Trex1 regulates lysosomal biogenesis and interferon-independent activation of antiviral genes.

The sensing of viral nucleic acids by the innate immune system triggers the production of type I interferons, which activates interferon-stimulated genes (ISGs) and directs a multifaceted antiviral response. ISGs can also be activated through interferon-independent pathways, although the precise mechanisms remain elusive. Here we found that the cytosolic exonuclease Trex1 regulated the activation of a subset of ISGs independently of interferon. Both Trex1(-/-) mouse cells and Trex1-mutant human cells had high expression of genes encoding antiviral molecules ('antiviral genes') and were refractory to viral infection. The interferon-independent activation of antiviral genes in Trex1(-/-) cells required the adaptor STING, the kinase TBK1 and the transcription factors IRF3 and IRF7. We also found that Trex1-deficient cells had an expanded lysosomal compartment, altered subcellular localization of the transcription factor TFEB and diminished activity of the regulator mTORC1. Together our data identify Trex1 as a regulator of lysosomal biogenesis and interferon-independent activation of antiviral genes and show that dysregulation of lysosomes can elicit innate immune responses.

Multifocal radiculoneuropathy during ipilimumab treatment of melanoma.

INTRODUCTION: Ipilimumab, a monoclonal anti-CTLA-4 antibody, is used to treat melanoma. Neuromuscular side effects, possibly autoimmune, may occur. METHODS: In this investigation we undertook a retrospective review of patient records. RESULTS: After 3 doses of ipilimumab, a 31-year-old man developed asymmetric, severe weakness involving all limbs, respiration, and cranial nerves, which was progressive over 2 weeks. EMG/NCS showed an axonal polyradiculoneuropathy with multifocal motor conduction blocks. CSF protein was 749 mg/dl. Nerve pathology showed inflammation around the endoneurial microvessels and subperineurial edema and inflammation. Spine MRI showed leptomeningeal and anterior and posterior root enhancement. Strength improved slowly over months after ipilimumab discontinuation and immunomodulating treatment. CONCLUSIONS: Ipilimumab toxicity presented as a monophasic, multifocal, asymmetric polyradiculoneuropathy involving roots and peripheral and cranial nerves. Ipilimumab may produce a polyradiculoneuropathy with disruption of the blood-nerve barrier due to a microvasculopathy.

Multiscale physics of rotating detonation waves: Autosolitons and modulational instabilities.

Proposed is a phenomenological modeling framework that is capable of reproducing the diverse experimental observations of the nonlinear, combustion wave propagation in a rotating detonation engine (RDE), specifically the nucleation and formation of combustion pulses, the soliton-like interactions between these combustion fronts, and the fundamental, underlying Hopf bifurcation to time-periodic modulation of the waves. In this framework, the mode-locked structures are classified as autosolitons or stably propagating nonlinear waves where the local physics of nonlinearity, gain, and dissipation exactly balance. We find that the global dominant balance physics in the RDE combustion chamber are dissipative and multiscale in nature: The fast combustion physics provide the energy input to form the fundamental mode-locked autosoliton state, while the slow physics of exhaust and propellant recovery shape the waveform and dictate the number of autosolitons. In this manner, the global multiscale balance physics give rise to the stable structures-not exclusively the frontal dynamics prescribed by classical detonation theory. Experimental observations and numerical models of the RDE combustion chamber are in strong qualitative agreement. Moreover, numerical continuation (computational bifurcation tracking) of the RDE analog system indicates that a Hopf bifurcation of the steadily propagating pulse train leads to the fundamental instability of the RDE, or time-periodic modulation of the waves. Along branches of Hopf orbits in parameter space exist a continuum of wave-pair interactions that exhibit solitonic interactions of varying strength.

Learning dominant physical processes with data-driven balance models.

