Comprehensive multimodal analysis of patients with neuroimmunological diseases

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications & trials

Abstract

Neuroimmunological diseases of the central nervous system (CNS) are a growing group of conditions, most of which are rare and not yet well understood. Effective treatments are limited. The most common of these diseases is multiple sclerosis (MS). In its early stage, called relapsing-remitting MS (RRMS), the disease can often be managed successfully with immune-modulating therapies—especially when treatment begins early, before significant damage to the brain and spinal cord occurs. Today, more than 20 treatments for MS are approved by the U.S. Food and Drug Administration (FDA). However, their ability to slow disability progression drops sharply with age. In fact, after about age 54, these treatments show no measurable benefit on disability progression at the group level. This research protocol aims to uncover disease mechanisms that current treatments do not address and to develop practical tools that can improve diagnosis, monitoring, and treatment decisions. This review period (September 2024-August 2025) we have generated following results: 1) Continued refinement of smartphone-based, self-administered Neurological Functions Test Suite (NeuFun-TS): For patients with neuroimmunological disorders, including infections, autoimmune diseases, and auto-inflammatory conditions of the central nervous system (CNS), timely access to a neurology specialist is critical for effective treatment. Yet in the United States, demand for neurological care, driven by an aging population, is growing far faster than the number of available neurologists. The COVID-19 pandemic proved that telemedicine can expand access, but it also revealed a critical weakness: current telemedicine tools cannot reliably detect or measure early neurological deficits. This is especially dangerous in immune-mediated diseases, where starting treatment early can prevent permanent brain and spinal cord injury. To close this gap, we are building the NeuFun-TS—a self-administered smartphone-based tool that recreates much of a traditional neurological examination. NeuFun-TS currently includes 12 short, easy-to-perform tests. We have already analyzed/optimized seven of them, showing that their digital biomarkers correlate strongly with results from expert neurological exams and brain/spinal cord MRI. This year, we fully analyzed two more tests: postural sway and pronator drift. a. Postural sway test: In just one minute, this simple balance test performed with a smartphone can detect subtle increases in body sway that occur with normal aging and distinguish them from the abnormal oscillations seen in neurological disease. Importantly, our results were validated in an independent cohort—a level of reproducibility achieved in minority of published studies. Falls are a leading cause of injury in older adults, and the ability to measure sway precisely with such a short, self-administered test is important advance. b. Pronator drift test: Although widely used in clinical exams, our analysis found it unreliable in this digital format, so we are removing it from NeuFun-TS. These results are now published. We have also completed analysis of two new cognitive tests in NeuFun-TS. The first is a digital adaptation of the established Paired-Associates Learning (PAL) test of verbal memory. The second is an entirely new paradigm we developed to measure both static and dynamic spatial memory. This novel test automatically adjusts its difficulty in real time based on the user’s performance, making it more comfortable to take while also delivering high-quality data. The new spatial memory test outperformed the PAL test in its ability to: (a) Differentiate between diagnostic categories and disease stages. (b) Correlate with clinician-derived cognitive assessments. (c) Correlate with neuroimaging biomarkers of brain injury. All of these results were confirmed in an independent validation cohort, underscoring the reproducibility. This manuscript is currently under review. By combining accessibility, scientific rigor, and independent validation, NeuFun-TS has the potential to bring high-quality neurological assessment into patients’ homes—filling a critical gap in early detection and monitoring of CNS diseases. 2) EBV-Specific CD8+ T Cells in the MS Central Nervous System May Protect Against Disease Progression EBV is strongly linked to MS risk in longitudinal epidemiology, but whether, and how, it contributes to MS progression within the CNS remains debated. Pathology studies report conflicting results on EBV detection in MS brain/CSF, and direct measurement is technically challenging, so quantifying anti-EBV immune responses in CSF provides a rigorous indirect approach. We profiled hundreds of CSF samples (BCR/TCR repertoires + bulk/scRNA-seq/CITE-seq), identifying intrathecal clonal expansion of B and T cells in pwMS, with BCR clonality increasing with progression. We found a higher proportion of TCRs annotated to EBV, especially lytic epitopes, in MS CSF vs controls, and greater TCR similarity suggestive of shared targets. This was not true for other viruses such as CMV and Influenza. Single-cell analysis pinpointed a GZMK⁺/GZMH⁺ double-positive (DP) CD8 T-cell population that is expanded, most differentiated by pseudotime, and enriched for EBV-reactive TCRs. Transcriptomic modules linked to this DP subset overlapped with top cytotoxic genes (CD8A, NKG7, GZMH, GZMK), tying TCR similarity to cytotoxic CD8 biology. Functionally, autologous co-culture assays showed that CD8 T cells proliferate and degranulate in response to EBV-reactivating CSF B-cell lines, and NKG7⁺ CD8 T cells kill EBV-infected targets, consistent with bona fide antiviral effector function. At the systems level, transcriptomic signatures of activated CSF B cells and DP CD8 T cells in pwMS correlated positively with brain MRI contrast-enhancing lesions, suggesting that activated B cells and anti-EBV CD8 T cell responses either partake in blood brain barrier disruption or are recruited to and/or expanded in newly formed lesions. Most importantly, when we adjusted for this lesional B cell enrichment by propensity score matching, we observed that pwMS with greater proportional expansion of anti-EBV DP CD8 T cells accumulated disability at slower pace. These findings provide strong, indirect evidence that ongoing EBV infection in the CNS may drive MS progression, and that robust CD8+ T cell responses against EBV-infected B cells may help restrain it. This opens new opportunities for therapies aimed at boosting protective antiviral immunity in MS. 3) Our work under this protocol also contributed to the following collaborator-led publications: (a) Discovery and validation of a plasma proteomic test for amyotrophic lateral sclerosis (ALS) that could speed diagnosis and enable earlier treatment decisions, with potential to improve outcomes. (b) Evidence that the apolipoprotein L1 (APOL1) G1 variant, a human risk variant for kidney disease that may affect blood lipids, promotes hydrocephalus (but not atherosclerosis) in apolipoprotein E (APOE) knockout mice. Analysis of the All of Us Research Program cohort also linked APOL1-G1 to hydrocephalus in humans, highlighting a novel role for APOL1 in the choroid plexus epithelium. (c) Identification of a CD4⁺CCR6⁺CCR2⁺ T-cell subset with a pathogenic Th17-like signature that can produce inflammatory cytokines without T-cell receptor activation and shows enhanced pathogenic/activation gene expression in the CSF of people with MS. In flow-chamber assays over activated endothelial cells, these cells transmigrate efficiently. Mechanistically, adhesion requires chemokines bound to the endothelial surface, while transendothelial migration requires a chemokine gradient—explaining why cells expressing two different chemokine receptors home to tissues more effectively than those with only one.