Cerebrospinal fluid proteomic profiling of cognitively unimpaired individuals with suspected non-Alzheimer's disease pathophysiology

Aurore Delvenne¹, Johan Gobom^{2

3}, Lianne M Reus⁴, Valerija Dobricic⁵, Mara Ten Kate^{4

6}, Suzanne E Schindler^{7

8}, Inez Ramakers¹, Betty M Tijms⁴, Rik Vandenberghe^{9

10}, Jolien Schaeverbeke^{9

10}, Pablo Martinez-Lage¹¹, Mikel Tainta¹¹, Charlotte E Teunissen¹², Julius Popp^{13

14}, Gwendoline Peyratout¹³, Magda Tsolaki¹⁵, Yvonne Freund-Levi^{16

17

18}, Simon Lovestone¹⁹, Johannes Streffer^{20

21}, Frederik Barkhof^{6

22}, Lars Bertram⁵, Kaj Blennow^{2

3

23

24}, Henrik Zetterberg^{2

3

25

26

27

28}, Pieter Jelle Visser^{1

4

29}, Stephanie J B Vos¹

Affiliations

¹ Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6229 ER, The Netherlands.
² Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 431 80, Sweden.
³ Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal 431 41, Sweden.
⁴ Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam 1081 HZ, The Netherlands.
⁵ Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck 23562, Germany.
⁶ Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam 1081 BT, The Netherlands.
⁷ Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
⁸ Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63108, USA.
⁹ Neurology Service, University Hospitals Leuven, Leuven 3000, Belgium.
¹⁰ Department of Neurosciences, Laboratory for Cognitive Neurology, KU Leuven, Leuven 3000, Belgium.
¹¹ Centre for Research and Memory Clinic, Fundación CITA-Alzhéimer Fundazioa, Donostia-San Sebastián Gipuzkoa 20009, Spain.
¹² Department of Clinical Chemistry, Neurochemistry Laboratory, Amsterdam University Medical Centers (AUMC), Amsterdam Neuroscience, Amsterdam 1081 HV, Netherlands.
¹³ Old Age Psychiatry, University Hospital Lausanne, Lausanne 1005, Switzerland.
¹⁴ Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatry University Hospital Zürich, Zürich 8008, Switzerland.
¹⁵ 1st Department of Neurology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 546 36, Greece.
¹⁶ Department of Neurobiology, Caring Sciences and Society (NVS), Division of Clinical Geriatrics, Karolinska Institutet, Stockholm 141 57, Sweden.
¹⁷ Department of Psychiatry in Region Örebro County and School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro 703 62, Sweden.
¹⁸ Department of Old Age Psychiatry, Psychology and Neuroscience, King's College, London SE5 8AB, United Kingdom.
¹⁹ Department of Psychiatry, University of Oxford, Oxford OX1 2JD, United Kingdom.
²⁰ Department of Biomedical Sciences, Reference Center for Biological Markers of Dementia (BIODEM), University of Antwerp, Antwerp 2610, Belgium.
²¹ H. Lundbeck A/S, Valby 2500, Denmark.
²² Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London WC1N 3BG, United Kingdom.
²³ Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris 75013, France.
²⁴ Division of Life Sciences and Medicine, and Department of Neurology, Neurodegenerative Disorder Research Center, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, Anhui 230026, PR China.
²⁵ Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, United Kingdom.
²⁶ Fluid Biomarker Laboratory, UK Dementia Research Institute at UCL, London W1T 7NF, United Kingdom.
²⁷ Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China.
²⁸ Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53792, USA.
²⁹ Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm 141 57, Sweden.

PMID: 40641595
PMCID: PMC12242384
DOI: 10.1093/braincomms/fcaf253

Cerebrospinal fluid proteomic profiling of cognitively unimpaired individuals with suspected non-Alzheimer's disease pathophysiology

Aurore Delvenne et al. Brain Commun. 2025.

. 2025 Jun 20;7(4):fcaf253.

doi: 10.1093/braincomms/fcaf253. eCollection 2025.

