2026

Do AN, Song S, Ali M, Timsina J, Wang L, Western D, Liu M, Sanford J, Rosende-Roca M, Boada M, Puerta R, Wilson EN, Ruiz A, Pastor P, ADNI, Wyss-Coray T & Cruchaga C “CSF proteomic profiling with amyloid and tau pathology identifies distinctive sex-specific alteration of multiple proteins involved in Alzheimer’s disease”  Alzheimer’s & Dementia. 22(1):e71063 (2026).  [PubMed]

Introduction: In Alzheimer’s disease (AD), females have higher prevalence and faster progression, but sex-specific molecular findings in AD are limited.

Methods: We comprehensively examined 6162 proteins in cerebrospinal fluid (CSF) from 2496 participants to identify sex-specific proteomic alteration by CSF amyloid beta (Aβ)42 and phosphorylated tau (p-tau) levels.

Results: We identified and replicated 68 male-specific and 116 female-specific proteins associated with Aβ42 and/or p-tau levels. Apolipoprotein E ε4 carrier status modified sex-specific alterations of multiple proteins including S100A9 and NEFL for Aβ42 and MAPK9 and MAPKAPK2 for p-tau. Male-specific proteins, enriched in microglia, were involved in activating innate immune response. The male network exhibited direct connections among 30 proteins and highlighted MAPKAPK2 as a hub. Female-specific proteins, enriched in endothelial cells, were involved in regulating protein metabolic process. The female network exhibited direct connections among 43 proteins and highlighted CSNK2A2 and PRKCA as hubs.

Discussion: Our findings provide insights into mechanistic understanding of sex differences in AD risk.

Highlights: Our proteomic study of 6162 proteins (targeted by 7006 aptamers) in cerebrospinal fluid (CSF) from 2496 participants identified and replicated 68 male-specific and 116 female-specific proteins associated with cerebrospinal fluid amyloid beta 42 and/or phosphorylated tau levels. Male-specific proteins, enriched in microglia, were involved in activation of innate immune response. The male network highlighted MAPKAPK2 involved in chronic neuronal neuroinflammation as a hub. Female-specific proteins, enriched in endothelial cells, were involved in regulation of protein metabolic process and response to external stimuli. The female network highlighted PRKCA regulating synaptic plasticity and CSNK2A2 protein involved in neuroplasticity as hubs.

2025

Winer, JR, Vossler H, Young CB, Smith V, Romero A, Shahid-Besanti M, Abdelnour C, Wilson EN, Anders D, Pacheco Morales A, Andreasson KI, Yutsis MV, Henderson VW, Davidzon GA, Mormino EC, Poston KL “18F-PI-2620 Tau PET is associated with cognitive and motor impairment in Lewy body disease” Brain Communications. 7(1) (2025).  [PubMed]

Co-pathology is frequent in Lewy body disease, which includes clinical diagnoses of both Parkinson’s disease and dementia with Lewy bodies. Measuring concomitant pathology in vivo can improve clinical and research diagnoses and prediction of cognitive trajectories. Tau PET imaging may serve a dual role in Lewy body disease by measuring cortical tau aggregation as well as assessing dopaminergic loss attributed to binding to neuromelanin within substantia nigra. We sought to characterize 18F-PI-2620, a next generation PET tracer, in individuals with Lewy body disease. We recruited 141 participants for 18F-PI-2620 PET scans from the Stanford Alzheimer’s Disease Research Center and the Stanford Aging and Memory Study, most of whom also had β-amyloid status available (139/141) from PET or cerebrospinal fluid. We compared 18F-PI-2620 uptake within entorhinal cortex, inferior temporal cortex, precuneus and lingual gyrus, as well as substantia nigra, across participants with Lewy body disease [Parkinson’s disease (n = 29), dementia with Lewy bodies (n = 14)] and Alzheimer’s disease (n = 28), in addition to cognitively unimpaired healthy older adults (n = 70). Mean bilateral signal was extracted from cortical regions of interest in 18F-PI-2620 standard uptake value ratio (inferior cerebellar grey reference) images normalized to template space. A subset of participants received cognitive testing and/or the Movement Disorders Society Unified Parkinson’s Disease Rating Scale Part III motor exam (off medication). 18F-PI-2620 uptake was low overall in Lewy body disease and correlated with β-amyloid PET in temporal lobe regions and precuneus. Moreover, inferior temporal 18F-PI-2620 uptake was significantly elevated in β-amyloid positive relative to β-amyloid negative participants with Lewy body disease. Temporal lobe 18F-PI-2620 signal was not associated with memory in Lewy body disease, but uptake within precuneus and lingual gyrus was associated with worse executive function and attention/working memory performance. Finally, substantia nigra 18F-PI-2620 signal was significantly reduced in participants with Parkinson’s disease, and lower substantia nigra signal was associated with greater motor impairment. These findings suggest that although levels are lower than in Alzheimer’s disease, small elevations in cortical tau are associated with cognitive function in Lewy body disease relevant domains, and that reduced 18F-PI-2620 binding in substantia nigra may represent loss of dopaminergic neurons. Cortical tau and neuromelanin binding within substantia nigra represent two unique signals in the same PET image that may be informative in the context of cognitive and motor deficits, respectively, in Lewy body disease.

