PreprintCited by 4Alzheimer's disease research and treatmentsDementia and Cognitive Impairment ResearchGenomic variations and chromosomal abnormalities

Mosaic chromosomal alterations in blood are associated with an increased risk of Alzheimer’s disease

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Naito, Tatsuhiko, Hirata, Kosei, Jang, Beomjin, Lakhani, Chirag M., Buonfiglioli, Alice, Lee, Wan-Ping, Valladares, Otto, Wang, Li-San +6 more·2025·medRxiv

Abstract

Mosaic chromosomal alterations (mCAs) in blood, a form of clonal hematopoiesis, have been linked to various diseases, but their role in Alzheimer’s disease (AD) remains unclear. We analyzed blood whole-genome sequencing (WGS) data from 24,049 individuals in the Alzheimer’s Disease Sequencing Project and found that autosomal mCAs were significantly associated with increased AD risk (odds ratio = 1.27; P = 1.3 × 10 −5 ). This association varied by ancestry, mCA subtype, APOE ε4 allele status, and chromosomal location. Using matched blood WGS and brain single-nucleus RNA-seq data, we identified microglia-annotated cells in the brain carrying the same mCAs found in blood. These findings suggest that blood mCAs may contribute to AD pathogenesis, potentially through infiltration into the brain and influencing local immune response.

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Crossref · 10.1101/2025.05.29.25328544

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  • Recent evidence identifies peripheral somatic clones within human brain-resident microglia.

    “This mechanism is supported by recent evidence identifying peripheral somatic clones within human brain-resident microglia [34]”

    From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]

    The Main section reports microglia-annotated brain cells carrying the same mosaic chromosomal alterations as cells in blood, supporting the presence of peripheral somatic alterations in that cell population. It does not establish that these cells are brain-resident microglia: the authors say the finding raises the possibility that blood-derived monocytes entered the brain. (LLM, conf=0.87)

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  • Mechanistic insights provide a plausible biological framework for the heterogeneous and sometimes contradictory epidemiological findings observed across studies, particularly those derived from shared cohorts such as the ADSP.

    “These mechanistic insights provide a plausible biological framework for the heterogeneous and sometimes contradictory epidemiological findings observed across studies, particularly those derived from shared cohorts such as the ADSP [10,13,34].”

    From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]

    The Main section reports contrasting findings: an earlier multicohort study found CHIP protective against Alzheimer’s disease, whereas this paper finds CHIP associated with increased risk. It also proposes a possible microglial mechanism and analyzes ADSP data. It does not establish that this mechanism explains differences across epidemiological studies, particularly studies using shared ADSP cohorts; that framework is the citing authors’ interpretation. (LLM, conf=0.82)

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  • The impact of somatic mosaicism on the brain depends heavily on the specific genetic architecture of the clonal expansion.

    “Collectively, these findings suggest that the impact of somatic mosaicism on the brain depends heavily on the specific genetic architecture of the clonal expansion.”

    From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]

    The Main section reports that Alzheimer’s disease risk associations differ by mCA type and chromosomal location, supporting the idea that genetic features matter. But the paper measures associations with Alzheimer’s disease, not whether the genetic architecture of a clonal expansion determines its impact on the brain; the Main section also says a causal relationship and the biological relevance of the brain-cell findings require further study. No page numbers are available in our copy. (LLM, conf=0.82)

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  • Three independent analytical frameworks have been applied to the same ADSP cohort, yielding disparate results.

    “Notably, three independent analytical frameworks have now been applied to the same ADSP cohort, yielding disparate results.”

    From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]

    The Methods section (page unavailable) confirms that this paper analyzes the ADSP release R4 cohort. The Main section reports an increased AD risk associated with CHIP in its data and contrasts this with a previously reported protective effect, but it does not identify three independent analytical frameworks applied to the same ADSP cohort or compare their results. (LLM, conf=0.82)

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  • Identical mCA clones were identified within a subset of brain-resident microglia exhibiting a pro-inflammatory transcriptional profile, providing direct evidence that large-scale somatic mosaicism in the blood can mirror pathological immune states in the CNS.

    “the study identified identical mCA clones within a subset of brain-resident microglia that exhibited a pro-inflammatory transcriptional profile characterized by the upregulation of MHC-II processing genes and markers of cellular senescence, providing direct evidence that large-scale somatic mosaicism in the blood can mirror pathological immune states in the CNS [34].”

    From Clonal Hematopoiesis of Indeterminate Potential as an Emerging Interdisciplinary Risk Factor in Alzheimer’s Disease: Current Evidence and Future Directions (2026) · cites this paper as [34]

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Research works printed but not linked: 23