Throughout the history of science, physics-based modeling has relied on judiciously approximating observed dynamics as a balance between a few dominant processes. However, this traditional approach is mathematically cumbersome and only applies in asymptotic regimes where there is a strict separation of scales in the physics. Here, we automate and generalize this approach to non-asymptotic regimes by introducing the idea of an equation space, in which different local balances appear as distinct subspace clusters. Unsupervised learning can then automatically identify regions where groups of terms may be neglected. We show that our data-driven balance models successfully delineate dominant balance physics in a much richer class of systems. In particular, this approach uncovers key mechanistic models in turbulence, combustion, nonlinear optics, geophysical fluids, and neuroscience.

Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, oncogenesis, and HER2 inhibitor sensitivity.

Activating mutations in HER2 (ERBB2) drive the growth of a subset of breast and other cancers and tend to co-occur with HER3 (ERBB3) missense mutations. The HER2 tyrosine kinase inhibitor neratinib has shown clinical activity against HER2-mutant tumors. To characterize the role of HER3 mutations in HER2-mutant tumors, we integrate computational structural modeling with biochemical and cell biological analyses. Computational modeling predicts that the frequent HER3E928G kinase domain mutation enhances the affinity of HER2/HER3 and reduces binding of HER2 to its inhibitor neratinib. Co-expression of mutant HER2/HER3 enhances HER2/HER3 co-immunoprecipitation and ligand-independent activation of HER2/HER3 and PI3K/AKT, resulting in enhanced growth, invasiveness, and resistance to HER2-targeted therapies, which can be reversed by combined treatment with PI3Kα inhibitors. Our results provide a mechanistic rationale for the evolutionary selection of co-occurring HER2/HER3 mutations and the recent clinical observations that HER3 mutations are associated with a poor response to neratinib in HER2-mutant cancers.

Mode-locked rotating detonation waves: Experiments and a model equation.

Direct observation of a rotating detonation engine combustion chamber has enabled the extraction of the kinematics of its detonation waves. These records exhibit a rich set of instabilities and bifurcations arising from the interaction of coherent wave fronts and global gain dynamics. We develop a model of the observed dynamics by recasting the Majda detonation analog as an autowave process. The solution fronts become attractors of the engine, i.e., mode-locked rotating detonation waves. We find that denotative energy release competes with dissipation and gain recovery to produce the observed dynamics and a bifurcation structure common to other driven-dissipative systems, such as mode-locked lasers.

Hyperactivation of TORC1 Drives Resistance to the Pan-HER Tyrosine Kinase Inhibitor Neratinib in HER2-Mutant Cancers.

We developed neratinib-resistant HER2-mutant cancer cells by gradual dose escalation. RNA sequencing identified TORC1 signaling as an actionable mechanism of drug resistance. Primary and acquired neratinib resistance in HER2-mutant breast cancer patient-derived xenografts (PDXs) was also associated with TORC1 hyperactivity. Genetic suppression of RAPTOR or RHEB ablated P-S6 and restored sensitivity to the tyrosine kinase inhibitor. The combination of the TORC1 inhibitor everolimus and neratinib potently arrested the growth of neratinib-resistant xenografts and organoids established from neratinib-resistant PDXs. RNA and whole-exome sequencing revealed RAS-mediated TORC1 activation in a subset of neratinib-resistant models. DNA sequencing of HER2-mutant tumors clinically refractory to neratinib, as well as circulating tumor DNA profiling of patients who progressed on neratinib, showed enrichment of genomic alterations that converge to activate the mTOR pathway.

Encephalopathy induced by Alzheimer brain inoculation in a non-human primate.