Oh HS, Urey DY, Karlsson L, Zhu Z, Shen Y, Farinas A, Timsina J, Duggan MR, Chen J, Guldner IH, Morshed N, Yang C, Western D, Ali M, Le Guen Y, Trelle A, Herukka SK, Rauramaa T, Hiltunen M, Lipponen A, Luikku AJ, Poston KL, Mormino E, Wagner AD, Wilson EN, Channappa D, Leinonen V, Stevens B, Ehrenberg AJ, Gottesman RF, Coresh J, Walker KA, Zetterberg H, Bennett DA, Franzmeier N, Hansson O, Cruchaga C, Wyss-Coray T “A Cerebrospinal Fluid Synaptic Protein Biomarker for Prediction of Resilience Versus Decline in Alzheimer’s Disease” Nature Medicine. 31:1592-1603 (2025).  [PubMed]

Rates of cognitive decline in Alzheimer’s disease (AD) are extremely heterogeneous. Although biomarkers for amyloid-beta (Aβ) and tau proteins, the hallmark AD pathologies, have improved pathology-based diagnosis, they explain only 20-40% of the variance in AD-related cognitive impairment (CI). To discover novel biomarkers of CI in AD, we performed cerebrospinal fluid (CSF) proteomics on 3,397 individuals from six major prospective AD case-control cohorts. Synapse proteins emerged as the strongest correlates of CI, independent of Aβ and tau. Using machine learning, we derived the CSF YWHAG:NPTX2 synapse protein ratio, which explained 27% of the variance in CI beyond CSF pTau181:Aβ42, 11% beyond tau positron emission tomography, and 28% beyond CSF neurofilament, growth-associated protein 43 and neurogranin in Aβ+ and phosphorylated tau+ (A+T1+) individuals. CSF YWHAG:NPTX2 also increased with normal aging and 20 years before estimated symptom onset in carriers of autosomal dominant AD mutations. Regarding cognitive prognosis, CSF YWHAG:NPTX2 predicted conversion from A+T1+ cognitively normal to mild cognitive impairment (standard deviation increase hazard ratio = 3.0, P = 7.0 × 10-4) and A+T1+ mild cognitive impairment to dementia (standard deviation increase hazard ratio = 2.2, P = 8.2 × 10-16) over a 15-year follow-up, adjusting for CSF pTau181:Aβ42, CSF neurofilament, CSF neurogranin, CSF growth-associated protein 43, age, APOE4 and sex. We also developed a plasma proteomic signature of CI, which we evaluated in 13,401 samples, which partly recapitulated CSF YWHAG:NPTX2. Overall, our findings underscore CSF YWHAG:NPTX2 as a robust prognostic biomarker for cognitive resilience versus AD onset and progression, highlight the potential of plasma proteomics in replacing CSF measurement and further implicate synapse dysfunction as a core driver of AD dementia.

Grandke F, Fehlmann T, Kern F, Gate DM, Wolff TW, Leventhal O, Channappa D, Hirsh P, Wilson EN, Meese E, Liu C, Shi Q, Flotho M, Lil Y, Chen C, Yu Y, Xu J, Junkin M, Wang Z, Wu T, Liu L, Hou Y, Andreasson KI, Gansen JS, Mass E, Poston KL, Wyss-Coray T, Keller A “A single-cell atlas to map sex-specific gene-expression changes in blood upon neurodegeneration” Nature Communications. 16 (1): 1965 (2025).

The clinical course and treatment of neurodegenerative disease are complicated by immune-system interference and chronic inflammatory processes, which remain incompletely understood. Mapping immune signatures in larger human cohorts through single-cell gene expression profiling supports our understanding of observed peripheral changes in neurodegeneration. Here, we employ single-cell gene expression profiling of over 909k peripheral blood mononuclear cells (PBMCs) from 121 healthy individuals, 48 patients with mild cognitive impairment (MCI), 46 with Parkinson’s disease (PD), 27 with Alzheimer’s disease (AD), and 15 with both PD and MCI. The dataset is interactively accessible through a freely available website ( https://www.ccb.uni-saarland.de/adrcsc ). In this work, we identify disease-associated changes in blood cell type composition and the gene expression in a sex-specific manner, offering insights into peripheral and solid tissue signatures in AD and PD.

Ali M, Shen Y, Do A, Wang L, Western D, Liu M, Beric A, Budde J, Gentsh J, Schindler S, Morris J, Holtzman D, Fernández M, Ruis A, Alvarez I, Aquilar M, Pastor P, Rutledge J, Oh H, Wilson EN, Le Guen Y, Khalid R, Robins C, Pulford D, Ibanez L, Wyss-Coray T, Ju Y, Cruchaga C. “Multi-cohort cerebrospinal fluid proteomics identifies robust molecular signatures for asymptomatic and symptomatic Alzheimer’s disease” Neuron. 113(9):1363-1379 (2025).  [PubMed]

Changes in β-amyloid (Aβ) and hyperphosphorylated tau (T) in brain and cerebrospinal fluid (CSF) precede Alzheimer’s disease (AD) symptoms, making the CSF proteome a potential avenue to understand disease pathophysiology and facilitate reliable diagnostics and therapies. Using the AT framework and a three-stage study design (discovery, replication, and meta-analysis), we identified 2,173 analytes (2,029 unique proteins) dysregulated in AD. Of these, 865 (43%) were previously reported, and 1,164 (57%) are novel. The identified proteins cluster in four different pseudo-trajectories groups spanning the AD continuum and were enriched in pathways including neuronal death, apoptosis, and tau phosphorylation (early stages), microglia dysregulation and endolysosomal dysfunction (mid stages), brain plasticity and longevity (mid stages), and microglia-neuron crosstalk (late stages). Using machine learning, we created and validated highly accurate and replicable (area under the curve [AUC] > 0.90) models that predict AD biomarker positivity and clinical status. These models can also identify people that will convert to AD.

