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In vivo profiling of astrocyte secretome reveals brain-region specific regulatory networks in a mouse model of amyloid pathology.

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Paper

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The authors' code

R · 47 lines · 1.6 KB · CC-BY-4.0

  1. # 01_data_preprocessing.R
  2. # Data input, missing value imputation, sample aggregation (technical replicates)
  4. rm(list = ls())
  5. library(openxlsx)
  6. source("scripts/utils.R") # if needed for later, but not used in this script
  8. # Input
  9. all_protein_imput <- read.xlsx("data/protein_Samplematrix_imputeNA.xlsx", rowNames = TRUE)
  10. all_protein <- read.xlsx("data/Protein_Matrix_annotation.xlsx", rowNames = TRUE)
  12. # Align column order
  13. all_protein <- all_protein[, colnames(all_protein_imput)]
  14. rownames(all_protein) <- rownames(all_protein_imput)
  15. colnames(all_protein) <- colnames(all_protein)[order(colnames(all_protein), decreasing = TRUE)]
  17. all_protein <- as.matrix(all_protein)
  18. all_protein[is.na(all_protein)] <- 0
  20. # Separate replicates and non-replicates
  21. rep <- all_protein[, c(4,5,27,28)]
  22. all_protein_nonrep <- all_protein[, -c(4,27)]
  24. # Average triplicates
  25. nonrep <- matrix(nrow = nrow(all_protein_nonrep), ncol = ncol(all_protein_nonrep)/3)
  26. rownames(nonrep) <- rownames(all_protein_nonrep)
  27. for (i in 1:nrow(nonrep)) {
  28. m <- c()
  29. for (j in seq(1, 36, 3)) {
  30. m <- c(m, mean(all_protein_nonrep[i, j], all_protein_nonrep[i, j+1], all_protein_nonrep[i, j+2]))
  31. }
  32. nonrep[i, ] <- m
  33. }
  34. colnames(nonrep) <- sapply(strsplit(colnames(all_protein_nonrep)[seq(1,36,3)], "-"), "[", 1)
  36. # Extract non-zero proteins per sample
  37. samples <- list()
  38. for (i in 1:ncol(nonrep)) {
  39. colname <- colnames(nonrep)
  40. rowname <- rownames(nonrep)
  41. samples[[colname[i]]] <- rowname[which(nonrep[, i] != 0)]
  42. }
  44. # Save samples list as RDS for later scripts
  45. saveRDS(samples, "data/samples_list.rds")
  47. # Note: samples2 is loaded from EXO_DEPs.xlsx in subsequent scripts

01_data_preprocessing.R, under CC-BY-4.0 · at the source

Overview

Authors: Qiu Jiang1,2, Jian-Ni Hu1,2,3, Hao-Min Dong4, Jia-Yan Xin1,2, An-Yu Shi1,2, Gui-Hua Zeng1,2, Jie Liu1,2,4, Yan-Jiang Wang1,2
ORCID iDs: Yan-Jiang Wang
  1. Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042 China
  2. Chongqing Key Laboratory of Ageing and Brain Diseases, Chongqing, 400042 China
  3. Shigatse Branch, Xinqiao Hospital, Army Medical University (Third Military Medical University), Tibet, 857012 China
  4. Department of Cognitive Impairment Research, Chongqing Institute for Brain and Intelligence, Guangyang Bay Laboratory, Chongqing, 401336 China
Institutions: Army Medical University (China); Daping Hospital (China); Xinqiao Hospital (China); Chongqing Institute for Brain and Intelligence (China)
Journal: Molecular neurodegeneration, volume 21, issue 1, article 39
Dates: received 29 November 2025; accepted 16 May 2026; published online 23 May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1186/s13024-026-00956-y · PMID 42177534 · PMCID PMC13393950 · OpenAlex W7162203673
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), Alzheimer's / dementia (population), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions
Keywords: Alzheimer’s disease, Astrocyte, Secretome, Entorhinal cortex, Hippocampus, Early pathogenesis
MeSH: Alzheimer Disease*, Astrocytes*, Brain*, Entorhinal Cortex*, Secretome*, Animals, Disease Models, Animal, Hippocampus, Mice, Mice, Transgenic, Neurons (* major topic)
Topic: Alzheimer's disease research and treatments (Physiology, Medicine), according to OpenAlex
Funding: the Natural Science Foundation of China (82120108010); the National Key Research and Development Program (2023YFC3605400)
Citations: not cited yet (Europe PMC); 75 references in the paper