Alzheimer's disease is characterized by cognitive alterations, cerebral atrophy and neuropathological lesions including neuronal loss, accumulation of misfolded and aggregated ß-amyloid peptides (Aß) and tau proteins. Iatrogenic induction of Aß is suspected in patients exposed to pituitary-derived hormones, dural grafts, or surgical instruments, presumably contaminated with Aß. Induction of Aß and tau lesions has been demonstrated in transgenic mice after contamination with Alzheimer's disease brain homogenates, with very limited functional consequences. Unlike rodents, primates naturally express Aß or tau under normal conditions and attempts to transmit Alzheimer pathology to primates have been made for decades. However, none of earlier studies performed any detailed functional assessments. For the first time we demonstrate long term memory and learning impairments in a non-human primate (Microcebus murinus) following intracerebral injections with Alzheimer human brain extracts. Animals inoculated with Alzheimer brain homogenates displayed progressive cognitive impairments (clinical tests assessing cognitive and motor functions), modifications of neuronal activity (detected by electroencephalography), widespread and progressive cerebral atrophy (in vivo MRI assessing cerebral volume loss using automated voxel-based analysis), neuronal loss in the hippocampus and entorhinal cortex (post mortem stereology). They displayed parenchymal and vascular Aß depositions and tau lesions for some of them, in regions close to the inoculation sites. Although these lesions were sparse, they were never detected in control animals. Tau-positive animals had the lowest performances in a memory task and displayed the greatest neuronal loss. Our study is timely and important as it is the first one to highlight neuronal and clinical dysfunction following inoculation of Alzheimer's disease brain homogenates in a primate. Clinical signs in a chronic disease such as Alzheimer take a long time to be detectable. Documentation of clinical deterioration and/or dysfunction following intracerebral inoculations with Alzheimer human brain extracts could lead to important new insights about Alzheimer initiation processes.

Available sight distance on existing highways: Meeting stopping sight distance requirements of an aging population.

An important element of highway design is ensuring that the available sight distance (ASD) on a highway meets driver needs. For instance, if the ASD at any point on a highway is less than the distance required to come to a complete stop after seeing a hazard (i.e. Stopping Sight Distance (SSD)), the driver will not be able to stop in time to avoid a collision. SSD is function of a number of variables which vary depending on the driver, the vehicle driven and surface conditions; examples of such variables include a driver's perception reaction time or PRT (i.e. the time required by the driver to perceive and react to a hazard) and the deceleration rate of the vehicle. Most design guides recommend deterministic values for PRT and deceleration rates. Although these values may serve the needs of the average driver, they may not satisfy the needs of drivers with limited abilities. In other words, even if the ASD exceeds required SSD defined in the design guide, it might not always satisfy the needs of all drivers. While it is impossible to design roads that satisfy the needs of all drivers, the fact that most developed countries suffer from an aging population, means that the number of old drivers on our roads is expected to increase. Since a large proportion of old drivers often have limited abilities, it is expected that the general population of drivers with limited abilities on our roads will increase with time. Accordingly, more efforts are required to ensure that existing road infrastructure is prepared to handle such a change. This paper aims to explore the extent to which ASD on highways satisfies the needs of drivers with limited abilities. The paper first develops MATLAB and Python codes to automatically estimate the ASD on highway point cloud data collected using Light Detection and Ranging (LiDAR) remote sensing technology. The developed algorithms are then used to estimate ASD on seven different crash prone segments in the Province of Alberta, Canada and the ASD is compared to the required SSD on each highway. Three different levels of SSD are defined (SSD for drivers with limited ability, AASHTOs SSD requirements and SSD for drivers with high skill). The results show that, when compared to SSD requirements which integrate limitations in cognitive abilities, a substantial portion of the analyzed segments do not meet the requirements (up to 20%). Similarly, when compared to AASHTO's SSD requirements, up to 6% of the analyzed segments do not meet the requirements. In an attempt to explore the effects of such design limitations on safety, the paper also explores crash rates in noncompliant regions (i.e. regions that do not provide sufficient SSD) and compares them to crash rates in compliant regions. On average, it was found that noncompliant regions experience crash rates that are 2.15 and 1.25 times higher than compliant regions for AASHTO's SSD requirements and those integrating driver limitations, respectively. Furthermore, the study found that a significantly higher proportion of drivers involved in collisions in the noncompliant regions were old drivers.

A Comparison of the Assay Sensitivity of Average and Worst Pain Intensity in Pharmacologic Trials: An ACTTION Systematic Review and Meta-Analysis.