Wilson EN, Umans J, Swarovski MS, Minhas PS, Mendiola, J.H., Midttun Ø, Ulvik A, Shahid-Besanti M, Linortner P, Mhatre SD, Wang Q, Channappa D, Corso NK, Tian L, Fredericks CA, Kerchner GA, Plowey ED, Cholerton B, Ueland PM, Zabetian CP, Gray NE, Quinn JF, Montine TJ, Sha SJ, Longo FM, Wolk DA, Chen-Plotkin A, Henderson VW, Wyss-Coray T, Wagner AD, Mormino EC, Aghaeepour N, Poston KL, Andreasson KI “Parkinson’s disease is characterized by vitamin B6-dependent inflammatory kynurenine pathway dysfunction” npj Parkinson’s Disease. 11(1):96 (2025).  [PubMed]

Recent studies demonstrate that Parkinson’s disease (PD) is associated with dysregulated metabolic flux through the kynurenine pathway (KP), in which tryptophan is converted to kynurenine (KYN), and KYN is subsequently metabolized to neuroactive compounds quinolinic acid (QA) and kynurenic acid (KA). Here, we used mass-spectrometry to compare blood and cerebral spinal fluid (CSF) KP metabolites between 158 unimpaired older adults and 177 participants with PD. We found increased neuroexcitatory QA/KA ratio in both plasma and CSF of PD participants associated with peripheral and cerebral inflammation and vitamin B6 deficiency. Furthermore, increased QA tracked with CSF tau, CSF soluble TREM2 (sTREM2) and severity of both motor and non-motor PD clinical symptoms. Finally, PD patient subgroups with distinct KP profiles displayed distinct PD clinical features. These data validate the KP as a site of brain and periphery crosstalk, integrating B-vitamin status, inflammation and metabolism to ultimately influence PD clinical manifestation.

Trelle AN, Young CB, Vossler H, Ramos Benitez J, Cody KC, Swarovski MS, Le Guen Y, Kasireddy NM, Feinstein I, Butler III RR, Channappa D, Romero A, Park J, Shahid-Besanti M, Corso NK, Chau K, Smith AN, Skylar-Scott I, Yutsis MV, Fredericks CA, Tian L, Younes K, Kerchner GA, Deutsch GK, Davidzon G, Sha SJ, Henderson VW, Longo FM, Greicius MD, Wyss-Coray T, Andreasson KI, Poston KL, Wagner AD, Mormino EC & Wilson EN “Plasma Aβ42/Aβ40 is sensitive to cerebral Aβ accumulation across the Alzheimer’s disease spectrum”. Alzheimer’s & Dementia. 21(2): e14442 (2025).  [PubMed]

Introduction: The availability of amyloid beta (Aβ) targeting therapies for Alzheimer’s disease (AD) is increasing the demand for scalable biomarkers that are sensitive to early cerebral Aβ accumulation.

Methods: We evaluated fully-automated Lumipulse plasma Aβ42/Aβ40 immunoassays for detecting cerebral Aβ in 457 clinically unimpaired (CU) and clinically impaired (CI) Stanford Alzheimer’s Disease Research Center (Stanford ADRC) participants and 186 CU in the Stanford Aging and Memory Study (SAMS). Longitudinal change in ADRC plasma Aβ42/Aβ40 and cognition and cross-sectional associations with SAMS memory and tau positron emission tomography (PET) were examined.

Results: Plasma Aβ42/Aβ40 exhibited high performance in detecting amyloid positivity defined by PET (area under the curve [AUC]: 0.885, 95% confidence interval [CI]: 0.816-0.955). Once abnomal, plasma Aβ42/Aβ40 remained low and predicted cognitive decline in both CU and CI individuals. Among SAMS CU, plasma Aβ42/Aβ40 was associated with poorer hippocampal-dependent memory and elevated tau accumulation.

Discussion: Lumipulse plasma Aβ42/Aβ40 is a scalable assay for detection of cerebral Aβ and prediction of risk for cognitive decline across the AD continuum.

Highlights: Lumipulse plasma amyloid beta (Aβ)42/Aβ40 exhibited high accuracy in detecting amyloid positivity. Plasma amyloid-positive (Aβ+) individuals exhibited stability of Aβ42/Aβ40 over time. Plasma Aβ42/Aβ40 predicted future cognitive decline across the Alzheimer’s disease (AD) spectrum. Plasma Aβ42/Aβ40 was sensitive to memory and tau burden in clinically unimpaired older adults.

Sheng J, Trelle AN, Romero A, Park J, Tran TT, Sha SJ, Andreasson KI, Wilson EN, Mormino EC & Wagner AD “Top-Down Attention and Alzheimer’s Pathology Affect Cortical Selectivity During Learning, Influencing Episodic Memory in Older Adults” Science Advances. 11(24) (2025).​  [PubMed]

Effective memory formation declines in human aging. Diminished neural selectivity-reduced differential responses to preferred versus nonpreferred stimuli-may contribute to memory decline, but its drivers remain unclear. We investigated the effects of top-down attention and preclinical Alzheimer’s disease (AD) pathology on neural selectivity in 166 cognitively unimpaired older participants using functional magnetic resonance imaging during a word-face/word-place associative memory task. During learning, neural selectivity in place- and, to a lesser extent, face-selective regions was greater for subsequently remembered than forgotten events; positively scaled with variability in dorsal attention network activity, within and across individuals; and negatively related to AD pathology, evidenced by elevated plasma phosphorylated Tau181 (pTau181). Path analysis revealed that neural selectivity mediated the effects of age, attention, and pTau181 on memory. These data reveal multiple pathways that contribute to memory differences among older adults-AD-independent reductions in top-down attention and AD-related pathology alter the precision of cortical representations of events during experience, with consequences for remembering.

2024

Minhas PS, Jones JR, Latif-Hernandez A, Sugiura Y, Durairaj AS, Wang Q, Mhatre SD, Uenaka T, Crapser J, Conley T, Ennerfelt H, Jung YJ, Liu L, Prasad P, Jenkins BC, Ay YA, Matrongolo M, Goodman R, Newmeyer T, Heard K, Kang A, Wilson EN, Yang T, Ullian EM, Serrano GS, Beach TG, Wernig M, Rabinowitz JD, Suematsu M, Longo FM, McReynolds MR, Gage FH & Andreasson KI ” Restoring hippocampal glucose metabolism rescues cognition across Alzheimer’s disease pathologies” Science. 385(6711):eabm6131 (2024).  [PubMed]

Impaired cerebral glucose metabolism is a pathologic feature of Alzheimer’s disease (AD), with recent proteomic studies highlighting disrupted glial metabolism in AD. We report that inhibition of indoleamine-2,3-dioxygenase 1 (IDO1), which metabolizes tryptophan to kynurenine (KYN), rescues hippocampal memory function in mouse preclinical models of AD by restoring astrocyte metabolism. Activation of astrocytic IDO1 by amyloid β and tau oligomers increases KYN and suppresses glycolysis in an aryl hydrocarbon receptor-dependent manner. In amyloid and tau models, IDO1 inhibition improves hippocampal glucose metabolism and rescues hippocampal long-term potentiation in a monocarboxylate transporter-dependent manner. In astrocytic and neuronal cocultures from AD subjects, IDO1 inhibition improved astrocytic production of lactate and uptake by neurons. Thus, IDO1 inhibitors presently developed for cancer might be repurposed for treatment of AD.

