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Multimodal atlas of single neuron metabolic electrophysiological coupling uncovers circadian rewiring.

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Paper

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The authors' code

R · 22 lines · 637 B · no license

  1. elec <- data.frame(elec)
  2. colnames(elec) <- c("Iamp","Tr","Td","Iauc","Freq")
  3. elec$Cluster <- as.factor(cluster)
  5. y_mean <- matrix(0,ncol(elec),length(clu))
  6. x_mean <- matrix(0,ncol(t(data)),length(clu))
  7. for(i in 1:length(clu)){
  8. y_mean[,i] <- apply(elec[cluster==clu[i],],2,function(x){mean(x)})
  9. x_mean[,i] <- apply(t(data)[cluster==clu[i],],2,function(x){mean(x)})
  10. }
  11. pheatmap::pheatmap(t(scale(t(y_mean))),cluster_cols = F,border_color = 'white',
  12. cluster_rows = F)
  14. x_y_mean_cor <- psych::corr.test(t(x_mean),t(y_mean))[['r']]
  15. x_y_mean_p <- psych::corr.test(t(x_mean),t(y_mean))[['p']]

correlation.R at commit dfb43e1, no license · at the source

Overview

Authors: Man Yuan1, Siyuan Ge1, Wenwei Qian1, Chenjian Miao1, Wei Liang1, Qi Chen1, Hongying Zhu1,2, Wei Xiong1,2
ORCID iDs: Wei Liang
  1. Department of Neurology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, State Key Laboratory of Eye Health, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
  2. Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
Institutions: University of Science and Technology of China (China)
Journal: iScience, volume 29, issue 7, article 116337
Dates: received 22 January 2026; accepted 26 May 2026; published online 11 June 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1016/j.isci.2026.116337 · PMID 42325561 · PMCID PMC13276300 · OpenAlex W7164355776
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Evoked potentials, Connectivity, Graphs
Keywords: cellular physiology, neuroscience, metabolomics
Topic: Circadian rhythm and melatonin (Endocrine and Autonomic Systems, Neuroscience), according to OpenAlex
Funding: National Key Research and Development Program of China (2021YFA0804900); Anhui Provincial Department of Science and Technology (202303a07020005); National Natural Science Foundation of China (82521101, 32121002, 32430045, 32225020, 32471080, 32541072, U25C2012, 32322033); Chinese Academy of Sciences (XDB39050000); Youth Innovation Promotion Association of the Chinese Academy of Sciences; Canadian Anesthesiologists&apos; Society; Key Research Program of Frontier Science, Chinese Academy of Sciences (ZDBS-LY-SM002); Fundamental Research Funds for the Central Universities
Citations: not cited yet (Europe PMC); 74 references in the paper

Abstract

Neuronal metabolism fundamentally modulates synaptic activity, yet how single-cell metabolic architecture aligns with electrophysiological diversity remains elusive. By integrating patch-clamp electrophysiology with single-neuron mass spectrometry (SNMS), we resolve metabolomic heterogeneity across suprachiasmatic nucleus (SCN) neurons, revealing six metabolic states with distinct synaptic dynamics, from lipid-enriched SCN1 exhibiting high-frequency presynaptic activity to quiescent SCN6. Pathway analysis linked metabolic state-specific signatures to sulfur metabolism, glutathione regulation, and citrate cycle dynamics. Machine learning and correlation networks mapped metabolites to functional parameters: histidine, carnitine, and creatinine regulated neuronal activity, validated by intracellular metabolite delivery experiments. Strikingly, light-dark cycles dynamically reconfigured most of the metabolite-postsynaptic current correlations, including light-induced taurine coupling to synaptic transmission. This multimodal platform establishes cellular metabolism as a tunable factor associated with neuronal heterogeneity and circadian plasticity, suggesting potential therapeutic avenues for circadian disorders.

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

Repository

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

SNMS-ctrl/SNMS

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: dfb43e1ff5423454273909425b5d6db1c2ae9c27, 20 February 2026
Languages: R (3), MATLAB (1)
Size: 4 files, 4 scripts
Software Heritage: not archived
Found in: “Data and code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: pheatmap (2 files), Seurat (2 files), ggplot2 (1 file), patchwork (1 file), psych (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
4 files
At the source: github.com/SNMS-ctrl/SNMS

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;
  • 4 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

No dataset and no data link were found in the paper.

Data and code availability

The raw single-cell mass spectrometry data and electrophysiological data generated in this study have been deposited in the MassIVE database under the accession code MassIVE: MSV000101065 and are publicly available as of the date of publication. The custom codes in this study are uploaded to GitHub (https://github.com/SNMS-ctrl/SNMS).

Reproduced under the paper's license (CC BY-NC), 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, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 3 keywords, 8 funders, 74 references.

Cite

This paper

Yuan, M., Ge, S., Qian, W., Miao, C., Liang, W., Chen, Q., Zhu, H., & Xiong, W. (2026). Multimodal atlas of single neuron metabolic electrophysiological coupling uncovers circadian rewiring. iScience, 29(7), 116337. https://doi.org/10.1016/j.isci.2026.116337

BibTeX

@article{yuan2026multimodal,
author = {Yuan, Man and Ge, Siyuan and Qian, Wenwei and Miao, Chenjian and Liang, Wei and Chen, Qi and Zhu, Hongying and Xiong, Wei},
title = {{Multimodal atlas of single neuron metabolic electrophysiological coupling uncovers circadian rewiring}},
journal = {iScience},
year = {2026},
month = jun,
volume = {29},
number = {7},
pages = {116337},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.116337},
url = {https://doi.org/10.1016/j.isci.2026.116337},
pmid = {42325561},
pmcid = {PMC13276300}
}

RIS

TY - JOUR
AU - Yuan, Man
AU - Ge, Siyuan
AU - Qian, Wenwei
AU - Miao, Chenjian
AU - Liang, Wei
AU - Chen, Qi
AU - Zhu, Hongying
AU - Xiong, Wei
TI - Multimodal atlas of single neuron metabolic electrophysiological coupling uncovers circadian rewiring
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/06/11
VL - 29
IS - 7
SP - 116337
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.116337
UR - https://doi.org/10.1016/j.isci.2026.116337
LA - en
ER -

CSL-JSON

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"issued": {
"date-parts": [
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}
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