Identifying methods to improve assay sensitivity in randomized clinical trials (RCTs) may facilitate the discovery of efficacious pain treatments. RCTs evaluating pain treatments typically use average pain intensity (API) or worst pain intensity (WPI) as the primary efficacy outcome. However, little evidence is available comparing the assay sensitivity of these 2 measures. In this systematic review and meta-analysis, we comprehensively reviewed all low back pain, osteoarthritis pain, fibromyalgia, diabetic peripheral neuropathy pain, and postherpetic neuralgia RCTs that used a parallel group design. Eligibility required: 1) primary RCT report published between 1980 and 2016, 2) comparing 1 or more active, efficacious pharmacologic pain treatment(s) with placebo, and 3) providing data on the standardized effect size (SES) for API as well as WPI for all treatment arms. Twenty-seven active versus placebo comparisons were identified in 23 eligible articles. Using a random-effects meta-analysis, API SES and WPI SES did not differ significantly (difference = -.021, 95% confidence interval = -.047 to .004, P = .12). The findings indicate that, depending on the objectives of the study, either API or WPI could be used as a primary outcome measure in clinical trials for the chronic pain conditions included in this analysis. PERSPECTIVE: Understanding the comparative assay sensitivity of API and WPI may advance pain treatment research. A meta-analysis of trials of efficacious pharmacologic treatments in 5 pain conditions did not show a statistically significant difference between the assay sensitivity of API and WPI.

Interpretation of CIs in clinical trials with non-significant results: systematic review and recommendations.

OBJECTIVES: Interpretation of CIs in randomised clinical trials (RCTs) with treatment effects that are not statistically significant can distinguish between results that are 'negative' (the data are not consistent with a clinically meaningful treatment effect) or 'inconclusive' (the data remain consistent with the possibility of a clinically meaningful treatment effect). This interpretation is important to ensure that potentially beneficial treatments are not prematurely abandoned in future research or clinical practice based on invalid conclusions. DESIGN: Systematic review of RCT reports published in 2014 in Annals of Internal Medicine, New England Journal of Medicine, JAMA, JAMA Internal Medicine and The Lancet (n=247). RESULTS: 85 of 99 articles with statistically non-significant results reported CIs for the treatment effect. Only 17 of those 99 articles interpreted the CI. Of the 22 articles in which CIs indicated an inconclusive result, only four acknowledged that the study could not rule out a clinically meaningful treatment effect. CONCLUSIONS: Interpretation of CIs is important but occurs infrequently in study reports of trials with treatment effects that are not statistically significant. Increased author interpretation of CIs could improve application of RCT results. Reporting recommendations are provided.

An Acquired HER2T798I Gatekeeper Mutation Induces Resistance to Neratinib in a Patient with HER2 Mutant-Driven Breast Cancer.

We report a HER2T798I gatekeeper mutation in a patient with HER2L869R-mutant breast cancer with acquired resistance to neratinib. Laboratory studies suggested that HER2L869R is a neratinib-sensitive, gain-of-function mutation that upon dimerization with mutant HER3E928G, also present in the breast cancer, amplifies HER2 signaling. The patient was treated with neratinib and exhibited a sustained partial response. Upon clinical progression, HER2T798I was detected in plasma tumor cell-free DNA. Structural modeling of this acquired mutation suggested that the increased bulk of isoleucine in HER2T798I reduces neratinib binding. Neratinib blocked HER2-mediated signaling and growth in cells expressing HER2L869R but not HER2L869R/T798I In contrast, afatinib and the osimertinib metabolite AZ5104 strongly suppressed HER2L869R/T798I-induced signaling and cell growth. Acquisition of HER2T798I upon development of resistance to neratinib in a breast cancer with an initial activating HER2 mutation suggests HER2L869R is a driver mutation. HER2T798I-mediated neratinib resistance may be overcome by other irreversible HER2 inhibitors like afatinib.Significance: We found an acquired HER2 gatekeeper mutation in a patient with HER2-mutant breast cancer upon clinical progression on neratinib. We speculate that HER2T798I may arise as a secondary mutation following response to effective HER2 tyrosine kinase inhibitors (TKI) in other cancers with HER2-activating mutations. This resistance may be overcome by other irreversible HER2 TKIs, such as afatinib. Cancer Discov; 7(6); 575-85. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 539.