Plastini, M.J., Abdelnour, C., Young C.B., Wilson, E.N., Shahid-Besanti, M., Lamoureux, J., Andreasson, Ki., Kerchner, G.A., Montine, T.J., Henderson, V.W., Poston, K.L. “Multiple biomarkers improve diagnostic accuracy across Lewy body and Alzheimer’s disease spectra” Annals of Clinical and Translational Neurology 11(5), 1197-1210 (2024).  [PubMed]

Objective: More than half of neurodegenerative disease patients have multiple pathologies at autopsy; however, most receive one diagnosis during life. We used the α-synuclein seed amplification assay (αSyn-SAA) and CSF biomarkers for amyloidosis and Alzheimer’s disease (AD) neuropathological change (ADNC) to determine the frequency of co-pathologies in participants clinically diagnosed with Lewy body (LB) disease or AD.

Methods: Using receiver operating characteristic analyses on retrospective CSF samples from 150 participants determined αSyn-SAA accuracy, sensitivity, and specificity for identifying clinically defined LB disease and predicting future change in clinical diagnosis. CSF biomarkers helped determine the frequency of concomitant Lewy body pathology, ADNC, and/or amyloidosis in participants with LB disease and AD, across clinical spectra.

Results: Following a decade-long follow-up, the clinically or autopsy-defined diagnosis changed for nine participants. αSyn-SAA demonstrated improved accuracy (91.3%), sensitivity (89.3%), and specificity (93.3%) for identifying LB disease compared to all non-LB disease, highlighting the limitations of clinical diagnosis alone. When examining biomarkers of co-pathology, amyloidosis was present in 18%, 48%, and 71% (χ2(2) = 13.56, p = 0.001) and AD biomarkers were present in 0%, 8.7%, and 42.9% (χ2(2) = 18.44, p < 0.001) of LB disease participants with different stages of cognitive impairment respectively. Co-occurring biomarkers for αSyn-SAA and amyloidosis were present in 12% and 14% of AD compared to 43% and 57% LB disease participants with different stages of cognitive impairment (χ2(3) = 13.87, p = 0.003).

Interpretation: Our study shows that using a combination of αSyn-SAA and AD biomarkers can identify people with αSyn, ADNC, and co-pathology better and earlier than traditional clinical diagnostic criteria alone.

Guilliot, S., Wilson, E.N., Touchon, J., Soto, M.E., “Nanolithium, a new treatment approach to Alzheimer’s disease: a review of existing evidence and clinical perspectives” The Journal of Prevention of Alzheimer’s Disease 11(2), 428-434 (2024).  [PubMed]

Lithium has been approved and used for several decades in the treatment of psychiatric disorders, and its potential effect in neurodegenerative diseases has been subject to increasing research interest in recent years. Nanolithium is a new experimental product using a novel drug-delivery technology (Aonys®), which optimizes its bioavailability while reducing its toxicity profile. Therapeutic doses of lithium used in Nanolithium are more than 50 times lower than the minimal dose of classical lithium salts. In this review we report data from non-clinical pharmacology studies supporting Nanolithium efficacy and the mechanism of action in Alzheimer’s disease. GSK-3β inhibition is thought to be central to Nanolithium’s mechanism of action, triggering a reduction of the production of toxic amyloid plaques and decrease in tau hyperphosphorylation, which could potentially benefit both neuropsychiatric symptoms and cognitive decline. We then summarize outcomes from non-clinical proof-of-concept studies. These data supported the initiation of a currently ongoing phase II proof-of-concept study to evaluate the safety and efficacy of Nanolithium in patients with mild-to-severe Alzheimer’s disease. We highlight key aspects of the study design. We finish this review with a discussion on the potential place of Nanolithium in the current and future Alzheimer’s disease treatment landscape.

Abdelnour C., Young C.B., Shahid-Besanti M., Smith A., Wilson E.N., Ramos Benitez J., Vossler H., Plastini M.J., Winer J.R., Kerchner G.A., Cholerton B., Andreasson K.I., Henderson V.W., Yutsis M., Montine T.J., Tian L., Mormino E.C., & Poston K.L. “Plasma pTau181 reveals a pathological signature that predicts cognitive outcomes in Lewy body disease” Annals of Neurology.  [PubMed]

Objective: To determine whether plasma phosphorylated-Tau181 (pTau181) could be used as a diagnostic biomarker of concurrent Alzheimer’s disease neuropathologic change (ADNC) or amyloidosis alone, as well as a prognostic, monitoring, and susceptibility/risk biomarker for clinical outcomes in Lewy body disease (LBD).

Methods: We studied 565 participants: 94 LBD with normal cognition, 83 LBD with abnormal cognition, 114 with Alzheimer’s disease, and 274 cognitively normal. Plasma pTau181 levels were measured with the Lumipulse G platform. Diagnostic accuracy for concurrent ADNC and amyloidosis was assessed with Receiver Operating Characteristic curves in a subset of participants with CSF pTau181/Aβ42, and CSF Aβ42/Aβ40 or amyloid-β PET, respectively. Linear mixed effects models were used to examine the associations between baseline and longitudinal plasma pTau181 levels and clinical outcomes.

