PreprintCited by 0Gene expression and cancer classificationSingle-cell and spatial transcriptomicsGenetics, Aging, and Longevity in Model Organisms

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A bird’s eye view to the homeostatic, Alzheimer and Glioblastoma attractors

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Nieves, Joan, Gil, Gabriel, Gonzalez, Augusto·2023·Heliyon

Preprint — published as 10.1016/j.heliyon.2025.e42445 · Paper page

Abstract

SUMMARY: Available data for white matter of the brain allows to locate the normal (homeostatic), Glioblastoma and Alzheimer’s disease attractors in gene expression space and to identify paths related to transitions like carcinogenesis or Alzheimer’s disease onset. A predefined path for aging is also apparent, which is consistent with the hypothesis of programmatic aging. In addition, reasonable assumptions about the relative strengths of attractors allow to draw a schematic landscape of fitness: a Wright’s diagram. These simple diagrams reproduce known relations between aging, Glioblastoma and Alzheimer’s disease, and rise interesting questions like the possible connection between programmatic aging and Glioblastoma in this tissue. We anticipate that similar multiple diagrams in other tissues could be useful in the understanding of the biology of apparently unrelated diseases or disorders, and in the discovery of unexpected clues for their treatment. Graphical abstract: In brief: Aging, carcinogenesis and Alzheimer’s disease onset in white matter of the brain are shown as paths or directions in gene-expression space, a simple view that allows the analysis of their mutual relations and to rise interesting questions such as whether programmatic aging could be related to avoiding the Glioblastoma. Highlights: Normal homeostatic, Glioblastoma and Alzheimer’s disease attractors are apparent in gene-expression space The relative disposition of paths for carcinogenesis and Alzheimer’s disease onset reproduce known relations between these diseases The observed corridor for aging is consistent with programmatic aging Avoiding the fall into the huge basin of the Glioblastoma could be the subject of selection pressure Aged normal samples could be captured by the weak Alzheimer’s disease attractor

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Crossref · 10.1101/2023.11.23.568350

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Graphical abstract Graphical abstract In brief:Aging, carcinogenesis and Alzheimer's disease onset in white matter of the brain are shown as paths or directions in gene-expression space, a simple view that allows the analysis of their mutual relations and to rise interesting questions such as whether programmatic aging could be related to avoiding the Glioblastoma.
Graphical abstract Graphical abstract In brief:Aging, carcinogenesis and Alzheimer's disease onset in white matter of the brain are shown as paths or directions in gene-expression space, a simple view that allows the analysis of their mutual relations and to rise interesting questions such as whether programmatic aging could be related to avoiding the Glioblastoma.CC BY-NC-ND · PubMed Central
Fig. 1 Gene expression diagrams and schematic fitness landscape. a) Principal component analysis of the data studied in the paper. N – Normal homeostatic state, GB – Glioblastoma, AD – Alzheimer's disease state. The normal old samples are denoted by O. b) Schematics of the transitions between attractors. c) A Wright diagram showing a hypothetical contour plot of fitness. The absolute maximum corresponds to the GB state. The AD attractor is represented as a slight local maximum. d) Violin plot for the log-fold changes of MMP9 and BCYRN1 genes in N, AD and GB states. The geometric mean of the expression in the N state is taken as reference in order to compute differential expression values.
Fig. 1 Gene expression diagrams and schematic fitness landscape. a) Principal component analysis of the data studied in the paper. N – Normal homeostatic state, GB – Glioblastoma, AD – Alzheimer's disease state. The normal old samples are denoted by O. b) Schematics of the transitions between attractors. c) A Wright diagram showing a hypothetical contour plot of fitness. The absolute maximum corresponds to the GB state. The AD attractor is represented as a slight local maximum. d) Violin plot for the log-fold changes of MMP9 and BCYRN1 genes in N, AD and GB states. The geometric mean of the expression in the N state is taken as reference in order to compute differential expression values.CC BY-NC-ND · PubMed Central

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Cites

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Metadata

Authors
Nieves, J., Gil, G., & Gonzalez, A.
Affiliations
Instituto de Cibernética Matemática y Física (CU)
Corresponding author
Nieves, Joan
Venue
Heliyon
Publisher
openRxiv
Published
2023-11-23
Volume
11
Issue
4
Pages
e42445-e42445
ISSN
2405-8440 (ISSN-L)
OpenAlex
W4407133599
Cited by
0
References
1
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Heliyon (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Aging › Genetics, Aging, and Longevity in Model Organisms
Keywords
Alzheimer's disease, glioblastoma, attractors, white matter, dimensional reduction, carcinogenesis, aging, fitness landscape, disease onset

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