Extracellular Matrix/Integrin Signaling Promotes Resistance to Combined Inhibition of HER2 and PI3K in HER2+ Breast Cancer.

PIK3CA mutations are associated with resistance to HER2-targeted therapies. We previously showed that HER2+/PIK3CAH1047R transgenic mammary tumors are resistant to the HER2 antibodies trastuzumab and pertuzumab but respond to PI3K inhibitor buparlisib (TPB). In this study, we identified mechanisms of resistance to combined inhibition of HER2 and PI3K. TPB-resistant tumors were generated by treating HER2+/PIK3CAH1047R tumor-bearing mice long term with the drug combination. RNA sequencing of TPB-resistant tumors revealed that extracellular matrix and cell adhesion genes, including collagen II (Col2a1), were markedly upregulated, accompanied by activation of integrin ß1/Src. Cells derived from drug-resistant tumors were sensitive to TBP when grown in vitro, but exhibited resistance when plated on collagen or when reintroduced into mice. Drug resistance was partially reversed by the collagen synthesis inhibitor ethyl-3,4-dihydroxybenzoate. Inhibition of integrin ß1/Src blocked collagen-induced resistance to TPB and inhibited growth of drug-resistant tumors. High collagen II expression was associated with significantly lower clinical response to neoadjuvant anti-HER2 therapy in HER2+ breast cancer patients. Overall, these data suggest that upregulation of collagen/integrin/Src signaling contributes to resistance to combinatorial HER2 and PI3K inhibition. Cancer Res; 77(12); 3280-92. ©2017 AACR.

HER2-Overexpressing Breast Cancers Amplify FGFR Signaling upon Acquisition of Resistance to Dual Therapeutic Blockade of HER2.

Purpose: Dual blockade of HER2 with trastuzumab and lapatinib or pertuzumab has been shown to be superior to single-agent trastuzumab. However, a significant fraction of HER2-overexpressing (HER2+) breast cancers escape from these drug combinations. In this study, we sought to discover the mechanisms of acquired resistance to the combination of lapatinib + trastuzumab.Experimental Design: HER2+ BT474 xenografts were treated with lapatinib + trastuzumab long-term until resistance developed. Potential mechanisms of acquired resistance were evaluated in lapatinib + trastuzumab-resistant (LTR) tumors by targeted capture next-generation sequencing. In vitro experiments were performed to corroborate these findings, and a novel drug combination was tested against LTR xenografts. Gene expression and copy-number analyses were performed to corroborate our findings in clinical samples.Results: LTR tumors exhibited an increase in FGF3/4/19 copy number, together with an increase in FGFR phosphorylation, marked stromal changes in the tumor microenvironment, and reduced tumor uptake of lapatinib. Stimulation of BT474 cells with FGF4 promoted resistance to lapatinib + trastuzumab in vitro Treatment with FGFR tyrosine kinase inhibitors reversed these changes and overcame resistance to lapatinib + trastuzumab. High expression of FGFR1 correlated with a statistically shorter progression-free survival in patients with HER2+ early breast cancer treated with adjuvant trastuzumab. Finally, FGFR1 and/or FGF3 gene amplification correlated with a lower pathologic complete response in patients with HER2+ early breast cancer treated with neoadjuvant anti-HER2 therapy.Conclusions: Amplification of FGFR signaling promotes resistance to HER2 inhibition, which can be diminished by the combination of HER2 and FGFR inhibitors. Clin Cancer Res; 23(15); 4323-34. ©2017 AACR.

Treatment of Triple-Negative Breast Cancer with TORC1/2 Inhibitors Sustains a Drug-Resistant and Notch-Dependent Cancer Stem Cell Population.