Results: Plasma pTau181 predicted concurrent ADNC and amyloidosis in LBD with abnormal cognition with 87% and 72% accuracy, respectively. In LBD patients with abnormal cognition, higher baseline plasma pTau181 was associated with worse baseline MoCA and CDR-SB, as well as accelerated decline in CDR-SB. Additionally, in this group, rapid increases in plasma pTau181 over 3 years predicted a faster decline in CDR-SB and memory. In LBD patients with normal cognition, there was no association between baseline or longitudinal plasma pTau181 levels and clinical outcomes; however, elevated pTau181 at baseline increased the risk of conversion to cognitive impairment.

Interpretation: Our findings suggest that plasma pTau181 is a promising biomarker for concurrent ADNC and amyloidosis in LBD. Furthermore, plasma pTau181 holds potential as a prognostic, monitoring, and susceptibility/risk biomarker, predicting disease progression in LBD. ANN NEUROL 2024;96:526-538.

Abiose, O., Rutledge, J., Moran-Losada, P., Belloy, M.E., Wilson E.N., He, Z., Trelle, A.N., Channappa, D., Romero, A., Park, J., Sha, S., Greicius, M., Andreasson, K.I., Poston, K.L., Henderson, V.W., Wagner, A.D., Wyss-Coray, T., Mormino, E.C. “Post-translational modifications linked to preclinical Alzheimer’s disease-related pathological and cognitive changes” Alzheimer’s & Dementia 20(3):1851-1867 (2024)  [PubMed]

Introduction: In this study, we leverage proteomic techniques to identify communities of proteins underlying Alzheimer’s disease (AD) risk among clinically unimpaired (CU) older adults.

Methods: We constructed a protein co-expression network using 3869 cerebrospinal fluid (CSF) proteins quantified by SomaLogic, Inc., in a cohort of participants along the AD clinical spectrum. We then replicated this network in an independent cohort of CU older adults and related these modules to clinically-relevant outcomes.

Results: We discovered modules enriched for phosphorylation and ubiquitination that were associated with abnormal amyloid status, as well as p-tau181 (M4: β = 2.44, p < 0.001, M7: β = 2.57, p < 0.001) and executive function performance (M4: β = -2.00, p = 0.005, M7: β = -2.39, p < 0.001).

Discussion: In leveraging CSF proteomic data from individuals spanning the clinical spectrum of AD, we highlight the importance of post-translational modifications for early cognitive and pathological changes.

Keywords: Alzheimer’s disease; aging; autophagy; cerebral spinal fluid; clinically unimpaired; protein co-expression network; ubiquitination.

Western D, Timsina J, Wang L, Wang C, Yang C, Phillips B, Wang Y, Liu M, Ali M, Beric A, Gorijala P, Kohlfeld P, Budde J, Levey AI, Morris JC, Perrin RJ, Ruiz A, Marquie M, Boada M, de Rojas I, Rutledge J, Oh H, Wilson EN, Le Guen Y, Reus LM, Tijms B, Visser PJ, van der Lee SJ, Pijnenburg YAL, Teunissen CE, del Campo Milan M, Alvarez I, Dominantly Inherited Alzheimer Network (DIAN), the Alzheimer’s Disease Neuroimaging Initiative (ADNI), Greicius MD, Pastor P, Pulford DJ, Ibanez L, Wyss-Coray T, Sung YJ & Cruchaga C “Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicated causal proteins for Alzheimer’s disease” Nature Genetics. 56, 2672-2684 (2024).  [PubMed]

The integration of quantitative trait loci (QTLs) with disease genome-wide association studies (GWASs) has proven successful in prioritizing candidate genes at disease-associated loci. QTL mapping has been focused on multi-tissue expression QTLs or plasma protein QTLs (pQTLs). We generated a cerebrospinal fluid (CSF) pQTL atlas by measuring 6,361 proteins in 3,506 samples. We identified 3,885 associations for 1,883 proteins, including 2,885 new pQTLs, demonstrating unique genetic regulation in CSF. We identified CSF-enriched pleiotropic regions on chromosome (chr)3q28 near OSTN and chr19q13.32 near APOE that were enriched for neuron specificity and neurological development. We integrated our associations with Alzheimer’s disease (AD) through proteome-wide association study (PWAS), colocalization and Mendelian randomization and identified 38 putative causal proteins, 15 of which have drugs available. Finally, we developed a proteomics-based AD prediction model that outperforms genetics-based models. These findings will be instrumental to further understand the biology and identify causal and druggable proteins for brain and neurological traits.

Minhas PS, Jones JR, Latif-Hernandez A, Sugiura Y, Durairaj AS, Wang Q, Mhatre SD, Uenaka T, Crapser J, Conley T, Ennerfelt H, Jung YJ, Liu L, Prasad P, Jenkins BC, Ay YA, Matrongolo M, Goodman R, Newmeyer T, Heard K, Kang A, Wilson EN, Yang T, Ullian EM, Serrano GS, Beach TG, Wernig M, Rabinowitz JD, Suematsu M, Longo FM, McReynolds MR, Gage FH & Andreasson KI "Restoring hippocampal glucose metabolism rescues cognition across Alzheimer’s disease pathologies" Science. 385(6711):eabm6131 (2024). PMID: 39172838  [PubMed]

Impaired cerebral glucose metabolism is a pathologic feature of Alzheimer’s disease (AD), with recent proteomic studies highlighting disrupted glial metabolism in AD. We report that inhibition of indoleamine-2,3-dioxygenase 1 (IDO1), which metabolizes tryptophan to kynurenine (KYN), rescues hippocampal memory function in mouse preclinical models of AD by restoring astrocyte metabolism. Activation of astrocytic IDO1 by amyloid β and tau oligomers increases KYN and suppresses glycolysis in an aryl hydrocarbon receptor-dependent manner. In amyloid and tau models, IDO1 inhibition improves hippocampal glucose metabolism and rescues hippocampal long-term potentiation in a monocarboxylate transporter-dependent manner. In astrocytic and neuronal cocultures from AD subjects, IDO1 inhibition improved astrocytic production of lactate and uptake by neurons. Thus, IDO1 inhibitors presently developed for cancer might be repurposed for treatment of AD.