  1. [2]Brown D. W. Shared and distinct genetic etiologies for different types of clonal hematopoiesis. Nat. Commun. 14, 5536 (2023). 37684235 PMC10491829
  2. [3]Xie M. Age-related mutations associated with clonal hematopoietic expansion and malignancies. Nat. Med. 20, 1472– 1478 (2014). 25326804 PMC4313872
  3. [4]Jaiswal S. Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease. N. Engl. J. Med. 377, 111– 121 (2017). 28636844 PMC6717509
  4. [5]Miller P. G. Association of clonal hematopoiesis with chronic obstructive pulmonary disease. Blood 139, 357– 368 (2022). 34855941 PMC8777202
  5. [8]Huang A. Y. Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer’s disease microglia. bioRxivorg (2024) doi: 10.1101/2024.01.03.574078. · DOI · Paper page
  6. [9]Kar S. P. Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis. Nat. Genet. 54, 1155– 1166 (2022). 35835912 PMC9355874
  7. [10]Jakubek Y. A. Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing. Nat. Genet. 55, 1912– 1919 (2023). 37904051 PMC10632132
  8. [11]Beecham G. W. The Alzheimer’s Disease Sequencing Project: Study design and sample selection. Neurol. Genet. 3, e194 (2017). 29184913 PMC5646177
  9. [12]Leung Y. Y. Alzheimer’s Disease Sequencing Project release 4 whole genome sequencing dataset. medRxiv (2024) doi: 10.1101/2024.12.03.24317000. PMC12100500 40407102 · DOI
  10. [13]Emrani S., Arain H. A., DeMarshall C. & Nuriel T. APOE4 is associated with cognitive and pathological heterogeneity in patients with Alzheimer’s disease: a systematic review. Alzheimers. Res. Ther. 12, 141 (2020). 33148345 PMC7643479
  11. [14]Abellanas M. A., Purnapatre M., Burgaletto C. & Schwartz M. Monocyte-derived macrophages act as reinforcements when microglia fall short in Alzheimer’s disease. Nat. Neurosci. 28, 436– 445 (2025). 39762659
  12. [15]Bennett D. A. Religious Orders Study and Rush Memory and Aging Project. J. Alzheimers. Dis. 64, S161– S189 (2018). 29865057 PMC6380522
  13. [16]Fujita M. Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain. Nat. Genet. 56, 605– 614 (2024). 38514782 PMC12288883
  14. [18]Gao T. Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes. Nat. Biotechnol. 41, 417– 426 (2023). 36163550 PMC10289836
  15. [19]Green G. S. Cellular communities reveal trajectories of brain ageing and Alzheimer’s disease. Nature 633, 634– 645 (2024). 39198642 PMC11877878
  16. [22]Wei Y. & Li X. Different phenotypes of microglia in animal models of Alzheimer disease. Immun. Ageing 19, 44 (2022). 36209099 PMC9547462
  17. [23]Manichaikul A. Robust relationship inference in genome-wide association studies. Bioinformatics 26, 2867– 2873 (2010). 20926424 PMC3025716
  18. [24]McLaren W. The Ensembl Variant Effect Predictor. Genome Biol. 17, 122 (2016). 27268795 PMC4893825
  19. [25]Wolf F. A., Angerer P. & Theis F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018). 29409532 PMC5802054
  20. [26]Wolock S. L., Lopez R. & Klein A. M. Scrublet: Computational identification of cell Doublets in Single-cell transcriptomic data. Cell Syst. 8, 281– 291.e9 (2019). 30954476 PMC6625319
  21. [27]Korsunsky I. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289– 1296 (2019). 31740819 PMC6884693
  22. [28]Zheng G. X. Y. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017). 28091601 PMC5241818
  23. [29]Sun N. Human microglial state dynamics in Alzheimer’s disease progression. Cell 186, 4386– 4403.e29 (2023). 37774678 PMC10644954

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Authors
Naito, T., Hirata, K., Jang, B., Lakhani, C. M., Buonfiglioli, A., Lee, W.-P., Valladares, O., Wang, L.-S., Okada, Y., Won, H.-H., Papapetrou, E. P., Marro, S. G., Knowles, D. A., & Raj, T.
Affiliations
  • New York Genome Center (US)
  • Icahn School of Medicine at Mount Sinai (US)
  • Samsung Medical Center (KR)
  • University of Pennsylvania (US)
  • RIKEN Center for Integrative Medical Sciences (JP)
  • Tisch Cancer Institute (US)
Corresponding author
Naito, Tatsuhiko
Venue
medRxiv
Publisher
openRxiv
Published
2025-06-04
OpenAlex
W4411016607
Cited by
4
References
6
Citations by year
2026: 2 · 2025: 2
Type
posted content
Language
en
Open access
Locations
  • medRxiv (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
Funders
  • BrightFocus Foundation
  • Georgia Clinical and Translational Science Alliance (UL1TR004419)
  • National Institutes of Health (1r21ag063130-01a1, 1s10od026880-01, 1rf1ag065926-01a1, 1r56ag055824-01a1, 1s10od030463-01, AG066514, NIA R01-AG054005, RF1-AG065926, UL1TR004419)
  • Japan Society for the Promotion of Science
  • National Institute on Aging (U01AG058635, R21-AG063130, U01AG068880, NIA R21-AG063130, R01AG054005, R56AG088669, R56- AG055824, RF1-AG065926, P30AG066514)
  • National Institute of Neurological Disorders and Stroke (U54NS123743, R01NS116006)
  • National Center for Advancing Translational Sciences (S10OD026880, S10OD030463)
Topics
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Keywords
mosaic chromosomal alterations, clonal hematopoiesis, Alzheimer's disease risk, microglia, APOE ε4, ancestry differences, neuroinflammation

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