Authors

Affiliations

¹ Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6229 ER, The Netherlands.
² Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 431 80, Sweden.
³ Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal 431 41, Sweden.
⁴ Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam 1081 HZ, The Netherlands.
⁵ Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck 23562, Germany.
⁶ Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam 1081 BT, The Netherlands.
⁷ Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
⁸ Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63108, USA.
⁹ Neurology Service, University Hospitals Leuven, Leuven 3000, Belgium.
¹⁰ Department of Neurosciences, Laboratory for Cognitive Neurology, KU Leuven, Leuven 3000, Belgium.
¹¹ Centre for Research and Memory Clinic, Fundación CITA-Alzhéimer Fundazioa, Donostia-San Sebastián Gipuzkoa 20009, Spain.
¹² Department of Clinical Chemistry, Neurochemistry Laboratory, Amsterdam University Medical Centers (AUMC), Amsterdam Neuroscience, Amsterdam 1081 HV, Netherlands.
¹³ Old Age Psychiatry, University Hospital Lausanne, Lausanne 1005, Switzerland.
¹⁴ Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatry University Hospital Zürich, Zürich 8008, Switzerland.
¹⁵ 1st Department of Neurology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 546 36, Greece.
¹⁶ Department of Neurobiology, Caring Sciences and Society (NVS), Division of Clinical Geriatrics, Karolinska Institutet, Stockholm 141 57, Sweden.
¹⁷ Department of Psychiatry in Region Örebro County and School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro 703 62, Sweden.
¹⁸ Department of Old Age Psychiatry, Psychology and Neuroscience, King's College, London SE5 8AB, United Kingdom.
¹⁹ Department of Psychiatry, University of Oxford, Oxford OX1 2JD, United Kingdom.
²⁰ Department of Biomedical Sciences, Reference Center for Biological Markers of Dementia (BIODEM), University of Antwerp, Antwerp 2610, Belgium.
²¹ H. Lundbeck A/S, Valby 2500, Denmark.
²² Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London WC1N 3BG, United Kingdom.
²³ Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris 75013, France.
²⁴ Division of Life Sciences and Medicine, and Department of Neurology, Neurodegenerative Disorder Research Center, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, Anhui 230026, PR China.
²⁵ Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, United Kingdom.
²⁶ Fluid Biomarker Laboratory, UK Dementia Research Institute at UCL, London W1T 7NF, United Kingdom.
²⁷ Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China.
²⁸ Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53792, USA.
²⁹ Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm 141 57, Sweden.

PMID: 40641595
PMCID: PMC12242384
DOI: 10.1093/braincomms/fcaf253

Abstract

Suspected non-Alzheimer's disease pathophysiology (SNAP) is a biomarker-based concept describing individuals with abnormal tau and/or neurodegeneration markers but normal amyloid levels. SNAP is common in individuals with normal cognition (NC), but its underlying pathophysiology is understudied, while being relevant for clinical trial design and treatment approaches. We aimed to investigate the pathophysiology of individuals with NC who are amyloid-negative and tau-positive (SNAP) through cerebrospinal fluid (CSF) proteomics. Two hundred and ninety-one individuals with NC were classified based on CSF amyloid β1-42 and phosphorylated tau 181, as amyloid-negative/tau-negative (controls), amyloid-negative/tau-positive (SNAP), amyloid-positive/tau-negative and amyloid-positive/tau-positive. We measured 3102 proteins in CSF using tandem mass tag proteomic analyses. We compared protein abundance between groups using analysis of covariance and identified enriched biological pathways using Gene Ontology. We also examined differences between groups in genetic risk for Alzheimer's disease, estimated using polygenic risk scores based on genome-wide association study data. SNAP individuals with NC showed mostly increased protein levels (n = 360) compared with controls, mainly associated with neuroplasticity, angiogenesis, and protein modification and degradation. The proteomic profile of SNAP was similar to that of amyloid-positive/tau-positive individuals, while distinct from amyloid-positive/tau-negative individuals, who showed mainly decreased proteins associated with neuroplasticity. Higher levels of amyloid β1-40 and amyloid β1-42 were observed in SNAP compared with the three other groups. Polygenic risk scores analyses showed no significant differences between SNAP, amyloid-positive/tau-negative, and amyloid-positive/tau-positive individuals, while SNAP showed some genetic differences from controls, which were driven by APOE. Individuals with NC and SNAP or amyloid-positive/tau-positive status showed similar CSF proteomic profiles, while amyloid-positive/tau-negative individuals showed a distinct CSF proteomic profile. This suggests that tau, rather than amyloid, might be the main driver of the proteomic profiles in SNAP and other amyloid/tau subgroups. This may have implications for future proteomic studies and clinical trial design, as these findings highlight the importance of considering tau status in future studies.