Wilson EN, Wang C, Swarovski MS, Zera KA, Ennerfelt HA, Wang Q, Chaney A, Gauba E, Ramos Benitez J, Le Guen Y, Minhas PS, Panchal M, Tan YJ, Blacher E, Iweka CA, Cropper H, Jain P, Liu Q, Mehta SS, Zuckerman AJ, Xin M, Umans J, Huang J, Durairaj AS, Serrano GE, Beach TG, Greicius MD, James ML, Buckwalter MS, McReynolds MR, Rabinowitz JD & Andreasson KI “TREM1 disrupts myeloid bioenergetics and cognitive function in aging and Alzheimer’s disease mouse models” Nature Neuroscience. 27, 873-885 (2024).  [PubMed]

Human genetics implicate defective myeloid responses in the development of late-onset Alzheimer disease. A decline in peripheral and brain myeloid metabolism, triggering maladaptive immune responses, is a feature of aging. The role of TREM1, a pro-inflammatory factor, in neurodegenerative diseases is unclear. Here we show that Trem1 deficiency prevents age-dependent changes in myeloid metabolism, inflammation and hippocampal memory function in mice. Trem1 deficiency rescues age-associated declines in ribose 5-phosphate. In vitro, Trem1-deficient microglia are resistant to amyloid-β42 oligomer-induced bioenergetic changes, suggesting that amyloid-β42 oligomer stimulation disrupts homeostatic microglial metabolism and immune function via TREM1. In the 5XFAD mouse model, Trem1 haploinsufficiency prevents spatial memory loss, preserves homeostatic microglial morphology, and reduces neuritic dystrophy and changes in the disease-associated microglial transcriptomic signature. In aging APPSwe mice, Trem1 deficiency prevents hippocampal memory decline while restoring synaptic mitochondrial function and cerebral glucose uptake. In postmortem Alzheimer disease brain, TREM1 colocalizes with Iba1+ cells around amyloid plaques and its expression is associated with Alzheimer disease clinical and neuropathological severity. Our results suggest that TREM1 promotes cognitive decline in aging and in the context of amyloid pathology.

2023

Oh, H., Rutledge, J., Pavlovics, R., Nachun, D., Pálovics, R., Abiose, O., Moran-Losada, P., Channappa D., Urey, D.Y., Kim, K., Sung Y.J., Wang, L., Timsina, J., Western, D., Liu, M., Kohlfeld, P., Budde, J., Wilson, E.N., Guen, Y., Maurer, T.M., Haney, M., Yang, A.C., He, Z., Greicius, M.D., Andreasson, K.I., Sathyan, S., Weiss, E.F., Milman, S., Barzilai, N., Cruchaga, C., Wagner, A.D., Mormino, E., Lehallier, B., Henderson, V.W., Longo, F.M., Montgomery, S.B., Wyss-Coray, T. “Organ-specific aging signatures in the plasma proteome track health and disease” Nature 624(7990):164-172 (2023).  [PubMed]

Animal studies show aging varies between individuals as well as between organs within an individual1-4, but whether this is true in humans and its effect on age-related diseases is unknown. We utilized levels of human blood plasma proteins originating from specific organs to measure organ-specific aging differences in living individuals. Using machine learning models, we analysed aging in 11 major organs and estimated organ age reproducibly in five independent cohorts encompassing 5,676 adults across the human lifespan. We discovered nearly 20% of the population show strongly accelerated age in one organ and 1.7% are multi-organ agers. Accelerated organ aging confers 20-50% higher mortality risk, and organ-specific diseases relate to faster aging of those organs. We find individuals with accelerated heart aging have a 250% increased heart failure risk and accelerated brain and vascular aging predict Alzheimer’s disease (AD) progression independently from and as strongly as plasma pTau-181 (ref. 5), the current best blood-based biomarker for AD. Our models link vascular calcification, extracellular matrix alterations and synaptic protein shedding to early cognitive decline. We introduce a simple and interpretable method to study organ aging using plasma proteomics data, predicting diseases and aging effects.

Chaney, A.M., Cropper, H.C., Jain, P., Wilson, E., Simonetta, F., Johnson, E.M., Alam, I.S., Patterson, I.T.J., Swarovski, M., Stevens, M.Y., Wang, Q., Azevedo, C., Nagy, S.C., Ramos Benitez, J., Deal, E.M., Vogel, H., Andreasson, K.I., & James., M.L. “PET imaging of TREM1 identifies CNS-infiltrating myeloid cells in a mouse model of multiple sclerosis,” Science Translational Medicine 15(702) (2023).  [PubMed]

Multiple sclerosis (MS) is an immune-mediated demyelinating disease of the central nervous system (CNS) that causes substantial morbidity and diminished quality of life. Evidence highlights the central role of myeloid lineage cells in the initiation and progression of MS. However, existing imaging strategies for detecting myeloid cells in the CNS cannot distinguish between beneficial and harmful immune responses. Thus, imaging strategies that specifically identify myeloid cells and their activation states are critical for MS disease staging and monitoring of therapeutic responses. We hypothesized that positron emission tomography (PET) imaging of triggering receptor expressed on myeloid cells 1 (TREM1) could be used to monitor deleterious innate immune responses and disease progression in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. We first validated TREM1 as a specific marker of proinflammatory, CNS-infiltrating, peripheral myeloid cells in mice with EAE. We show that the 64Cu-radiolabeled TREM1 antibody-based PET tracer monitored active disease with 14- to 17-fold higher sensitivity than translocator protein 18 kDa (TSPO)-PET imaging, the established approach for detecting neuroinflammation in vivo. We illustrate the therapeutic potential of attenuating TREM1 signaling both genetically and pharmacologically in the EAE mice and show that TREM1-PET imaging detected responses to an FDA-approved MS therapy with siponimod (BAF312) in these animals. Last, we observed TREM1+ cells in clinical brain biopsy samples from two treatment-naïve patients with MS but not in healthy control brain tissue. Thus, TREM1-PET imaging has potential for aiding in the diagnosis of MS and monitoring of therapeutic responses to drug treatment.

