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Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma.

Code ↔ Paper

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The 3 matches
  1. [1] § Results › Transcriptomic analysis reveals potential mechanisms underlying both innate and acquired TMZ resistance in GBOs with MGMT methylation ↔ Code/RNA_analysis.R, lines 276–352 · score 0.69 · Gene Ontology, pathway enrichment, fold changes, DEGs, KEGG, GO
  2. [2] § Results › Transcriptomic analysis reveals potential mechanisms underlying both innate and acquired TMZ resistance in GBOs with MGMT methylation ↔ Code/RNA_analysis.R, lines 276–352 · score 0.56 · fold changes, expressed genes, enriched, DEGs, enrichment, pathways
  3. [3] § Results › Transcriptomic analysis reveals potential mechanisms underlying both innate and acquired TMZ resistance in GBOs with MGMT methylation ↔ Code/RNA_analysis.R, lines 51–104 · score 0.54 · mismatch repair, KEGG pathway, MMR, gene

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

R · 352 lines · 13 KB · no license · 3 matches

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It can be read at the source: Code/RNA_analysis.R.

Overview

Authors: Jisu Park1,2, Meiyu Qiu3,2, Eun Jeong Cho4, Sanghee Seo5, Ji-Hoon Moon3,2, Minji Kim3,2, Hyemin Mun4, Hyounji Yun3,2, Hoewon Park3,2, Arim Lim3,2, Younsoo Kang4,6, Jeong-woo Oh4, Heejeong Youk4, Seon-Hwan Kim7, Yeongbeom Seo8, Sae Min Kwon9, Kyoung Su Sung10, Hyuk-Jin Oh11, Kyung Rae Cho12, Kyungtae Yoon5, Nam-Shik Kim5, Se Jin Jang4,13, Kyung Hwan Kim7, Ki-Jun Yoon3,1,2
13 affiliations
  1. Graduate School of Stem Cell and Regeneration Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
  2. KAIST Stem Cell Center, KAIST, Daejeon 34141, Republic of Korea
  3. Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
  4. SG BioScience, Inc., Seoul 02637, Republic of Korea
  5. Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
  6. Department of Medical Science, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
  7. Department of Neurosurgery, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
  8. Department of Neurosurgery, Yeungnam University Hospital, Yeungnam University School of Medicine, Daegu 42415, Republic of Korea
  9. Department of Neurosurgery, Dongsan Medical Center, Keimyung University School of Medicine, Daegu 41931, Republic of Korea
  10. Department of Neurosurgery, Dong-A University Hospital, Dong-A University, College of Medicine, Busan 49201, Republic of Korea
  11. Department of Neurosurgery, Soonchunhyang University Hospital Cheonan, Soonchunhyang University School of Medicine, Cheonan 31151, Republic of Korea
  12. Department of Neurosurgery, Konkuk University Medical Center, Seoul 05030, Republic of Korea
  13. Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
Institutions: Korea Advanced Institute of Science and Technology (South Korea); Chungnam National University (South Korea); Asan Medical Center (South Korea); University of Ulsan (South Korea); Chungnam National University Hospital (South Korea); Yeungnam University Medical Center (South Korea); Yeungnam University (South Korea); Keimyung University Dongsan Medical Center (South Korea); Keimyung University Dongsan Hospital (South Korea); Keimyung University (South Korea); Dong-A University Hospital (South Korea); Dong-A University (South Korea); Soonchunhyang University Hospital Cheonan (South Korea); Konkuk University Medical Center (South Korea)
Journal: Cell reports. Medicine, volume 7, issue 7, article 102850
Dates: received 22 February 2025; accepted 14 May 2026; published online 11 June 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.xcrm.2026.102850 · PMID 42276053 · PMCID PMC13400186 · OpenAlex W7164364482
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism), other condition (population), clinical / translational (subfield)
Methods: Statistics, Connectivity
Keywords: glioblastoma, patient-derived organoid, precision oncology, personalized medicine, organoid-based drug screening, temozolomide resistance, lazertinib
MeSH: Brain Neoplasms*, Glioblastoma*, Organoids*, Precision Medicine*, Animals, Cell Line, Tumor, DNA Modification Methylases, DNA Repair Enzymes, Drug Resistance, Neoplasm, Female, Gene Expression Regulation, Neoplastic, Humans, Mice, Temozolomide, Tumor Suppressor Proteins, Xenograft Model Antitumor Assays (* major topic)
Topic: Glioma Diagnosis and Treatment (Genetics, Medicine), according to OpenAlex
Funding: Ministry of Health and Welfare (RS-2024-00439675, RS-2025-24536373); National Research Foundation of Korea (RS-2025-02214081, RS-2024-00332454, RS-2026-25488918, RS-2023-00209833, RS-2024-00440778, RS-2025-02219306); Korea Health Industry Development Institute; Ministry of Science, ICT and Future Planning; Korea Foundation for Women In Science, Engineering and Technology (WISET 2024-764)
Citations: cited by 1 paper (Europe PMC); 82 references in the paper
Research resources: Mouse anti-SOX2 RRID:AB_10843364, Rabbit anti-OLIG2 RRID:AB_10861310, Rabbit anti-PTPRZ1 RRID:AB_11127912, Alexa 594 donkey-anti chicken IgG RRID:AB_2340377, Alexa 594 donkey-anti rabbit IgG RRID:AB_2340621, Alexa 488 donkey-anti-mouse IgG RRID:AB_2340846, Alexa 647 donkey-anti mouse IgG RRID:AB_2340862, Alexa 647 donkey-anti rabbit IgG RRID:AB_2492288, Rabbit anti-Ki67 RRID:AB_2756525, Mouse Anti-STEM121 RRID:AB_2801314, RRID:AB_2885016, Chicken anti-GFAP RRID:AB_304558, Mouse anti-NCAM1 RRID:AB_306945, RRID:AB_309864, NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ RRID:IMSR_JAX:005557