Keywords: biomarkers; cognitively unimpaired; proteomics; suspected non-Alzheimer’s disease pathophysiology; tau.

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Conflict of interest statement

A.D. received funding from Alzheimer Nederland (grant number WE.15-2022-01). J.G. has nothing to disclose. S.E.S. has analyzed data provided by C2N Diagnostics to Washington University. She has served on scientific advisory boards for Eisai. M.t.K. has nothing to disclose. L.M.R. was funded by the Memorabel fellowship (ZonMW (the Netherlands Organisation for Health Research and Development) projectnumber: 10510022110012). V.D. has nothing to disclose. B.M.T. has nothing to disclose. TLSB has investigator-initiated research funding from the National Institutes of Health, the Alzheimer’s Association, the Barnes-Jewish Hospital Foundation and Siemens. She participates as a site investigator in clinical trials sponsored by Avid Radiopharmaceuticals, Eli Lilly, Biogen, Eisai, Janssen, and Roche. She serves as a consultant to Biogen, Lilly, Eisai, and Siemens. CC has nothing to disclose. C.E.T. has nothing to disclose. I.R. has nothing to disclose. P.M.-L. has nothing to disclose. M.T. has nothing to disclose. R.V.’s institution has clinical trial agreements (R.V. as PI) with Alector, Biogen, Denali, Eli Lilly, Johnson & Johnson and UCB (Union Chimique Belge). R.V.’s institution has consultancy agreements (R.V. as Data Safety Monitoring Board member) with AC Immune. J.S. is a senior postdoctoral fellow [12Y1623N] of FWO (Research Foundation Flanders). J.S. receives funding from Stichting Alzheimer Onderzoek [SAO-FRA 2021/0022]. S.E.S. has nothing to disclose. EDR has nothing to disclose. J.P. served as a consultant and at advisory boards for the Nestlé Institute of Health Sciences, Ono Pharma, OM Pharma, Schwabe Pharma, Lilly, Roche, and Fujirebio Europe. All his disclosures are unrelated to the present work. The VD cohort was supported by grants from the Swiss National Research Foundation (SNF 320030_204886), Synapsis Foundation—Dementia Research Switzerland (Grant number 2017-PI01). G.P. has nothing to disclose. M.T. has nothing to disclose. Y.F.-L. has nothing to disclose. S.L. has nothing to disclose. J.S. has nothing to disclose. F.B. is a steering committee or Data Safety Monitoring Board member for Biogen, Merck, Eisai and Prothena, an advisory board member for Combinostics, Scottish Brain Sciences, a consultant for Roche, Celltrion, Rewind Therapeutics, Merck, Bracco. F.B. has research agreements with Alzheimer's Disease Data Initiative, Merck, Biogen, GE Healthcare, Roche. F.B. is co-founder and shareholder of Queen Square Analytics LTD. L.B. has nothing to disclose. K.B. has served as a consultant and at advisory boards for AC Immune, Acumen, ALZPath, AriBio, BioArctic, Biogen, Eisai, Lilly, Moleac Pte. Ltd, Novartis, Ono Pharma, Prothena, Roche Diagnostics, and Siemens Healthineers; has served at data monitoring committees for Julius Clinical and Novartis; has given lectures, produced educational materials and participated in educational programmes for AC Immune, Biogen, Celdara Medical, Eisai and Roche Diagnostics; and is a co-founder of Brain Biomarker Solutions in Gothenburg AB (BBS), which is a part of the GU Ventures Incubator Programme, outside the work presented in this paper. H.Z. has served at scientific advisory boards and/or as a consultant for Abbvie, Acumen, Alector, Alzinova, ALZPath, Amylyx, Annexon, Apellis, Artery Therapeutics, AZTherapies, Cognito Therapeutics, CogRx, Denali, Eisai, Merry Life, Nervgen, Novo Nordisk, Optoceutics, Passage Bio, Pinteon Therapeutics, Prothena, Red Abbey Labs, reMYND, Roche, Samumed, Siemens Healthineers, Triplet Therapeutics, and Wave, has given lectures in symposia sponsored by Alzecure, Biogen, Cellectricon, Fujirebio, Lilly, Novo Nordisk, and Roche, and is a co-founder of Brain Biomarker Solutions in Gothenburg AB (BBS), which is a part of the GU Ventures Incubator Programme (outside submitted work). P.J.V. received funding from the European Commission, IMI 2 Joint Undertaking (JU), AMYPAD, grant n° 115952; European Commission, IMI 2 JU, RADAR-AD, grant n°806999; European Commission, IMI 2 JU, EPND, grant n°101034344. The IMI JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. P.J.V. received also funding from Zon-MW, Redefining Alzheimer's disease, grant n°733050824736; and Biogen (Amyloid biomarker study group). Grants were paid to the university. S.J.B.V. received funding from ZonMW (the Netherlands Organisation for Health Research and Development; SNAP VIMP grant n°7330505021), Stichting Adriana van Rinsum-Ponssen, and the European Platform for Neurodegenerative Diseases (EPND) project, which received funding from the European Commision, IMI 2 Joint Undertaking (JU) under grant agreement n°101034344. The IMI JU receives support from the European Union’s Horizon 2020 research and innovation programme and European Federation of Pharmaceutical Industries and Associations.

