Functional Hierarchy Disruption: A Mechanistic Link to Cognitive Decline and Treatment Targets in Alzheimer’s Disease

Functional Hierarchy Disruption: A Mechanistic Link to Cognitive Decline and Treatment Targets in Alzheimer’s Disease | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Biological Sciences - Article Functional Hierarchy Disruption: A Mechanistic Link to Cognitive Decline and Treatment Targets in Alzheimer’s Disease Kun Zhao, Rongshen Zhou, Pindong Chen, Dong Wang, Yating Li, Sheng Bi, and 11 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8184263/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Alzheimer’s disease (AD) is marked by disrupted brain network connectivity, which impairs functional hierarchy and contributes to cognitive decline. Two fundamental questions, however, remain open: what specific changes occur in the hierarchical organization of the AD brain, and whether rectifying these changes can restore cognitive function. To answer these, we first analyzed individualized functional hierarchical architecture across three large, independent fMRI datasets (MCADI, N = 711; ADNI, N = 621; OASIS-3, N = 506). We identified a reproducible pattern of hierarchical remodeling in AD, characterized by expansion of the dorsal attention network A and shrinkage of the control network A, with spatial variability shaped by underlying brain tissue properties. To evaluate the therapeutic relevance of this signature, we conducted a randomized controlled trial of transcranial alternating current stimulation (tACS; N=44). Targeted stimulation selectively reversed the remodeling trajectory, suppressing dorsal attention network expansion and countering control network contraction. These network improvements persisted for three months and were accompanied by sustained cognitive gains, with 80% of participants showing measurable improvement. Our results reveal a functional hierarchical signature of AD and establish its potential as a novel interventional target, while also providing mechanistic insights into the action of non-invasive neuromodulation. Biological sciences/Neuroscience/Cognitive neuroscience Health sciences/Biomarkers/Prognostic markers Biological sciences/Neuroscience/Diseases of the nervous system/Alzheimer's disease Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Full Text Additional Declarations There is NO Competing Interest. Supplementary Files suppltacs251121zrs.docx Supplementary Material Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8184263","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":549996406,"identity":"c43adde3-7e70-45e8-afc5-cba01a7ed6f9","order_by":0,"name":"Kun 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Hospital","correspondingAuthor":false,"prefix":"","firstName":"Xi","middleName":"","lastName":"Zhang","suffix":""},{"id":549996420,"identity":"1fa6a63a-0db1-4a8c-ba1e-dfc8424092a5","order_by":14,"name":"Jie Lu","email":"","orcid":"https://orcid.org/0000-0003-0425-3921","institution":"Xuanwu Hospital, Capital Medical University","correspondingAuthor":false,"prefix":"","firstName":"Jie","middleName":"","lastName":"Lu","suffix":""},{"id":549996421,"identity":"8bb86ae7-d30d-4c3a-bc6e-4f9605a3987e","order_by":15,"name":"Yong Liu","email":"","orcid":"https://orcid.org/0000-0002-1862-3121","institution":"Beijing University of Posts and Telecommunications","correspondingAuthor":false,"prefix":"","firstName":"Yong","middleName":"","lastName":"Liu","suffix":""},{"id":549996422,"identity":"5ffacb6f-fe90-404c-acfd-d37d9b564cbe","order_by":16,"name":"Shao-Zhen Yan","email":"","orcid":"","institution":"Department of Radiology and Nuclear Medicine, Xuanwu Hospital, Capital Medical University","correspondingAuthor":false,"prefix":"","firstName":"Shao-Zhen","middleName":"","lastName":"Yan","suffix":""}],"badges":[],"createdAt":"2025-11-23 08:25:07","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8184263/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8184263/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":96805973,"identity":"0512dd52-5adb-46bc-86c3-0a6628006d4a","added_by":"auto","created_at":"2025-11-26 09:13:24","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":809368,"visible":true,"origin":"","legend":"\u003cp\u003eSchematic workflow from network mapping to targeted modulation in Alzheimer’s disease. (A) An iteration based method was employed to establish the IFN, starting with the Yeo parcellation as the initialization. The mean time \u0026nbsp;series of each functional network were weighted by variability and tSNR. Then, vertices were assigned to different \u0026nbsp;functional networks based on the correlation between the time series of each vertex and each functional network, with the \u0026nbsp;parcellation updated accordingly. This process was repeated 10 times to achieve convergence. (B) The functional \u0026nbsp;topography was used to identify subjects, ensuring their individual-specific characteristics. (C) Machine learning \u0026nbsp;techniques were applied to validate the clinical relevance of functional network topography. A classification model and a \u0026nbsp;regression model were employed to classify patients and predict their cognition, respectively. (D) The relationships \u0026nbsp;between functional network alterations and structural atrophy were also explored. (E) tACS flowchart. (F) tACS-induced \u0026nbsp;modifications of IFN topography in AD were assessed.