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.

Repository

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SGMedical/GBO

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 3bd53b6dc092698e780cb000c474f91f8e6ebba8, 14 February 2025
Languages: R (2)
Size: 3 files, 2 scripts
Software Heritage: not archived
Found in: “Data and code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ComplexHeatmap (2 files), ggpubr (2 files), tidyverse (2 files), circlize (1 file), clusterProfiler (1 file), edgeR (1 file), limma (1 file), pheatmap (1 file), reshape2 (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
3 files, not copied: shown from their source

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At the source: github.com/SGMedical/GBO

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

Tracing map

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What the map holds:

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  • 2 scripts, each with its path and the digest of its content;
  • 3 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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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.

Code and data availability statement

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Read it in the paper: doi.org/10.1016/j.xcrm.2026.102850.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 24 authors, 7 keywords, 16 MeSH terms, 5 funders, 80 references, 15 RRIDs.

Cite

This paper

Park, J., Qiu, M., Cho, E. J., Seo, S., Moon, J.-H., Kim, M., Mun, H., Yun, H., Park, H., Lim, A., Kang, Y., Oh, J.-w., Youk, H., Kim, S.-H., Seo, Y., Kwon, S. M., Sung, K. S., Oh, H.-J., Cho, K. R., . . . Yoon, K.-J. (2026). Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma. Cell reports. Medicine, 7(7), 102850. https://doi.org/10.1016/j.xcrm.2026.102850

BibTeX

@article{park2026patient,
author = {Park, Jisu and Qiu, Meiyu and Cho, Eun Jeong and Seo, Sanghee and Moon, Ji-Hoon and Kim, Minji and Mun, Hyemin and Yun, Hyounji and Park, Hoewon and Lim, Arim and Kang, Younsoo and Oh, Jeong-woo and Youk, Heejeong and Kim, Seon-Hwan and Seo, Yeongbeom and Kwon, Sae Min and Sung, Kyoung Su and Oh, Hyuk-Jin and Cho, Kyung Rae and Yoon, Kyungtae and Kim, Nam-Shik and Jang, Se Jin and Kim, Kyung Hwan and Yoon, Ki-Jun},
title = {{Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma}},
journal = {Cell reports. Medicine},
year = {2026},
month = jun,
volume = {7},
number = {7},
pages = {102850},
publisher = {Elsevier},
issn = {2666-3791},
doi = {10.1016/j.xcrm.2026.102850},
url = {https://doi.org/10.1016/j.xcrm.2026.102850},
pmid = {42276053},
pmcid = {PMC13400186}
}

RIS

TY - JOUR
AU - Park, Jisu
AU - Qiu, Meiyu
AU - Cho, Eun Jeong
AU - Seo, Sanghee
AU - Moon, Ji-Hoon
AU - Kim, Minji
AU - Mun, Hyemin
AU - Yun, Hyounji
AU - Park, Hoewon
AU - Lim, Arim
AU - Kang, Younsoo
AU - Oh, Jeong-woo
AU - Youk, Heejeong
AU - Kim, Seon-Hwan
AU - Seo, Yeongbeom
AU - Kwon, Sae Min
AU - Sung, Kyoung Su
AU - Oh, Hyuk-Jin
AU - Cho, Kyung Rae
AU - Yoon, Kyungtae
AU - Kim, Nam-Shik
AU - Jang, Se Jin
AU - Kim, Kyung Hwan
AU - Yoon, Ki-Jun
TI - Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma
T2 - Cell reports. Medicine
J2 - Cell Rep Med
PY - 2026
DA - 2026/06/11
VL - 7
IS - 7
SP - 102850
SN - 2666-3791
PB - Elsevier
DO - 10.1016/j.xcrm.2026.102850
UR - https://doi.org/10.1016/j.xcrm.2026.102850
LA - en
ER -

CSL-JSON

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