Figures

**Figure 1**
**Differential levels of CSF proteins across groups.** (**A–C**) Volcano plots showing the CSF proteins with significantly different levels in NC A−T+, NC A+T−, or NC A+T+ versus controls. CSF protein levels were compared between groups using ANCOVA corrected for age and sex. Each dot represents a protein. The log₂ fold change are plotted versus the −log₁₀ P-values. For graphs (B) and (C), significant proteins overlapping with the different proteins in the comparison NC A−T+ versus controls are in blue. The name of the top 20 significantly different CSF proteins are annotated. The total number of proteins that are decreased (left) or increased (right) is indicated. Horizontal dotted line indicates the significance threshold. NC, normal cognition; SNAP, Suspected non-Alzheimer’s disease pathophysiology (A−T+); A+, abnormal levels of CSF Aβ42; T+, abnormal levels of CSF phosphorylated-tau.

**Figure 2**
**CSF proteomics in NC-SNAP (A−T+) compared with controls.** (A) Selected biological processes GO terms for the increased proteins in the comparison NC A−T+ versus controls. (B) Selected biological processes GO terms for the decreased proteins in the comparison NC A−T+ versus controls. Pathway enrichment analyses were performed using Fisher’s exact test with false discovery rate (using the Benjamini-Hochberg procedure). GO, Gene Ontology; NC, normal cognition; SNAP, Suspected non-Alzheimer’s disease pathophysiology (A−T+); A+, abnormal levels of CSF Aβ42; T+, abnormal levels of CSF phosphorylated-tau; NC, normal cognition; SNAP, Suspected non-Alzheimer’s disease pathophysiology (A−T+); A+, abnormal levels of CSF Aβ42; T+, abnormal levels of CSF phosphorylated-tau.

