TGF-β signaling promotes astroglial activation and TDP-43 proteinopathy in organoid models of frontotemporal lobar degeneration.
The 16 matches
- [1] § Results › Precocious neurogenesis and astrogliogenesis in GRN–/– cortical organoids. ↔ B. Clustering_GRNKO.ipynb, lines 540–554 · score 0.89 · CT neuroblasts, mixed identity, early neuroblasts, ependymal cells, radial glia, inhibitory neuron
- [2] § Methods › Transcriptomics › Cell-cell communication analysis. ↔ C. Analysis_GRNKO.ipynb, lines 478–559 · score 0.85 · receiver cell, potential target genes, cell communication, cutoff, infer, predict
- [3] § Results › GRNR493X cortical organoids phenocopy astroglial phenotypes in GRN–/– cortical organoids. ↔ B. Clustering_GRNKO.ipynb, lines 540–554 · score 0.81 · LGE inhibitory neurons, mixed identity, ependymal cells, radial glia, neuroblasts, OPCs
- [4] § Methods › Transcriptomics › Reanalysis of other datasets. ↔ D. Subclustering_Ast_GRNKO.ipynb, lines 398–455 · score 0.78 · FindTransferAnchors, find anchors, reference UMAP, query, Sadick
- [5] § Results › GRNR493X cortical organoids phenocopy astroglial phenotypes in GRN–/– cortical organoids. ↔ B. Clustering_R493X.ipynb, lines 517–530 · score 0.72 · LGE inhibitory neurons, ependymal cells, radial glia, neuroblasts, OPCs, glioblasts
- [6] § Results › Precocious neurogenesis and astrogliogenesis in GRN–/– cortical organoids. ↔ B. Clustering_R493X.ipynb, lines 517–530 · score 0.69 · ependymal cells, radial glia, inhibitory neuron, neuroblasts, OPC, LGE
- [7] § Methods › Transcriptomics › Comparison with Bhaduri et al., 2020. ↔ D. Subclustering_Ast_GRNKO.ipynb, lines 398–455 · score 0.65 · MapQuery, FindTransferAnchors, UMAP
- [8] § Methods › Transcriptomics › Astroglia subclustering. ↔ B. Clustering_R493X.ipynb, lines 352–361 · score 0.61 · FindClusters, FindNeighbors, RunUMAP, resolution
- [9] § Methods › Transcriptomics › Astroglia subclustering. ↔ B. Clustering_GRNKO.ipynb, lines 148–159 · score 0.61 · FindClusters, FindNeighbors, RunUMAP, resolution
- [10] § Methods › Transcriptomics › Clustering and annotation. ↔ B. Clustering_R493X.ipynb, lines 352–361 · score 0.61 · FindClusters, FindNeighbors, RunUMAP, resolution, Clustering
- [11] § Methods › Transcriptomics › Clustering and annotation. ↔ B. Clustering_GRNKO.ipynb, lines 148–159 · score 0.61 · FindClusters, FindNeighbors, RunUMAP, resolution, Clustering
- [12] § Results › Precocious neurogenesis and astrogliogenesis in GRN–/– cortical organoids. ↔ C. Analysis_GRNKO.ipynb, lines 73–86 · score 0.60 · TMEM106B, EMX2, FOXG1, PSAP, WNT1, STMN2
- [13] § Results › Precocious neurogenesis and astrogliogenesis in GRN–/– cortical organoids. ↔ C. Analysis_R493X.ipynb, lines 78–85 · score 0.60 · TMEM106B, EMX2, FOXG1, PSAP, WNT1, STMN2
- [14] § Methods › Transcriptomics › Quality control, normalization, and dimensional reduction. ↔ B. Clustering_GRNKO.ipynb, lines 105–121 · score 0.54 · DoubletFinder, variable features, Elbow
- [15] § Results › Loss of PGRN leads to aberrant growth in cortical organoids. ↔ B. Clustering_GRNKO.ipynb, lines 484–523 · score 0.51 · S100B, radial glia, NES, progenitor, GFAP, SOX9
- [16] § Results › Loss of PGRN leads to aberrant growth in cortical organoids. ↔ B. Clustering_R493X.ipynb, lines 454–497 · score 0.51 · S100B, radial glia, NES, progenitor, GFAP, SOX9
Paper
Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC
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The authors' code
Jupyter notebook · 634 lines · 37 KB · no license · 6 matches
B. Clustering_GRNKO.ipynb at commit 7da0b92, no license · at the source
Overview
- Department of Pathology
- BMS Graduate Program, and
- Weill Institute for Neurosciences, UCSF, San Francisco, California, USA
- Department of Biological Chemistry, UCLA, Los Angeles, California, USA
- Department of Pathology & Immunology and
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research and
- Department of Neurology, UCSF, San Francisco, California, USA
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, Maryland, USA
Abstract
Dominant mutations in progranulin (GRN) gene cause frontotemporal lobar degeneration (FTLD-GRN), whereas homozygous GRN mutations lead to neuronal ceroid lipofuscinosis, a childhood neurodegenerative disorder. While recent transcriptomic studies reveal profound glial and neuronal pathology in FTLD-GRN at the disease end stage, the mechanism that disrupts glia-neuron homeostasis remains unclear. Using induced pluripotent stem cell–derived cortical organoids, we showed that GRN–/
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above, with 16 matches between paragraphs and lines of code.