\u003c/p\u003e","description":"","filename":"Figure1XXX.png","url":"https://assets-eu.researchsquare.com/files/rs-8184263/v1/cd47615d1d11efc391fe3f61.png"},{"id":96805976,"identity":"076ee8bd-8c99-496f-ab28-02a949585b2e","added_by":"auto","created_at":"2025-11-26 09:13:24","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1405708,"visible":true,"origin":"","legend":"\u003cp\u003eFunctional fingerprints and hierarchical network disruption in AD. (A) The three participants include a normal \u0026nbsp;control, a participant with mild cognitive impairment (MCI), and a patient with AD. The first column shows the template \u0026nbsp;of each functional network in color, and the black bold line labels the network belonging whose probability is no less than \u0026nbsp;5% in NC (i.e. normative range). Each of the other columns represents a subject. The first row represents the whole-brain \u0026nbsp;discrete network parcellation, whereas the subsequent three rows represent the dorsal attention B, control C, and default A \u0026nbsp;networks. For each network, the discrete parcellation and the network weight map are displayed. (B) The activity \u0026nbsp;homogeneity inside each functional network. ****P \u0026lt; 0.0001. (C) The performance of network topography in individual \u0026nbsp;recognition. (D) The across-subject variability of NC and AD are displayed. (E) Cortical thinning potentially drives \u0026nbsp;alterations in the brain's hierarchical structure. Left: spatial distribution of across-subject variability alterations in AD; \u0026nbsp;Center: cortical atrophy map derived from vertex-wise t-tests comparing AD and NC; Right: vertex-wise correlation \u0026nbsp;between cortical atrophy and alterations in across-subject variability of functional topography, inset histograms represent \u0026nbsp;null distributions from permutation testing.\u003c/p\u003e","description":"","filename":"Figure2XXXBC.png","url":"https://assets-eu.researchsquare.com/files/rs-8184263/v1/eadfeccd695334a6206172ae.png"},{"id":96916265,"identity":"7b84c6b0-07d9-4364-90b6-34a241a1c957","added_by":"auto","created_at":"2025-11-27 14:08:20","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":643210,"visible":true,"origin":"","legend":"\u003cp\u003eAlterations of functional networks area in Alzheimer’s disease. (A) The group-average parcellation of NC \u0026nbsp;and AD is displayed, showing high similarity to both the group-level initialization and between NC and AD. (B) The \u0026nbsp;differences in the functional network topographic structure between the NC and AD groups, with the location and area of \u0026nbsp;the differences highlighted. Vertices are colored according to the average partition pattern of the NC group. (C) \u0026nbsp;Reproducibility of altered functional network topography patterns in AD across independent datasets. (D) The alterations \u0026nbsp;of FN’s areas in AD in MCAD, show the differences in the spatial patterns of the limbic networks among the NC, MCI, \u0026nbsp;and AD groups. *p \u0026lt; 0.05, **p \u0026lt; 0.01, ***p \u0026lt; 0.001, ****p \u0026lt; 0.0001.\u003c/p\u003e","description":"","filename":"Figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-8184263/v1/b3ada53276344732ec41f462.png"},{"id":96917243,"identity":"f519ba66-24b6-46db-9532-98fb7b23ba8a","added_by":"auto","created_at":"2025-11-27 14:09:25","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":515830,"visible":true,"origin":"","legend":"\u003cp\u003eDeviation patterns of IFN topography in Alzheimer’s disease. The alterations of network distribution in AD \u0026nbsp;were using the Mann-Whitney U test.