2022

Shuken, S.R., Rutledge, J., Iram, T., Moran Losada, P., Wilson, E.N., Andreasson, K.I., Leib, R.D., Wyss-Coray, T., “Limited proteolysis–mass spectrometry reveals aging-associated changes in cerebrospinal fluid protein abundances and structures,” Nature Aging 2, 379-388 (2022).  [PubMed]

Cerebrospinal fluid (CSF) proteins and their structures have been implicated repeatedly in aging and neurodegenerative diseases. Limited proteolysis-mass spectrometry (LiP-MS) is a method that enables proteome-wide screening for changes in both protein abundance and structure. To screen for novel aging-associated changes in the CSF proteome, we performed LiP-MS on CSF from young and old mice with a modified analysis pipeline. We found 38 protein groups change in abundance with aging, most dominantly immunoglobulins of the IgM subclass. We discovered six high-confidence candidates that appeared to change in structure with aging, of which Kng1, Itih2, Lp-PLA2, and 14-3-3 proteins have binding partners or proteoforms known previously to change in the brain with Alzheimer’s disease. Intriguingly, using orthogonal validation by Western blot we found the LiP-MS hit Cd5l forms a covalent complex with IgM in mouse and human CSF whose abundance increases with aging. SOMAmer probe signals for all six LiP-MS hits in human CSF, especially 14-3-3 proteins, significantly associate with several clinical features relevant to cognitive function and neurodegeneration. Together, our findings show that LiP-MS can uncover age-related structural changes in CSF with relevance to neurodegeneration.

Wilson, E.N., Young, C.B., Ramos Benitez, J., Swarovski, M.S., Feinstein, I., Vandijck, M., Le Guen, Y., Kasireddy, N.M., Shalid, M., Corso, N.K., Wang, Q., Kennedy, G., Trelle, A., Lind, B., Channappa, D., Belnap, M., Ramirez, V., Skylar-Scott, I., Younes, K., Yutsis, M.V., Le Bastard, N., Quinn, J.F., van Dyck, C.H., Nairn, A., Fredericks, C.A., Tian, L., Kerchner, G.A., Montine, T.J., Sha, S.J., Davidzon, G., Henderson, V.W., Longo, F.M., Greicius, M.D., Wagner, A.D., Wyss-Coray, T., Poston, K.L., Mormino, E.C. & Andreasson, K.I. “Performance of a Fully-Automated Lumipulse Plasma Phospho-Tau181 Assay for Alzheimer’s Disease,” Alzheimer’s Research & Therapy 14, 172 (2022).  [PubMed]

Background: The recent promise of disease-modifying therapies for Alzheimer’s disease (AD) has reinforced the need for accurate biomarkers for early disease detection, diagnosis and treatment monitoring. Advances in the development of novel blood-based biomarkers for AD have revealed that plasma levels of tau phosphorylated at various residues are specific and sensitive to AD dementia. However, the currently available tests have shortcomings in access, throughput, and scalability that limit widespread implementation.

Methods: We evaluated the diagnostic and prognostic performance of a high-throughput and fully-automated Lumipulse plasma p-tau181 assay for the detection of AD. Plasma from older clinically unimpaired individuals (CU, n = 463) and patients with mild cognitive impairment (MCI, n = 107) or AD dementia (n = 78) were obtained from the longitudinal Stanford University Alzheimer’s Disease Research Center (ADRC) and the Stanford Aging and Memory Study (SAMS) cohorts. We evaluated the discriminative accuracy of plasma p-tau181 for clinical AD diagnosis, association with amyloid β peptides and p-tau181 concentrations in CSF, association with amyloid positron emission tomography (PET), and ability to predict longitudinal cognitive and functional change.

Results: The assay showed robust performance in differentiating AD from control participants (AUC 0.959, CI: 0.912 to 0.990), and was strongly associated with CSF p-tau181, CSF Aβ42/Aβ40 ratio, and amyloid-PET global SUVRs. Associations between plasma p-tau181 with CSF biomarkers were significant when examined separately in Aβ+ and Aβ- groups. Plasma p-tau181 significantly increased over time in CU and AD diagnostic groups. After controlling for clinical diagnosis, age, sex, and education, baseline plasma p-tau181 predicted change in MoCA overall and change in CDR Sum of Boxes in the AD group over follow-up of up to 5 years.

Conclusions: This fully-automated and available blood-based biomarker assay therefore may be useful for early detection, diagnosis, prognosis, and treatment monitoring of AD.

Keywords: Alzheimer’s disease; Biomarkers; Phospho-tau; Plasma.

Arnold, M.R., Coughlin, D.G., Brumbach, B.H., Smirnov, D.S., Concha-Marambio, L., Farris, C.M., Ma, Y., Kim, Y., Wilson, E.N., Kaye, J.A., Hiniker, A., Woltjer, R.L., Galasko, D.R., Quinn, J.F. “α-Synuclein Seed Amplification in CSF and Brain from Patients with Different Brain Distributions of Pathological α-Synuclein in the Context of Co-Pathology and Non-LBD Diagnoses,” Annals of Neurology (2022).  [PubMed]

Objective: The purpose of this study was to determine the sensitivity and specificity of α-synuclein seed amplification assay (αSyn-SAA) in antemortem and postmortem cerebrospinal fluid (CSF) of autopsy-confirmed patients with different distributions of pathological αSyn, co-pathologies, and clinical diagnoses.

Methods: The αSyn-SAA was used to test antemortem CSF samples from 119 subjects with a variety of clinical syndromes and standardized neuropathological examinations from Oregon Health and Science University (OHSU) and University of California San Diego (UCSD; 56 additional postmortem CSF samples available). The αSyn-SAA was also applied to frontal cortex and amygdala homogenates. Sensitivity and specificity were compared across distributions of αSyn pathology. Clinical data and co-pathologies were compared across αSyn-SAA positive and negative groups.

