Pan-Cancer, Genome-Scale Metabolic Network Analysis of over 10,000 Patients Elucidates Relationship between Metabolism and Survival.

Despite the high variability in cancer biology, cancers nevertheless exhibit cohesive hallmarks across multiple cancer types, notably dysregulated metabolism. Metabolism plays a central role in cancer biology, and shifts in metabolic pathways have been linked to tumor aggressiveness and likelihood of response to therapy. We therefore sought to interrogate metabolism across cancer types and understand how intrinsic modes of metabolism vary within and across indications and how they relate to patient prognosis. We used context specific genome-scale metabolic modeling to simulate metabolism across 10,915 patients from 34 cancer types from The Cancer Genome Atlas and the MMRF-COMMPASS study. We found that cancer metabolism clustered into modes characterized by differential glycolysis, oxidative phosphorylation, and growth rate. We also found that the simulated activities of metabolic pathways are intrinsically prognostic across cancer types, especially tumor growth rate, fatty acid biosynthesis, folate metabolism, oxidative phosphorylation, steroid metabolism, and glutathione metabolism. This work shows the prognostic power of individual patient metabolic modeling across multiple cancer types. Additionally, it shows that analyzing large-scale models of cancer metabolism with survival information provides unique insights into underlying relationships across cancer types and suggests how therapies designed for one cancer type may be repurposed for use in others.

Validation of a parameterized, open-source model of nerve stimulation.

Peripheral nerve stimulation is an effective treatment for various neurological disorders. The method of activation and stimulation parameters used impact the efficacy of the therapy, which emphasizes the need for tools to model this behavior. Computational modeling of nerve stimulation has proven to be a useful tool for estimating stimulation thresholds, optimizing electrode design, and exploring previously untested stimulation methods. Despite their utility, these tools require access to and familiarity with several pieces of specialized software. A simpler, streamlined process would increase accessibility significantly. We developed an open-source, parameterized model with a simple online user interface that allows user to adjust up to 36 different parameters (https://nervestimlab.utdallas.edu). The model accurately predicts fiber activation thresholds for nerve and electrode combinations reported in literature. Additionally, it replicates characteristic differences between stimulation methods, such as lower thresholds with monopolar stimulation as compared to tripolar stimulation. The model predicted that the difference in threshold between monophasic and biphasic waveforms, a well-characterized phenomenon, is not present during stimulation with bipolar electrodes.In vivotesting on the rat sciatic nerve validated this prediction, which has not been previously reported. The accuracy of the model when compared to previous experiments, as well as the ease of use and accessibility to generate testable hypotheses, indicate that this software may represent a useful tool for a variety of nerve stimulation applications.

Parametric characterization of the rat Hering-Breuer reflex evoked with implanted and non-invasive vagus nerve stimulation.

Vagus nerve stimulation (VNS) has rapidly gained interest as a treatment for a variety of disorders. A number of methods have been employed to stimulate the vagus nerve, but the most common relies on a cuff electrode implanted around the cervical branch of the nerve. Recently, two non-invasive methods have increased in popularity: transcutaneous cervical VNS (tcVNS) and transcutaneous auricular VNS (taVNS). Despite promising clinical results, there has been little direct comparison of these methods to stimulation delivered via an implanted device. In this study, we directly compared both non-invasive strategies to stimulation with an implanted cuff electrode on activation of the Hering-Breuer (HB) reflex, a non-invasive biomarker of A-fiber activation in the vagus. Stimulation was delivered across a wide range of parameters using tcVNS, taVNS, and an implanted cuff electrode in female rats. Activation of the HB reflex, changes in heart rate, and neck muscle twitch force were recorded. Consistent with low thresholds reported in previous studies, we found that the threshold to activate the HB reflex using an implanted cuff electrode was 0.406 ± 0.066 mA. tcVNS was capable of activating the HB reflex, but the threshold was 34.18 ± 1.86 mA, over 15 fold higher than the stimulation intensity that caused twitching of the neck muscles (2.09 ± 0.16 mA). No activation of the HB reflex was observed with taVNS at any parameters. These results describe activation of the HB reflex with each strategy and provide initial evidence regarding differences in the activation of the vagus nerve with invasive and non-invasive methods.

Acute Cardiovascular Responses to Vagus Nerve Stimulation after Experimental Spinal Cord Injury.

Pairing vagus nerve stimulation (VNS) with rehabilitation has emerged as a potential strategy to enhance plasticity and improve recovery in a range of neurological disorders. A recent study highlights the therapeutic promise of VNS in promoting motor recovery after spinal cord injury (SCI). We investigated the safety of acute VNS in a rat model of chronic SCI. We measured the cardiovascular response to various VNS paradigms following chronic high-thoracic SCI that is known to deleteriously impact cardiovascular control. Dose-response experiments with continuous VNS revealed an SCI-dependent increase in sensitivity for heart rate (HR) and blood pressure (BP) compared with controls. A clinically relevant intermittent VNS resulted in transient reduction in HR in rats with SCI; however, BP remained unaltered. In all experiments, the effect lasted only while the VNS stimulus train was present, as HR and BP restored to baseline values as soon as VNS ended. No prolonged episodes of persisting hypotension were seen in either group. Further, VNS did not trigger autonomic dysreflexia or exacerbate the severity of autonomic dysreflexia when induced during or after stimulation sessions. Overall, these findings provide initial evidence that intermittent VNS at parameters used for targeted plasticity therapy (30 Hz, 0.8 mA) appears safe and supports further investigation of this potential therapy for use following SCI.