Zenodo 20709533
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
11 files
- A. Filtering_GRNKO.ipynb — Jupyter, 178 lines
- A. Filtering_R493X.ipynb — Jupyter, 156 lines
- B. Clustering_GRNKO.ipynb — Jupyter, 634 lines
- B. Clustering_R493X.ipynb — Jupyter, 604 lines
- C. Analysis_GRNKO.ipynb — Jupyter, 784 lines
- C. Analysis_R493X.ipynb — Jupyter, 248 lines
- D. Subclustering_Ast_GRNKO.
ipynb — Jupyter, 455 lines - D. Subclustering_Ast_Mouse_
12m.ipynb — Jupyter, 322 lines - D. Subclustering_Ast_Mouse_
19m.ipynb — Jupyter, 329 lines - D. Subclustering_Ast_R493X.
ipynb — Jupyter, 396 lines - README.md — Text, 14 lines
arrenramsey/ramsey_et_al_2026
7da0b9261780f9da662acfc306cbf22121c13adf, 17 June 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
11 files, not copied: shown from their source
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- A. Filtering_GRNKO.ipynb — Jupyter, 178 lines, shown from its source
- A. Filtering_R493X.ipynb — Jupyter, 156 lines, shown from its source
- B. Clustering_GRNKO.ipynb — Jupyter, 634 lines, 6 matches, shown from its source
- B. Clustering_R493X.ipynb — Jupyter, 604 lines, 5 matches, shown from its source
- C. Analysis_GRNKO.ipynb — Jupyter, 784 lines, 2 matches, shown from its source
- C. Analysis_R493X.ipynb — Jupyter, 248 lines, 1 match, shown from its source
- D. Subclustering_Ast_GRNKO.
ipynb — Jupyter, 455 lines, 2 matches, shown from its source - D. Subclustering_Ast_Mouse_
12m.ipynb — Jupyter, 322 lines, shown from its source - D. Subclustering_Ast_Mouse_
19m.ipynb — Jupyter, 329 lines, shown from its source - D. Subclustering_Ast_R493X.
ipynb — Jupyter, 396 lines, shown from its source - README.md — Text, 16 lines, shown from its source
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scRNA-seq data have been deposited at GEO, and the accession number is GSE282668. All original code has been deposited at Zenodo (https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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Recorded: type, language, journal, volume, issue, pages, dates, 15 authors, 5 keywords, 12 MeSH terms, 5 funders, 50 references, 62 RRIDs.
Cite
This paper
Ramsey, A. C., Tang, X.-Y., Macias, M. J., Nano, P. R., Lu, R., Benito, B., Lau, C. M., Park, J., Zhang, J., Beatty, W., Mukhtar, T., Kriegstein, A. R., Bhaduri, A., Marsan, E., & Huang, E. J. (2026). TGF-β signaling promotes astroglial activation and TDP-43 proteinopathy in organoid models of frontotemporal lobar degeneration. The Journal of clinical investigation, 136(14), e190035. https://
BibTeX
@article{ramsey2026tgf,
author = {Ramsey, Arren C. and Tang, Xiao-Yan and Macias, Magdalena J. and Nano, Patricia R. and Lu, Rufei and Benito, Brian and Lau, Cameron M. and Park, Jisu and Zhang, Jiasheng and Beatty, Wandy and Mukhtar, Tanzila and Kriegstein, Arnold R. and Bhaduri, Aparna and Marsan, Elise and Huang, Eric J.},
title = {{TGF-β signaling promotes astroglial activation and TDP-43 proteinopathy in organoid models of frontotemporal lobar degeneration}},
journal = {The Journal of clinical investigation},
year = {2026},
month = jun,
volume = {136},
number = {14},
pages = {e190035},
publisher = {American Society for Clinical Investigation},
issn = {0021-9738},
doi = {10.1172/
url = {https://
pmid = {42302828},
pmcid = {PMC13367973}
}
RIS
TY - JOUR
AU - Ramsey, Arren C.
AU - Tang, Xiao-Yan
AU - Macias, Magdalena J.
AU - Nano, Patricia R.
AU - Lu, Rufei
AU - Benito, Brian
AU - Lau, Cameron M.
AU - Park, Jisu
AU - Zhang, Jiasheng
AU - Beatty, Wandy
AU - Mukhtar, Tanzila
AU - Kriegstein, Arnold R.
AU - Bhaduri, Aparna
AU - Marsan, Elise
AU - Huang, Eric J.
TI - TGF-β signaling promotes astroglial activation and TDP-43 proteinopathy in organoid models of frontotemporal lobar degeneration
T2 - The Journal of clinical investigation
J2 - J Clin Invest
PY - 2026
DA - 2026/
VL - 136
IS - 14
SP - e190035
SN - 0021-9738
PB - American Society for Clinical Investigation
DO - 10.1172/
UR - https://
LA - en
ER -
CSL-JSON
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