Results: Fifty-three individuals without and 66 with αSyn-pathology (neocortical [n = 38], limbic [n = 7], and amygdala-predominant [n = 21]) were included. There was a sensitivity of 97.8% and specificity of 98.1% of the αSyn-SAA to identify patients with limbic/neocortical pathology from antemortem CSF. Sensitivity to detect amygdala-predominant pathology was only 14.3%. Postmortem CSF and brain tissue αSyn-SAA analyses also showed higher assay positivity in samples from limbic/neocortical cases.

Interpretation: CSF αSyn-SAA reliably identifies αSyn seeds in patients with diffuse αSyn pathology in the context of co-pathology and non-Lewy body disease (LBD) diagnoses. The analysis of brain homogenates suggests that pathological αSyn in the amygdala might differ from pathological αSyn in the frontal cortex. The αSyn-SAA might facilitate the differential diagnosis of dementias with mixed pathologies. ANN NEUROL 2022;92:650-662.

2021

Feinstein I, Wilson EN, Swarovski MS, Andreasson KI, Angst MS, Greicius MD, “Plasma Biomarkers of Tau and Neurodegeneration During Major Cardiac and Non-Cardiac Surgery,” JAMA Neurology 78(11), 1407-1409 (2021).  [PubMed]

This analysis compares plasma biomarkers of tau and neurodegeneration during major cardiac and noncardiac surgeries.

Wilson EN & Andreasson KI  “TAM-ping Down Amyloid in Alzheimer’s Disease,” Nature Immunology 22, 543-544 (2021).  [PubMed]

The TAM receptor kinases Axl and Mer are critical for microglial recognition and clearance of accumulating amyloid in transgenic models of Alzheimer’s disease.

Trelle AN, Carr VA, Wilson EN, Swarovski MS, Hunt MP, Toueg TN, Tran TT, Channappa D, Corso NK, Thieu MK, Jayakumar M, Nadiadwala A, Guo W, Tanner NJ, Bernstein JD, Litovsky CP, Guerin SA, Khazenzon AM, Harrison MB, Rutt BK, Deutsch GK, Chin FT, Davidzon GA, Hall JN, Sha SJ, Fredericks CA, Andreasson KI, Kerchner GA, Wagner AD, Mormino EC  “Association of CSF Biomarkers with Hippocampal-dependent Memory in Preclinical Alzheimer Disease” Neurology 96 (10), 1470-1481 (2021).  [PubMed]

Objective: To determine whether memory tasks with demonstrated sensitivity to hippocampal function can detect variance related to preclinical Alzheimer disease (AD) biomarkers, we examined associations between performance in 3 memory tasks and CSF β-amyloid (Aβ)42/Aβ40 and phosopho-tau181 (p-tau181) in cognitively unimpaired older adults (CU).

Methods: CU enrolled in the Stanford Aging and Memory Study (n = 153; age 68.78 ± 5.81 years; 94 female) completed a lumbar puncture and memory assessments. CSF Aβ42, Aβ40, and p-tau181 were measured with the automated Lumipulse G system in a single-batch analysis. Episodic memory was assayed using a standardized delayed recall composite, paired associate (word-picture) cued recall, and a mnemonic discrimination task that involves discrimination between studied “target” objects, novel “foil” objects, and perceptually similar “lure” objects. Analyses examined cross-sectional relationships among memory performance, age, and CSF measures, controlling for sex and education.

Results: Age and lower Aβ42/Aβ40 were independently associated with elevated p-tau181. Age, Aβ42/Aβ40, and p-tau181 were each associated with (1) poorer associative memory and (2) diminished improvement in mnemonic discrimination performance across levels of decreased task difficulty (i.e., target-lure similarity). P-tau mediated the effect of Aβ42/Aβ40 on memory. Relationships between CSF proteins and delayed recall were similar but nonsignificant. CSF Aβ42 was not significantly associated with p-tau181 or memory.

Conclusions: Tests designed to tax hippocampal function are sensitive to subtle individual differences in memory among CU and correlate with early AD-associated biomarker changes in CSF. These tests may offer utility for identifying CU with preclinical AD pathology.

2020

Wilson EN, Swarovski MS, Linortner P, Shahid M, Zuckerman AJ, Wang Q, Channappa D, Minhas PS, Mhatre SD, Plowey ED, Quinn JF, Zabetian CP, Tian L, Longo FM, Cholerton B, Montine TJ, Poston KL, Andreasson KI   “Soluble TREM2 is elevated in Parkinson’s disease subgroups with elevated CSF tau,” Brain 143 (3), 932-943 (2020).  [PubMed]

Parkinson’s disease is the second most common neurodegenerative disease after Alzheimer’s disease and affects 1% of the population above 60 years old. Although Parkinson’s disease commonly manifests with motor symptoms, a majority of patients with Parkinson’s disease subsequently develop cognitive impairment, which often progresses to dementia, a major cause of morbidity and disability. Parkinson’s disease is characterized by α-synuclein accumulation that frequently associates with amyloid-β and tau fibrils, the hallmarks of Alzheimer’s disease neuropathological changes; this co-occurrence suggests that onset of cognitive decline in Parkinson’s disease may be associated with appearance of pathological amyloid-β and/or tau. Recent studies have highlighted the appearance of the soluble form of the triggering receptor expressed on myeloid cells 2 (sTREM2) receptor in CSF during development of Alzheimer’s disease. Given the known association of microglial activation with advancing Parkinson’s disease, we investigated whether CSF and/or plasma sTREM2 differed between CSF biomarker-defined Parkinson’s disease participant subgroups. In this cross-sectional study, we examined 165 participants consisting of 17 cognitively normal elderly subjects, 45 patients with Parkinson’s disease with no cognitive impairment, 86 with mild cognitive impairment, and 17 with dementia. Stratification of subjects by CSF amyloid-β and tau levels revealed that CSF sTREM2 concentrations were elevated in Parkinson’s disease subgroups with a positive tau CSF biomarker signature, but not in Parkinson’s disease subgroups with a positive CSF amyloid-β biomarker signature. These findings indicate that CSF sTREM2 could serve as a surrogate immune biomarker of neuronal injury in Parkinson’s disease.