Abstract

Coordinated cell-to-cell communications is crucial for the proper functioning and maintenance of brain activities, and its disruption contributes to neurological disorders, including Alzheimer’s disease (AD). Altered astrocyte-neuron communications have been implicated in AD progression, yet the underlying regulatory networks remain poorly understood. Given that secretory proteins mediate both local and long-range intercellular signaling, we constructed a spatiotemporal profile of the astrocyte-derived secretome using in vivo TurboID proximity labeling in mice of amyloid pathology. Early alterations in the entorhinal cortex secretome were identified and enriched in metabolic pathways, whereas changes in the hippocampus were observed later, correlating with neuronal and synaptic maintenance. These findings suggest that early remodeling of the astrocyte secretome in the entorhinal cortex may be involved in AD pathogenesis, while later changes in the hippocampus contribute to neurodegeneration and cognitive decline. This work provides a systematic map of the dynamic, region-specific remodeling of the astrocyte secretome in AD, identifying novel spatiotemporal vulnerabilities and potential therapeutic targets.

Supplementary Information: The online version contains supplementary material available at 10.1186/s13024-026-00956-y.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

Zenodo 20131790

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (5 files), clusterProfiler (2 files), car (1 file), cowplot (1 file), patchwork (1 file), reshape2 (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
8 files
At the source:

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 7 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (https://proteomecentral.proteomexchange.org) via the iProX partner repository [74, 75] with the dataset identifier PXD078262 and PXD078308. All bioinformatics analysis scripts are publicly available in the Zenodo repository at 10.5281/zenodo.20131790.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 6 keywords, 11 MeSH terms, 2 funders, 75 references.

Cite

This paper

Jiang, Q., Hu, J.-N., Dong, H.-M., Xin, J.-Y., Shi, A.-Y., Zeng, G.-H., Liu, J., & Wang, Y.-J. (2026). In vivo profiling of astrocyte secretome reveals brain-region specific regulatory networks in a mouse model of amyloid pathology. Molecular neurodegeneration, 21(1), 39. https://doi.org/10.1186/s13024-026-00956-y

BibTeX

@article{jiang2026vivo,
author = {Jiang, Qiu and Hu, Jian-Ni and Dong, Hao-Min and Xin, Jia-Yan and Shi, An-Yu and Zeng, Gui-Hua and Liu, Jie and Wang, Yan-Jiang},
title = {{In vivo profiling of astrocyte secretome reveals brain-region specific regulatory networks in a mouse model of amyloid pathology}},
journal = {Molecular neurodegeneration},
year = {2026},
month = may,
volume = {21},
number = {1},
pages = {39},
publisher = {BMC},
issn = {1750-1326},
doi = {10.1186/s13024-026-00956-y},
url = {https://doi.org/10.1186/s13024-026-00956-y},
pmid = {42177534},
pmcid = {PMC13393950}
}

RIS

TY - JOUR
AU - Jiang, Qiu
AU - Hu, Jian-Ni
AU - Dong, Hao-Min
AU - Xin, Jia-Yan
AU - Shi, An-Yu
AU - Zeng, Gui-Hua
AU - Liu, Jie
AU - Wang, Yan-Jiang
TI - In vivo profiling of astrocyte secretome reveals brain-region specific regulatory networks in a mouse model of amyloid pathology
T2 - Molecular neurodegeneration
J2 - Mol Neurodegener
PY - 2026
DA - 2026/05/23
VL - 21
IS - 1
SP - 39
SN - 1750-1326
PB - BMC
DO - 10.1186/s13024-026-00956-y
UR - https://doi.org/10.1186/s13024-026-00956-y
LA - en
ER -

CSL-JSON

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"author": [
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"family": "Jiang",
"given": "Qiu"
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"container-title-short": "Mol Neurodegener",
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"PMCID": "PMC13393950",
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"date-parts": [
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23
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}
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The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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