Approximately 30% of triple-negative breast cancers (TNBC) harbor molecular alterations in PI3K/mTOR signaling, but therapeutic inhibition of this pathway has not been effective. We hypothesized that intrinsic resistance to TORC1/2 inhibition is driven by cancer stem cell (CSC)-like populations that could be targeted to enhance the antitumor action of these drugs. Therefore, we investigated the molecular mechanisms by which PI3K/mTOR inhibitors affect the stem-like properties of TNBC cells. Treatment of established TNBC cell lines with a PI3K/mTOR inhibitor or a TORC1/2 inhibitor increased the expression of CSC markers and mammosphere formation. A CSC-specific PCR array revealed that inhibition of TORC1/2 increased FGF1 and Notch1 expression. Notch1 activity was also induced in TNBC cells treated with TORC1/2 inhibitors and associated with increased mitochondrial metabolism and FGFR1 signaling. Notably, genetic and pharmacologic blockade of Notch1 abrogated the increase in CSC markers, mammosphere formation, and in vivo tumor-initiating capacity induced by TORC1/2 inhibition. These results suggest that targeting the FGFR-mitochondrial metabolism-Notch1 axis prevents resistance to TORC1/2 inhibitors by eradicating drug-resistant CSCs in TNBC, and may thus represent an attractive therapeutic strategy to improve drug responsiveness and efficacy.

Unmet visual needs of Alzheimer's disease patients in long-term care facilities.

INTRODUCTION: The purpose of this study was to determine the prevalence of uncorrected visual disorders in nursing home patients with Alzheimer's disease (AD) and to determine whether appropriate corrective measures were taken by nursing home staff. This study was conducted at 2 community nursing homes in the St Louis area. Whereas previous studies have shown that visual impairment is common among all residents of nursing facilities, our study was focused specifically on residents with AD. This population is less able to effectively express needs and more likely to endure unaddressed visual deficits. For AD patients, it is important to offer appropriate corrective remedies in order to maintain as much functional independence as possible. METHODS: A retrospective cohort study was conducted in 2 private, skilled nursing facilities in St Louis County thought to be representative of community nursing homes in the United States. All subjects were patients with a diagnosis of dementia of probable AD. Demographic information collected included age, sex, and race. Mini-Mental State Examination scores were also obtained. The patients, their families, and nursing staff were interviewed to determine the patients' visual history, corrective measures, and the usage of corrective eyewear before and after admission to the nursing homes. The data were summarized to demonstrate how many patients suffered from uncorrected errors of refraction and what factors contributed to their visual status. RESULTS: Of the total of 85 patients included in the study, 80 (94.1%) required glasses for correction of presbyopia, myopia, or both. However, 25 of the 80 residents had not actively been using glasses since entering the nursing home. Of these 25 residents not wearing proper eyewear, 9 residents were too cognitively impaired to request them, 8 residents had broken or misplaced them, and 8 residents had prescriptions that were no longer sufficient to correct their vision. DISCUSSION: Our study found that nearly one third of the visually impaired nursing home residents with AD (25 of 80 patients) were not using their required eyewear. These 25 patients were the population of most interest because they were most likely to benefit from intervention. Many of these patients were not using glasses because they had been lost, damaged, or were no longer sufficient to correct their vision. CONCLUSIONS: We have presented 3 recommendations intended to prevent uncorrected visual acuity in nursing home residents with dementia: (1) Label eyewear in appropriate patient populations to provide rapid identification in the event of misplacement, (2) recommend that an extra pair of glasses be made available if the current pair would be lost or damaged, and (3) ensure that all residents have annual or biannual eye exams. If adequate steps are taken to prevent unnecessary visual impairment in AD patients, it would limit their dependence on others, reduce the burden on nursing staff, and improve the patients' overall quality of life.

Effects of the cannabinoid antagonists AM281 and AM630 on deprivation-induced intake in Lewis rats.

Male Lewis rats (two groups of 10) received intracerebroventricular injections of either AM 630 (vehicle, 2.5, 5, 10 and 20 microg) or AM 281 (vehicle, 5, 10, 20 and 40 microg) following overnight food deprivation. The CB2 antagonist AM 630 failed to block deprivation-induced intake at 0.5, 1, 2, 4 and 6 h. The CB1 antagonist AM 281 significantly blocked intake following 20 microg (1 h) and 40 microg (1, 2, 4 and 6 h). Results are discussed with respect to cannabinoid receptor systems' involvement in ingestion and the differential pharmacological profiles of AM 630 and AM 281.