NeuroBooster Array: A Genome-Wide Genotyping Platform to Study Neurological Disorders Across Diverse Populations.

BACKGROUND: Commercial genome-wide genotyping arrays have historically neglected coverage of genetic variation across populations. OBJECTIVE: We aimed to create a multi-ancestry genome-wide array that would include a wide range of neuro-specific genetic content to facilitate genetic research in neurological disorders across multiple ancestral groups, fostering diversity and inclusivity in research studies. METHODS: We developed the Illumina NeuroBooster Array (NBA), a custom high-throughput and cost-effective platform on a backbone of 1,914,934 variants from the Infinium Global Diversity Array and added custom content comprising 95,273 variants associated with more than 70 neurological conditions or traits, and we further tested its performance on more than 2000 patient samples. This novel platform includes approximately 10,000 tagging variants to facilitate imputation and analyses of neurodegenerative disease-related genome-wide association study loci across diverse populations. RESULTS: In this article, we describe NBA's potential as an efficient means for researchers to assess known and novel disease genetic associations in a multi-ancestry framework. The NBA can identify rare genetic variants and accurately impute more than 15 million common variants across populations. Apart from enabling sample prioritization for further whole-genome sequencing studies, we envisage that NBA will play a pivotal role in recruitment for interventional studies in the precision medicine space. CONCLUSIONS: From a broader perspective, the NBA serves as a promising means to foster collaborative research endeavors in the field of neurological disorders worldwide. Ultimately, this carefully designed tool is poised to make a substantial contribution to uncovering the genetic etiology underlying these debilitating conditions. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Cycles of self-reported seizure likelihood correspond to yield of diagnostic epilepsy monitoring.

OBJECTIVE: Video-electroencephalography (vEEG) is an important component of epilepsy diagnosis and management. Nevertheless, inpatient vEEG monitoring fails to capture seizures in up to one third of patients. We hypothesized that personalized seizure forecasts could be used to optimize the timing of vEEG. METHODS: We used a database of ambulatory vEEG studies to select a cohort with linked electronic seizure diaries of more than 20 reported seizures over at least 8 weeks. The total cohort included 48 participants. Diary seizure times were used to detect individuals' multiday seizure cycles and estimate times of high seizure risk. We compared whether estimated seizure risk was significantly different between conclusive and inconclusive vEEGs, and between vEEG with and without recorded epileptic activity. vEEGs were conducted prior to self-reported seizures; hence, the study aimed to provide a retrospective proof of concept that cycles of seizure risk were correlated with vEEG outcomes. RESULTS: Estimated seizure risk was significantly higher for conclusive vEEGs and vEEGs with epileptic activity. Across all cycle strengths, the average time in high risk during vEEG was 29.1% compared with 14% for the conclusive/inconclusive groups and 32% compared to 18% for the epileptic activity/no epileptic activity groups. On average, 62.5% of the cohort showed increased time in high risk during their previous vEEG when epileptic activity was recorded (compared to 28% of the cohort where epileptic activity was not recorded). For conclusive vEEGs, 50% of the cohort had increased time in high risk, compared to 21.5% for inconclusive vEEGs. SIGNIFICANCE: Although retrospective, this study provides a proof of principle that scheduling monitoring times based on personalized seizure risk forecasts can improve the yield of vEEG. Forecasts can be developed at low cost from mobile seizure diaries. A simple scheduling tool to improve diagnostic outcomes may reduce cost and risks associated with delayed or missed diagnosis in epilepsy.

Proceedings of the 2020 Epilepsy Foundation Pipeline Conference: Emerging Drugs and Devices.

From August 27-28, 2020 the Epilepsy Foundation hosted the Pipeline Conference, exploring emerging issues related to antiepileptic drug and device development. The conference featured epilepsy therapeutic companies and academic laboratories developing drugs for focal epilepsies, innovations for rare and ultra-rare diseases, and devices both in clinical trials and approved for use. In this paper, we outline the virtual presentations by the authors, including novel data from their development pipeline.

Forecasting cycles of seizure likelihood.