Efficient parameters of vagus nerve stimulation to enhance extinction learning in an extinction-resistant rat model of PTSD.

Vagus nerve stimulation (VNS) has shown promise as an adjuvant treatment for posttraumatic stress disorder (PTSD), as it enhances fear extinction and reduces anxiety symptoms in multiple rat models of this condition. Yet, identification of the optimal stimulation paradigm is needed to facilitate clinical translation of this potential therapy. Using an extinction-resistant rat model of PTSD, we tested whether varying VNS intensity and duration could maximize extinction learning while minimizing the total amount of stimulation. We confirmed that sham rats failed to extinguish after a week of extinction training. Delivery of the standard LONG VNS trains (30 s) at 0.4 mA enhanced extinction and reduced anxiety but did not prevent fear return. Increasing the intensity of LONG VNS trains to 0.8 mA prevented fear return and attenuated anxiety symptoms. Interestingly, delivering 1, 4 or 16 SHORT VNS bursts (0.5 s) at 0.8 mA during each cue presentation in extinction training also enhanced extinction. LONG VNS trains or multiple SHORT VNS bursts at 0.8 mA attenuated fear renewal and reinstatement, promoted extinction generalization and reduced generalized anxiety. Delivering 16 SHORT VNS bursts also facilitated extinction in fewer trials. This study provides the first evidence that brief bursts of VNS can enhance extinction training, reduce relapse and support symptom remission using much less VNS than previous protocols. These findings suggest that VNS parameters can be adjusted in order to minimize total charge delivery and maximize therapeutic effectiveness.

Flat electrode contacts for vagus nerve stimulation.

The majority of available systems for vagus nerve stimulation use helical stimulation electrodes, which cover the majority of the circumference of the nerve and produce largely uniform current density within the nerve. Flat stimulation electrodes that contact only one side of the nerve may provide advantages, including ease of fabrication. However, it is possible that the flat configuration will yield inefficient fiber recruitment due to a less uniform current distribution within the nerve. Here we tested the hypothesis that flat electrodes will require higher current amplitude to activate all large-diameter fibers throughout the whole cross-section of a nerve than circumferential designs. Computational modeling and in vivo experiments were performed to evaluate fiber recruitment in different nerves and different species using a variety of electrode designs. Initial results demonstrated similar fiber recruitment in the rat vagus and sciatic nerves with a standard circumferential cuff electrode and a cuff electrode modified to approximate a flat configuration. Follow up experiments comparing true flat electrodes to circumferential electrodes on the rabbit sciatic nerve confirmed that fiber recruitment was equivalent between the two designs. These findings demonstrate that flat electrodes represent a viable design for nerve stimulation that may provide advantages over the current circumferential designs for applications in which the goal is uniform activation of all fascicles within the nerve.

Protocol for Construction of Rat Nerve Stimulation Cuff Electrodes.

Peripheral nerve stimulation has emerged as a platform therapy to treat a wide range of disorders. Continued development and translation of these strategies requires that researchers have access to reliable, customizable electrodes for nerve stimulation. Here, we detail procedures to build three different configurations of cuff electrodes with varying numbers and orientations of contacts for nerve stimulation in rats. These designs are built with simple, widely available materials, using platinum-iridium electrodes assembled into polyurethane tubing. Moreover, the designs can easily be customized to increase versatility and individualize for specific stimulation applications. This protocol provides a resource to facilitate the construction and customization of stimulation cuffs to support preclinical nerve stimulation research.

ReStore: A wireless peripheral nerve stimulation system.

BACKGROUND: The growing use of neuromodulation techniques to treat neurological disorders has motivated efforts to improve on the safety and reliability of implantable nerve stimulators. NEW METHOD: The present study describes the ReStore system, a miniature, implantable wireless nerve stimulator system that has no battery or leads and is constructed using commercial components and processes. The implant can be programmed wirelessly to deliver charge-balanced, biphasic current pulses of varying amplitudes, pulse widths, frequencies, and train durations. Here, we describe bench and in vivo testing to evaluate the operational performance and efficacy of nerve recruitment. Additionally, we also provide results from a large-animal chronic active stimulation study assessing the long-term biocompatibility of the device. RESULTS: The results show that the system can reliably deliver accurate stimulation pulses through a range of different loads. Tests of nerve recruitment demonstrate that the implant can effectively activate peripheral nerves, even after accelerated aging and post-chronic implantation. Biocompatibility and hermeticity tests provide an initial indication that the implant will be safe for use in humans. COMPARISON WITH EXISTING METHOD(S): Most commercially available nerve stimulators include a battery and wire leads which often require subsequent surgeries to address failures in these components. Though miniaturized battery-less stimulators have been prototyped in academic labs, they are often constructed using custom components and processes that hinder clinical translation. CONCLUSIONS: The results from testing the performance and safety of the ReStore system establish its potential to advance the field of peripheral neuromodulation.