Evidence map›Paper›PMID 40675983›Full record

ArticleNature communications2025

Cellular crosstalk mediated by TGF-β drives epithelial-mesenchymal transition in patient-derived multi-compartment biliary organoids.

Hiroaki Ayabe, Erica A K DePasquale, Surya P Amarachintha, Reena Mourya, Wenqi Li, Shreya Nalluri, Sejal R Fox, Kenichiro Konishi, Pranavkumar Shivakumar, Jorge A Bezerra

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
–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

9 citing papers in PubMed.

  1. Article
  2. Melatonin Alleviates Graft Biliary Fibrosis by Inhibiting VIMAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  3. Review
  4. Review
  5. Article
  6. Review
  7. Biliary atresia-related liver fibrosis.Frontiers in cell and developmental biology · 2026
    Review
  8. Article
  9. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Hiroaki AyabeDepartment of Pediatrics, University of Texas Southwestern Medical Center and Children's Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0009-0007-2476-037X
Erica A K DePasqualeDivision of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID http://orcid.org/0000-0002-2430-6982
Surya P AmarachinthaDepartment of Biology, Georgia Southwestern State University, Americus, GA, USA.
Reena MouryaDepartment of Pediatrics, University of Texas Southwestern Medical Center and Children's Medical Center, Dallas, TX, USA.
Wenqi LiDepartment of Pediatrics, University of Texas Southwestern Medical Center and Children's Medical Center, Dallas, TX, USA.
Shreya NalluriGraduate Program in Bioinformatics, Boston University Center for Computing and Data Sciences, Boston, MA, USA.
Sejal R FoxDivision of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Kenichiro KonishiDivision of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Pranavkumar ShivakumarDepartment of Pediatrics, University of Texas Southwestern Medical Center and Children's Medical Center, Dallas, TX, USA. Pranavkumar.Shivakumar@utsouthwestern.edu.ORCID http://orcid.org/0000-0002-2095-0623
Jorge A BezerraDepartment of Pediatrics, University of Texas Southwestern Medical Center and Children's Medical Center, Dallas, TX, USA. Jorge.Bezerra@utsouthwestern.edu.ORCID http://orcid.org/0000-0001-9667-7742

Funding

Stem Cell/Organoid and Genome Editing CoreP30DK078392 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI LEE ARMISTEAD DENSON · 2007 to 2026
$24.4M
Immunologic Dysfunction in Biliary AtresiaR01DK064008 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI DENSON, LEE ARMISTEAD · 2003 to 2022
$6.7M
Biological Basis of Phenotypes and Clinical Outcomes in Biliary AtresiaR01DK083781 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI BEZERRA, JORGE A. · 2009 to 2023
$6.1M
Laser Scanning Confocal for UT Southwestern Live Cell Imaging FacilityS10OD021684 · OD · UT SOUTHWESTERN MEDICAL CENTER · PI LUBY-PHELPS, KATHERINE J · 2016 to 2016
$455k
NIDDK NIH HHS P30 DK078392NIDDK NIH HHS R01 DK064008NIDDK NIH HHS R01 DK083781NIH HHS S10 OD021684
6 · The paper itself

Abstract

Deficiencies in the development of epithelial structures and delays in cellular maturation can increase the susceptibility of neonates to disease early in life. To investigate human biliary development and its vulnerability to biliary atresia, a severe pediatric cholangiopathy, we engineered multi-compartment biliary organoids (MBOs) from co-cultures of human liver-derived epithelial organoid cells with human endothelial and mesenchymal cells. MBOs derived from normal livers effectively replicated the epithelial structure of the bile duct epithelium and peribiliary glands (PBGs). Conversely, MBOs from diseased livers exhibited defective epithelial layers, a significant epithelial-mesenchymal transition (EMT), and an activation of the TGF-β/Activin-SMAD2/3 signaling, primarily due to intermediary cell sub-populations. Inhibition of TGF-β signaling suppressed EMT and promoted biliary epithelial development in human MBOs and suppressed the phenotype of experimental biliary atresia in neonatal mice. Thus, the modulation of TGF-β-dependent EMT regulates bile duct epithelial development and influences the susceptibility of neonates to biliary injuries.

Indexed as

Bile DuctsCell CommunicationEpithelial-Mesenchymal TransitionOrganoidsTransforming Growth Factor betaActivinsAnimalsBiliary AtresiaCoculture TechniquesEpithelial CellsHumansLiverMiceSignal TransductionSmad2 ProteinSmad3 ProteinActivinsSmad2 ProteinSmad3 ProteinTransforming Growth Factor beta

Identifiers

PMID40675983
PMCPMC12271497

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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 OpenQuestion graph.