OBJECTIVE: Seizure unpredictability is rated as one of the most challenging aspects of living with epilepsy. Seizure likelihood can be influenced by a range of environmental and physiological factors that are difficult to measure and quantify. However, some generalizable patterns have been demonstrated in seizure onset. A majority of people with epilepsy exhibit circadian rhythms in their seizure times, and many also show slower, multiday patterns. Seizure cycles can be measured using a range of recording modalities, including self-reported electronic seizure diaries. This study aimed to develop personalized forecasts from a mobile seizure diary app. METHODS: Forecasts based on circadian and multiday seizure cycles were tested pseudoprospectively using data from 50 app users (mean of 109 seizures per subject). Individuals' strongest cycles were estimated from their reported seizure times and used to derive the likelihood of future seizures. The forecasting approach was validated using self-reported events and electrographic seizures from the Neurovista dataset, an existing database of long-term electroencephalography that has been widely used to develop forecasting algorithms. RESULTS: The validation dataset showed that forecasts of seizure likelihood based on self-reported cycles were predictive of electrographic seizures for approximately half the cohort. Forecasts using only mobile app diaries allowed users to spend an average of 67.1% of their time in a low-risk state, with 14.8% of their time in a high-risk warning state. On average, 69.1% of seizures occurred during high-risk states and 10.5% of seizures occurred in low-risk states. SIGNIFICANCE: Seizure diary apps can provide personalized forecasts of seizure likelihood that are accurate and clinically relevant for electrographic seizures. These results have immediate potential for translation to a prospective seizure forecasting trial using a mobile diary app. It is our hope that seizure forecasting apps will one day give people with epilepsy greater confidence in managing their daily activities.

Proceedings of the 15th Antiepileptic Drug and Device Trials Meeting: State of the Science.

On May 22-24, 2019, the 15th Antiepileptic Drug and Device (AEDD) Trials Conference was held, which focused on current issues related to AEDD development from preclinical models to clinical prognostication. The conference featured regulatory agencies, academic laboratories, and healthcare companies involved in emerging epilepsy therapies and research. The program included discussions around funding and support for investigations in epilepsy and neurologic research, clinical trial design and integrated outcome measures for people with epilepsy, and drug development and upcoming disease-modifying therapies. Finally, the conference included updates from the preclinical, clinical, and device pipeline. Summaries of the talks are provided in this paper, with the various pipeline therapeutics in the listed tables to be outlined in a subsequent publication.

Patient and caregiver preferences for the potential benefits and risks of a seizure forecasting device: A best-worst scaling.

BACKGROUND: Epilepsy is the 4th most common neurological disorder and is characterized by recurrent, unpredictable seizures. The ability to forecast seizures is a significant unmet need and would have a transformative effect on the lives of people living with epilepsy. In an effort to address this need, the Epilepsy Foundation has committed effort and resources to promote the development of seizure forecasting devices (SFD). OBJECTIVE: To promote user-centered design of future SFD, we sought to quantify patient and caregiver preferences for the potential benefits and risks of SFD. METHODS: A community-centered approach was used to develop a survey incorporating a novel best-worst scaling (BWS) to assess preferences for SFD. A main-effect orthogonal array was used to design and generate 18 "prototypes" that systematically varied across six attributes: seizure forecasting probability, seizure forecasting range, inaccuracy of forecasting, amount of time required to use the device, how the device is worn, and cost. The dependent variable was the attributes that respondents selected the best and worst in each profile, and a choice model was estimated using conditional logistic regression, which was also stratified and compared across patients and caregivers. Respondents also indicated that they would accept each of the prototype SFDs if it were real. These acceptance data and net monetary benefits (relative to the least preferred SFD) were explored. RESULTS: There were 633 eligible respondents; 493 (78%) completed at least one task. Responses indicated that 346 (68%) had epilepsy, and 147 (29%) were primary caregivers or family members of someone with epilepsy. The data show that short forecasting range is the most favored among experimental attributes, followed by mid forecasting range and notification of high chance of seizure. Having the device implanted is the least favorable attribute. Stated preferences differed between patients and caregivers (p < 0.001) for range of forecasting and inaccuracy of device. Caregivers preferred any range of forecasting, regardless of length, more than patients. Patients cared less about inaccuracy of the device compared to caregivers. The groups also differ in impact of fear of having seizures (versus actually having seizures) (p = 0.034) and on device acceptance. The acceptance of devices ranged from 42.3% to 95%, with caregivers being more likely to use a device (p < 0.05) for the majority of device profiles. Acceptance of devices varied with net monetary benefit of the best device being $717.44 more per month relative to the least preferred device. CONCLUSION: Our finding extends previous calls for seizure forecasting devices by demonstrating the value that they might provide to patients and caregivers affected by epilepsy and the feature that might be most and least desirable. In addition to guiding device development, the data can help inform regulatory decisions makers.

