feedback mechanism. Thus, the distinct biological responses to LPS and TNFalpha depend on signaling pathway-specific mechanisms that regulate the temporal profile of IKK activity.