OSCR

Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment.

Overview

Authors: Thomas Simon1, David N Buckley1, Zeyi Yang1, Chikako Matsuba1, Ben Y Tew1, Gerald C Gooden1, Kyle Hurth2, Steven A Toms3, David D Tran4,5, Gabriel Zada4,5, Matthew P Salomon1, Bodour Salhia1,5
  1. Department of Cancer Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
  2. Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
  3. Department of Neurosurgery and Medicine, Brown University Health, The Warren Alpert Medical School of Brown University, Providence, RI USA
  4. Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
  5. Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
Institutions: University of Southern California (United States); Brown University (United States); USC Norris Comprehensive Cancer Center (United States)
Journal: Communications biology, volume 9, issue 1, article 714
Dates: received 30 July 2024; accepted 12 March 2026; published online 1 April 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s42003-026-09915-1 · PMID 41917370 · PMCID PMC13201622 · OpenAlex W7147575840
Open access: gold, a free copy (OpenAlex)
Status: code on request
Categories: genetics / omics (modality), human (organism), other condition (population), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, fMRI & imaging
Keywords: Cancer microenvironment, CNS cancer, Cancer genomics, Next-generation sequencing
MeSH: Brain Neoplasms*, Cancer-Associated Fibroblasts*, Single-Cell Analysis*, Tumor Microenvironment*, Cell Communication, Cell Line, Tumor, Extracellular Matrix, Gene Expression Regulation, Neoplastic, Humans (* major topic)
Topic: Brain Metastases and Treatment (Pulmonary and Respiratory Medicine, Medicine), according to OpenAlex
Funding: NCI NIH HHS (P30 CA014089)
Citations: not cited yet (Europe PMC); 70 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Code

The paper says that its authors' code is available on request: it was not published with the paper, so there is nothing to verify.

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it says that the code is available on request

Read it in the paper: doi.org/10.1038/s42003-026-09915-1.

Tracing map

A tracing map links a paper to the code its authors published: this paper has none (its code is available on request), so it has no map.

Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it points to a dataset: NCBI GEO GSE322964
  • it says that the data are available on request
  • it says that the code is available on request

Read it in the paper: doi.org/10.1038/s42003-026-09915-1.

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, 12 authors, 4 keywords, 9 MeSH terms, 1 funder, 70 references.

Cite

This paper

Simon, T., Buckley, D. N., Yang, Z., Matsuba, C., Tew, B. Y., Gooden, G. C., Hurth, K., Toms, S. A., Tran, D. D., Zada, G., Salomon, M. P., & Salhia, B. (2026). Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment. Communications biology, 9(1), 714. https://doi.org/10.1038/s42003-026-09915-1

BibTeX

@article{simon2026single,
author = {Simon, Thomas and Buckley, David N and Yang, Zeyi and Matsuba, Chikako and Tew, Ben Y and Gooden, Gerald C and Hurth, Kyle and Toms, Steven A and Tran, David D and Zada, Gabriel and Salomon, Matthew P and Salhia, Bodour},
title = {{Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment}},
journal = {Communications biology},
year = {2026},
month = apr,
volume = {9},
number = {1},
pages = {714},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-026-09915-1},
url = {https://doi.org/10.1038/s42003-026-09915-1},
pmid = {41917370},
pmcid = {PMC13201622}
}

RIS

TY - JOUR
AU - Simon, Thomas
AU - Buckley, David N
AU - Yang, Zeyi
AU - Matsuba, Chikako
AU - Tew, Ben Y
AU - Gooden, Gerald C
AU - Hurth, Kyle
AU - Toms, Steven A
AU - Tran, David D
AU - Zada, Gabriel
AU - Salomon, Matthew P
AU - Salhia, Bodour
TI - Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/04/01
VL - 9
IS - 1
SP - 714
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/s42003-026-09915-1
UR - https://doi.org/10.1038/s42003-026-09915-1
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s42003-026-09915-1",
"type": "article-journal",
"title": "Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment",
"container-title": "Communications biology",
"author": [
{
"family": "Simon",
"given": "Thomas"
},
{
"family": "Buckley",
"given": "David N"
},
{
"family": "Yang",
"given": "Zeyi"
},
{
"family": "Matsuba",
"given": "Chikako"
},
{
"family": "Tew",
"given": "Ben Y"
},
{
"family": "Gooden",
"given": "Gerald C"
},
{
"family": "Hurth",
"given": "Kyle"
},
{
"family": "Toms",
"given": "Steven A"
},
{
"family": "Tran",
"given": "David D"
},
{
"family": "Zada",
"given": "Gabriel"
},
{
"family": "Salomon",
"given": "Matthew P"
},
{
"family": "Salhia",
"given": "Bodour"
}
],
"container-title-short": "Commun Biol",
"volume": "9",
"issue": "1",
"page": "714",
"DOI": "10.1038/s42003-026-09915-1",
"PMID": "41917370",
"PMCID": "PMC13201622",
"ISSN": "2399-3642",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s42003-026-09915-1",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
1
]
]
}
}

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1038/s41419-026-08807-w [code]
Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.
Journal: Cell death & disease
In common: genetics / omics, other condition, cellular / molecular, 6 references
[2] doi:10.1016/j.xcrm.2026.102766 [code]
A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.
Journal: Cell reports. Medicine
In common: genetics / omics, other condition, cellular / molecular, 6 references
[3] doi:10.1038/s41467-026-70715-6
Identification of altered immune landscape at single-cell resolution in NSCLC brain metastasis and its association with poor immune checkpoint inhibitor responses.
Journal: Nature communications
In common: other condition, cellular / molecular, 4 references
[4] doi:10.1038/s41467-026-75722-1 [code]
Single-nucleus analysis of the adult human olfactory epithelium uncovers shared neurogenesis programs with the brain.
Journal: Nature communications
In common: genetics / omics, 5 references
[5] doi:10.1038/s41467-026-71803-3 [code]
Charting the transition from in vitro gliogenesis to the in vivo maturation of human glial progenitor cells transplanted into the hypomyelinated mouse brain.
Journal: Nature communications
In common: genetics / omics, cellular / molecular, 4 references
[6] doi:10.1038/s41593-026-02367-0 [code]
A reproducible three-dimensional model of human brain tissue to investigate physiological and disease-associated microglia phenotypes.
Journal: Nature neuroscience
In common: cellular / molecular, 5 references
[7] doi:10.1038/s41598-026-51295-3
Immune landscape of the affected brain in Rasmussen encephalitis.
Journal: Scientific reports
In common: genetics / omics, other condition, cellular / molecular, 4 references
[8] doi:10.1186/s40478-026-02402-y
Overactivation of SHH signaling induces a cascade of dedifferentiation and oncogenesis in a new mouse model for choroid plexus carcinoma.
Journal: Acta neuropathologica communications
In common: genetics / omics, other condition, cellular / molecular, 4 references
[9] doi:10.1371/journal.pone.0343734
Single-cell transcriptomic profiling of C. elegans Q neuroblast lineage during migration and differentiation.
Journal: PloS one
In common: genetics / omics, 4 references
[10] doi:10.1093/brain/awaf426 [code]
Single-nucleus multiome shows motor neuron glutamate overactivation in amyotrophic lateral sclerosis.
Journal: Brain : a journal of neurology
In common: genetics / omics, other condition, 4 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.