Opportunities for epilepsy: Outcomes of the Milken Institute State of the Science Retreat.

The Milken Institute Center for Strategic Philanthropy has launched a Giving Smarter Program in Epilepsy to inform philanthropists on the state of the science for the epilepsy field, key challenges, and solutions to address them. As part of the program, the Milken Institute Center for Strategic Philanthropy hosted a retreat to identify strategic investments that would accelerate epilepsy research to ultimately improve care. The top three prioritized opportunities from the retreat were to 1) invest in data standards and analytical tool development, 2) support young investigators, and 3) promote cross-sector collaborations especially between basic scientists, preclinical researchers, clinicians, and patients.

Distinct Functions for Anterograde and Retrograde Sorting of SORLA in Amyloidogenic Processes in the Brain.

SORLA is a neuronal sorting receptor implicated both in sporadic and familial forms of AD. SORLA reduces the amyloidogenic burden by two mechanisms, either by rerouting internalized APP molecules from endosomes to the trans-Golgi network (TGN) to prevent proteolytic processing or by directing newly produced Aß to lysosomes for catabolism. Studies in cell lines suggested that the interaction of SORLA with cytosolic adaptors retromer and GGA is required for receptor sorting to and from the TGN. However, the relevance of anterograde or retrograde trafficking for SORLA activity in vivo remained largely unexplored. Here, we generated mouse models expressing SORLA variants lacking binding sites for GGA or retromer to query this concept in the brain. Disruption of retromer binding resulted in a retrograde-sorting defect with accumulation of SORLA in endosomes and depletion from the TGN, and in an overall enhanced APP processing. In contrast, disruption of the GGA interaction did not impact APP processing but caused increased brain Aß levels, a mechanism attributed to a defect in anterograde lysosomal targeting of Aß. Our findings substantiated the significance of adaptor-mediated sorting for SORLA activities in vivo, and they uncovered that anterograde and retrograde sorting paths may serve discrete receptor functions in amyloidogenic processes. SIGNIFICANCE STATEMENT: SORLA is a sorting receptor that directs target proteins to distinct intracellular compartments in neurons. SORLA has been identified as a genetic risk factor for sporadic, but recently also for familial forms of AD. To confirm the relevance of SORLA sorting for AD processes in the brain, we generated mouse lines, which express trafficking mutants instead of the wild-type form of this receptor. Studying neuronal activities in these mutant mice, we dissected distinct trafficking routes for SORLA guided by two cytosolic adaptors termed GGA and retromer. We show that these sorting pathways serve discrete functions in control of amyloidogenic processes and may represent unique therapeutic targets to interfere with specific aspects of neurodegenerative processes in the diseased brain.

Very low density lipoprotein receptor regulates dendritic spine formation in a RasGRF1/CaMKII dependent manner.

Very Low Density Lipoprotein Receptor (VLDLR) is an apolipoprotein E receptor involved in synaptic plasticity, learning, and memory. However, it is unknown how VLDLR can regulate synaptic and cognitive function. In the present study, we found that VLDLR is present at the synapse both pre- and post-synaptically. Overexpression of VLDLR significantly increases, while knockdown of VLDLR decreases, dendritic spine number in primary hippocampal cultures. Additionally, knockdown of VLDLR significantly decreases synaptophysin puncta number while differentially regulating cell surface and total levels of glutamate receptor subunits. To identify the mechanism by which VLDLR induces these synaptic effects, we investigated whether VLDLR affects dendritic spine formation through the Ras signaling pathway, which is involved in spinogenesis and neurodegeneration. Interestingly, we found that VLDLR interacts with RasGRF1, a Ras effector, and knockdown of RasGRF1 blocks the effect of VLDLR on spinogenesis. Moreover, we found that VLDLR did not rescue the deficits induced by the absence of Ras signaling proteins CaMKIIα or CaMKIIß. Taken together, our results suggest that VLDLR requires RasGRF1/CaMKII to alter dendritic spine formation.

Human APOE genotype affects intraneuronal Aß1-42 accumulation in a lentiviral gene transfer model.

