Evidence map›Paper›PMID 39332415›Full record

ArticleCell reports. Medicine2024

A living organoid biobank of patients with Crohn's disease reveals molecular subtypes for personalized therapeutics.

Courtney Tindle, Ayden G Fonseca, Sahar Taheri, Gajanan D Katkar, Jasper Lee, Priti Maity, Ibrahim M Sayed, Stella-Rita Ibeawuchi, Eleadah Vidales, Rama F Pranadinata and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports. Medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Gut microbes · 2026
    Article
  3. New developments and applications of human organoids.Nature reviews. Molecular cell biology · 2026
    Review
  4. Review
  5. Article
  6. Review
  7. New approach methodologies in Crohn's disease link molecular disease subtypes to clinical outcomes.American journal of physiology. Gastrointestinal and liver physiology · 2026
    Article
  8. Review
  9. Review
  10. Review
  11. Review
  12. Review
  13. From AI-AssistedPharmaceuticals (Basel, Switzerland) · 2025
    Review
  14. Review
  15. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Courtney TindleDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA.
Ayden G FonsecaDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA.
Sahar TaheriDepartment of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
Gajanan D KatkarDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Jasper LeeDepartment of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
Priti MaityDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA.
Ibrahim M SayedDepartment of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
Stella-Rita IbeawuchiDepartment of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
Eleadah VidalesDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA.
Rama F PranadinataDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA.
Mackenzie FullerDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA.
Dominik L StecDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA.
Mahitha Shree AnandacharDepartment of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
Kevin PerryDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA.
Helen N LeDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Jason EarDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Brigid S BolandDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: bboland@health.ucsd.edu.
William J SandbornDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: wsandborn@health.ucsd.edu.
Debashis SahooDepartment of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: dsahoo@ucsd.edu.
Soumita DasHUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA; Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: soumita_das@uml.edu.
Pradipta GhoshDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: prghosh@ucsd.edu.

Funding

San Diego Digestive Diseases Research CenterP30DK120515 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Bernd G. Schnabl · 2019 to 2026
$10.8M
Predoctoral and Postdoctoral Training in Cancer Cell BiologyT32CA067754 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEAN Y.J. WANG · 1995 to 2026
$6.5M
Macrophage Polarization in Response to Infections and InflammationR01AI155696 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GHOSH, PRADIPTA, SAHOO, DEBASHIS · 2020 to 2024
$4.9M
Modulation of Macrophage Polarization by Heterotrimeric G proteins: Implications of Gastrointestinal InflammationR01AI141630 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Pradipta Ghosh · 2019 to 2026
$3.2M
Innate responses following infection with enteric microbesR01DK107585 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DAS, SOUMITA · 2016 to 2020
$2.2M
Summer Student Research on the Application of Boolean AnalysisR01GM138385 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SAHOO, DEBASHIS · 2020 to 2023
$2.0M
Network-Based Novel Therapeutics in Colorectal CancersUG3TR002968 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DAS, SOUMITA, GHOSH, PRADIPTA · 2019 to 2021
$946k
Precision therapeutics of inflammatory bowel disease guided by Boolean logicUG3TR003355 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DAS, SOUMITA, GHOSH, PRADIPTA · 2020 to 2022
$937k
USING SINGLE-CELL RNA AND PROTEIN APPROACHES TO ELUCIDATE MOLECULAR DETERMINANTSAND PREDICTORS OF INFLAMMATORY BOWEL DISEASESK23DK123406 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BOLAND, BRIGID S · 2020 to 2022
$720k
Illumina NovaSeq 6000 Sequencing SystemS10OD026929 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEPSEN, KRISTEN LYNN · 2019 to 2019
$600k
The host-microbe-metformin interplay in the aged gutR56AG069689 · NIA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DAS, SOUMITA · 2020 to 2020
$394k
Precision therapeutics of inflammatory bowel disease guided by Boolean logicUH3TR003355 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GHOSH, PRADIPTA, SAHOO, DEBASHIS · 2023 to 2023
$356k
NCATS NIH HHS UG3 TR002968NCATS NIH HHS UG3 TR003355NCATS NIH HHS UH3 TR003355NCI NIH HHS T32 CA067754NIAID NIH HHS R01 AI141630NIAID NIH HHS R01 AI155696NIA NIH HHS R56 AG069689NIDDK NIH HHS K23 DK123406NIDDK NIH HHS P30 DK120515NIDDK NIH HHS R01 DK107585NIGMS NIH HHS R01 GM138385NIH HHS S10 OD026929
6 · The paper itself

Abstract

Crohn's disease (CD) is a complex and heterogeneous condition with no perfect preclinical model or cure. To address this, we explore adult stem cell-derived organoids that retain their tissue identity and disease-driving traits. We prospectively create a biobank of CD patient-derived organoid cultures (PDOs) from colonic biopsies of 53 subjects across all clinical subtypes and healthy subjects. Gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and identified two major molecular subtypes: immune-deficient infectious CD (IDICD) and stress and senescence-induced fibrostenotic CD (S2FCD). Each subtype shows internal consistency in the transcriptome, genome, and phenome. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. Drug screens reverse subtype-specific phenotypes, suggesting phenotyped-genotyped CD PDOs can bridge basic biology and patient trials by enabling preclinical phase "0" human trials for personalized therapeutics.

Indexed as

Biological Specimen BanksCrohn DiseaseOrganoidsPrecision MedicineAdultAdult Stem CellsColonFemaleHumansMaleMiddle AgedPhenotypeTranscriptomebarrier integrityhost-microbe interactioninflammatory bowel diseasepatient-derived organoidstherapeutics

Identifiers

PMID39332415
PMCPMC11513829

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.