**Figure 3**
**Overlap of significantly dysregulated CSF proteins in NC A/T groups versus controls.** (A) Proportional Venn diagram showing the overlap in proteins with significantly different levels between NC A−T+ and controls as well as between NC A+T− and controls and between NC A+T+ and controls. (B) Table depicting the number and direction of the proteins with significantly different levels from the comparisons shown in the Venn diagram.

**Figure 4**
**CSF proteomics in NC-SNAP (A−T+) compared with NC A+T−.** (A) Volcano plots showing the CSF proteins that were significantly different in NC A−T+ versus NC A+T−. CSF protein levels were compared between groups using ANCOVA corrected for age and sex. Each dot represents a protein. The log2 fold change are plotted versus the −log10 P-values. The name of the top 20 significant CSF proteins are annotated. The total number of proteins that are decreased (left) or increased (right) is indicated. Horizontal dotted line indicates the significance threshold. (B) Selected biological processes GO terms for the increased proteins in the comparison NC A−T+ versus NC A+T−. (C) Selected biological processes GO terms for the decreased proteins in the comparison NC A−T+ versus NC A+T−. Pathway enrichment analyses were performed using Fisher’s exact test with false discovery rate (using the Benjamini-Hochberg procedure). GO, Gene Ontology; NC, normal cognition; SNAP, Suspected non-Alzheimer’s disease pathophysiology (A−T+); A+, abnormal levels of CSF Aβ42; T+, abnormal levels of CSF phosphorylated-tau.

**Figure 5**
**CSF proteomics in NC-SNAP (A−T+) compared with NC A+T+.** (A) Volcano plots showing the CSF proteins that were significantly different in NC A−T+ versus NC A+T+. CSF protein levels were compared between groups using ANCOVA corrected for age and sex. Each dot represents a protein. The log2 fold change are plotted versus the −log10 P-values. The name of the top 20 significant CSF proteins are annotated. The total number of proteins that are decreased (left) or increased (right) is indicated. Horizontal dotted line indicates the significance threshold. (B) Selected biological processes GO terms for the increased proteins in the comparison NC A−T+ versus NC A+T+. (C) Selected biological processes GO terms for the decreased proteins in the comparison NC A−T+ versus NC A+T+. Pathway enrichment analyses were performed using Fisher’s exact test with false discovery rate (using the Benjamini-Hochberg procedure). GO, Gene Ontology; NC, normal cognition; SNAP, Suspected non-Alzheimer’s disease pathophysiology (A−T+); A+, abnormal levels of CSF Aβ42; T+, abnormal levels of CSF phosphorylated-tau.

**Figure 6**
**CSF proteomic profiles of the different comparisons and proteins uniquely associated with NC-SNAP (A−T+).** (A) Proportional Venn diagram showing the overlap in proteins with significantly different levels between NC A−T+ and controls, between NC A−T+ and NC A+T− and between NC A−T+ and NC A+T+. The total number of proteins with significantly different levels in each of the groups is annotated. (B) Table depicting the number and direction of the different proteins as showed in the Venn diagram. (C) Heatmap representing the log2 fold-change values of the proteins with significantly different levels in each comparison. Statistical analysis was performed using ANCOVA corrected for age and gender. Significant differences were determined based on P-values < 0.05. NC, normal cognition; SNAP, Suspected non-Alzheimer’s disease pathophysiology (A−T+); A+, abnormal levels of CSF Aβ42; T+, abnormal levels of CSF phosphorylated-tau.

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Cerebrospinal fluid proteomic profiling of cognitively unimpaired individuals with suspected non-Alzheimer's disease pathophysiology

Affiliations

Cerebrospinal fluid proteomic profiling of cognitively unimpaired individuals with suspected non-Alzheimer's disease pathophysiology

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

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