Intraneuronal accumulation of ß-amyloid (Aß)42 is one of the earliest pathological events in humans and in animal models of Alzheimer's disease (AD). Apolipoprotein E 4 (APOE4) is the major identified genetic risk factor for late-onset AD, with Aß deposition beginning earlier in apoE4-positive subjects. To directly determine the effects of APOE genotype on intraneuronal accumulation of Aß1-42 at the onset of AD pathogenesis, we introduced lentiviral Aß1-42 into the cortex of APOE targeted replacement (TR) mice at the age of 8-9 months. We demonstrated a significant isoform-dependent effect of human APOE, with dramatically enhanced intracellular Aß1-42 deposits in the cerebral cortex of APOE4-TR mice 2 weeks after injection. Double-immunofluorescent staining showed that intracellular accumulation of lentiviral Aß1-42 was mainly present in neurons, localized to late endosomes/lysosomes. This intraneuronal accumulation of Aß1-42 correlated with increased tau phosphorylation and cell death in the ipsilateral cortex around the injection site. Aß1-42 was also observed in microglia, but not in astrocytes. Quantitative analysis revealed more neurons with Aß1-42 while less microglia with Aß1-42 nearest to the injection site of Aß1-42 lentivirus in APOE4-TR mice. Finally, apoE was present in neurons of the ipsilateral cortex of APOE-TR mice at 2 weeks after lentivirus injection, in addition to astrocytes and microglia in both the ipsilateral and contralateral cerebral cortex. Taken together, these results demonstrate that apoE4 tips the balance of the glial and neuronal Aß toward the intraneuronal accumulation of Aß.

APOE genotype affects the pre-synaptic compartment of glutamatergic nerve terminals.

Apolipoprotein E (APOE) genotype affects outcomes of Alzheimer's disease and other conditions of brain damage. Using APOE knock-in mice, we have previously shown that APOE-ε4 Targeted Replacement (TR) mice have fewer dendritic spines and reduced branching in cortical neurons. As dendritic spines are post-synaptic sites of excitatory neurotransmission, we used APOE TR mice to examine whether APOE genotype affected the various elements of the glutamate-glutamine cycle. We found that levels of glutamine synthetase and glutamate uptake transporters were unchanged among the APOE genotypes. However, compared with APOE-ε3 TR mice, APOE-ε4 TR mice had decreased glutaminase levels (18%, p < 0.05), suggesting decreased conversion of glutamine to glutamate. APOE-ε4 TR mice also had increased levels of the vesicular glutamate transporter 1 (20%, p < 0.05), suggesting that APOE genotype affects pre-synaptic terminal composition. To address whether these changes affected normal neurotransmission, we examined the production and metabolism of glutamate and glutamine at 4-5 months and 1 year. Using high-frequency (13)C/(1)H nuclear magnetic resonance spectroscopy, we found that APOE-ε4 TR mice have decreased production of glutamate and increased levels of glutamine. These factors may contribute to the increased risk of neurodegeneration associated with APOE-ε4, and also act as surrogate markers for Alzheimer's disease risk.

Wild type and P301L mutant Tau promote neuro-inflammation and α-Synuclein accumulation in lentiviral gene delivery models.

Neurodegeneration involves multiple pathogenic proteins, including Tau, Aß, TDP-43 and α-Synuclein, but there is little information how these pathogenic proteins interact. We cloned human wild type 4 repeat Tau (Tau(wt)) and mutant Tau(P301L) into a lentivirus and performed stereotaxic injection into the rat motor cortex to examine Tau modification, neuro-inflammation and changes of other proteins associated with neurodegeneration. Tau(P301L) was associated with more phosphorylation of Tau, including Thr 181 and Ser 262 residues and resulted in more aggregation. Both forms of Tau expression increased glycogen synthase kinase-3 (GSK-3) activity, polo-like kinase-2 (PLK2) levels and decreased protein phosphatase activity, but had no effects on casein kinase-1 (CK1). No changes were observed in glial fibrillary acidic protein (GFAP) staining with either Tau(wt) or Tau(P301L), but both caused microglial changes and higher interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) levels. Tau(wt) and Tau(P301L) increased the levels of endogenous α-Synuclein, but not ß-amyloid precursor protein (ßAPP) or Tar-DNA binding protein (TDP-43). The levels of phosphorylated Ser-129 α-Synuclein (p-Ser129) were also increased with Tau(wt) and Tau(P301L) expressing animals. These data suggest that Tau(wt) and Tau(P301L) alter kinase activities, but they differentially induce inflammation, Tau modification and α-Synuclein phosphorylation. This change of α-Synuclein in Tau gene transfer models suggests that Tau pathology may lead to α-Synuclein modification in neurodegenerative diseases.