\u003c/p\u003e","description":"","filename":"Figure4.png","url":"https://assets-eu.researchsquare.com/files/rs-8184263/v1/f5f7e3aa3ce39db61526a7b7.png"},{"id":96805974,"identity":"e93af1ff-fb94-40b0-8c77-8ecb300d035b","added_by":"auto","created_at":"2025-11-26 09:13:24","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":811492,"visible":true,"origin":"","legend":"\u003cp\u003etACS stimulation suppresses alterations in functional brain network topology in AD. (A) Cognitive changes \u0026nbsp;across groups. (B) It shows a significant increase in the number of participants with improved MMSE after 3 weeks of real \u0026nbsp;tACS. (C) Deviation patterns of IFN topography across four networks showing significant alterations after tACS. The first \u0026nbsp;row depicts contraction–expansion patterns identified in the MCADI cohort; the second row shows significant changes in \u0026nbsp;the same regions between active and sham groups after three weeks of stimulation; and the third row illustrates alterations \u0026nbsp;in these regions at the three-month follow-up. Highlighted regions showing significant group differences. (C) Differences \u0026nbsp;between the active groups at the three-week and three-month time points, where no significant effects were observed. \u0026nbsp;Colored regions indicate z-value changes falling within the range of deviations identified in the MCADI dataset. (D) Cross dataset reproducibility of the similarity between tACS-induced patterns and the AD-HC deviation pattern.\u003c/p\u003e","description":"","filename":"figure5XXXXXXXXXXXX3w.png","url":"https://assets-eu.researchsquare.com/files/rs-8184263/v1/640a67dfc5d3ea62701d8674.png"},{"id":98629653,"identity":"145d1e45-229c-410c-b58b-d904249ddf9d","added_by":"auto","created_at":"2025-12-19 17:14:25","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2412470,"visible":true,"origin":"","legend":"Article File","description":"","filename":"manuscript251123.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8184263/v1_covered_756fb391-583d-465b-abdf-86c2037b8c80.pdf"},{"id":96805977,"identity":"31b63d18-86dd-4ad1-b640-7a01c40408cd","added_by":"auto","created_at":"2025-11-26 09:13:24","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":7645205,"visible":true,"origin":"","legend":"Supplementary Material","description":"","filename":"suppltacs251121zrs.docx","url":"https://assets-eu.researchsquare.com/files/rs-8184263/v1/dffac8dec7156536717bf427.docx"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Functional Hierarchy Disruption: A Mechanistic Link to Cognitive Decline and Treatment Targets in Alzheimer’s Disease","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-8184263/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8184263/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Alzheimer’s disease (AD) is marked by disrupted brain network connectivity, which impairs functional hierarchy and contributes to cognitive decline. Two fundamental questions, however, remain open: what specific changes occur in the hierarchical organization of the AD brain, and whether rectifying these changes can restore cognitive function. To answer these, we first analyzed individualized functional hierarchical architecture across three large, independent fMRI datasets (MCADI, N = 711; ADNI, N = 621; OASIS-3, N = 506). We identified a reproducible pattern of hierarchical remodeling in AD, characterized by expansion of the dorsal attention network A and shrinkage of the control network A, with spatial variability shaped by underlying brain tissue properties. To evaluate the therapeutic relevance of this signature, we conducted a randomized controlled trial of transcranial alternating current stimulation (tACS; N=44). Targeted stimulation selectively reversed the remodeling trajectory, suppressing dorsal attention network expansion and countering control network contraction. These network improvements persisted for three months and were accompanied by sustained cognitive gains, with 80% of participants showing measurable improvement. Our results reveal a functional hierarchical signature of AD and establish its potential as a novel interventional target, while also providing mechanistic insights into the action of non-invasive neuromodulation.","manuscriptTitle":"Functional Hierarchy Disruption: A Mechanistic Link to Cognitive Decline and Treatment Targets in Alzheimer’s Disease","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-26 09:13:20","doi":"10.21203/rs.3.rs-8184263/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"bd2eddcd-e2e7-4006-88e2-9d62193f5b7b","owner":[],"postedDate":"November 26th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":58516521,"name":"Biological sciences/Neuroscience/Cognitive neuroscience"},{"id":58516522,"name":"Health sciences/Biomarkers/Prognostic markers"},{"id":58516523,"name":"Biological sciences/Neuroscience/Diseases of the nervous system/Alzheimer's disease"}],"tags":[],"updatedAt":"2026-02-02T11:30:55+00:00","versionOfRecord":[],"versionCreatedAt":"2025-11-26 09:13:20","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8184263","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8184263","identity":"rs-8184263","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}