NeuroBooster Array: A Genome-Wide Genotyping Platform to Study Neurological Disorders Across Diverse Populations.

Genome-wide genotyping platforms have the capacity to capture genetic variation across different populations, but there have been disparities in the representation of population-dependent genetic diversity. The motivation for pursuing this endeavor was to create a comprehensive genome-wide array capable of encompassing a wide range of neuro-specific content for the Global Parkinson's Genetics Program (GP2) and the Center for Alzheimer's and Related Dementias (CARD). CARD aims to increase diversity in genetic studies, using this array as a tool to foster inclusivity. GP2 is the first supported resource project of the Aligning Science Across Parkinson's (ASAP) initiative that aims to support a collaborative global effort aimed at significantly accelerating the discovery of genetic factors contributing to Parkinson's disease and atypical parkinsonism by generating genome-wide data for over 200,000 individuals in a multi-ancestry context. Here, we present the Illumina NeuroBooster array (NBA), a novel, high-throughput and cost-effective custom-designed content platform to screen for genetic variation in neurological disorders across diverse populations. The NBA contains a backbone of 1,914,934 variants (Infinium Global Diversity Array) complemented with custom content of 95,273 variants implicated in over 70 neurological conditions or traits with potential neurological complications. Furthermore, the platform includes over 10,000 tagging variants to facilitate imputation and analyses of neurodegenerative disease-related GWAS loci across diverse populations. The NBA can identify low frequency variants and accurately impute over 15 million common variants from the latest release of the TOPMed Imputation Server as of August 2023 (reference of over 300 million variants and 90,000 participants). We envisage this valuable tool will standardize genetic studies in neurological disorders across different ancestral groups, allowing researchers to perform genetic research inclusively and at a global scale.

APOE genotype alters glial activation and loss of synaptic markers in mice.

The ε4 allele of the Apolipoprotein E (APOE) gene is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), and affects clinical outcomes of chronic and acute brain damages. The mechanisms by which apoE affect diverse diseases and disorders may involve modulation of the glial response to various types of brain damage. We examined glial activation in a mouse model where each of the human APOE alleles are expressed under the endogenous mouse APOE promoter, as well as in APOE knock-out mice. APOE4 mice displayed increased glial activation in response to intracerebroventricular lipopolysaccharide (LPS) compared to APOE2 and APOE3 mice by several measures. There were higher levels of microglia/macrophage, astrocytes, and invading T-cells after LPS injection in APOE4 mice. APOE4 mice also displayed greater and more prolonged increases of cytokines (IL-1ß, IL-6, TNF-α) than APOE2 and APOE3 mice. We found that APOE4 mice had greater synaptic protein loss after LPS injection, as measured by three markers: PSD-95, drebin, and synaptophysin. In all assays, APOE knock-out mice responded similar to APOE4 mice, suggesting that the apoE4 protein may lack anti-inflammatory characteristics of apoE2 and apoE3. Together, these findings demonstrate that APOE4 predisposes to inflammation, which could contribute to its association with Alzheimer's disease and other disorders.

Drugs, the brain, and behavior: a graduate student-run comprehensive course in neuroscience.

Drugs, the Brain, and Behavior is an interdisciplinary two-semester upper level course at Georgetown University designed to expose undergraduate and graduate students to broad areas of the neurosciences, to promote the development of scientific literacy in these students, and to provide pedagogical experience for Ph.D. students in the Interdisciplinary Program in Neuroscience (IPN) at all stages of training. Drugs, the Brain, and Behavior fulfills these goals through a unique model of student-teaching. This lecture-based, team-taught course is completely run and taught by Ph.D. students in the IPN. It is designed to gradually increase the teaching duties of new instructors, providing a structured setting for them to develop their pedagogical skills. We encourage scientific literacy in our students through the incorporation of primary literature and experimental results throughout the course. The strategies we have employed have increased student confidence on a variety of measures of scientific literacy. While running a team-taught course, we have also developed several strategies for coordinating team-taught courses within semesters and across years, which could easily be adapted to other courses.