Evidence map›Paper›PMID 39798574›Full record

ArticleDevelopmental cell2025

A spatiotemporal and machine-learning platform facilitates the manufacturing of hPSC-derived esophageal mucosa.

Ying Yang, Carmel Grace McCullough, Lucas Seninge, Lihao Guo, Woo-Joo Kwon, Yongchun Zhang, Nancy Yanzhe Li, Sadhana Gaddam, Cory Pan, Hanson Zhen and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Developmental cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Epithelial architecture and signaling activity in the adult human esophagus.Frontiers in cell and developmental biology · 2025
    Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Ying YangProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
Carmel Grace McCulloughProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
Lucas SeningeDepartment of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Lihao GuoDepartment of Pharmacy Practice and Science, University of Arizona, Tucson, AZ, USA.
Woo-Joo KwonProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
Yongchun ZhangState Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Nancy Yanzhe LiProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
Sadhana GaddamProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
Cory PanProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
Hanson ZhenProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
Jessica TorkelsonProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA.
Ian A GlassBirth Defect Research Laboratory Department of Pediatrics, University of Washington, Seattle, WA, USA.
Birth Defects Research LaboratoryBirth Defect Research Laboratory Department of Pediatrics, University of Washington, Seattle, WA, USA.
Gregory W CharvilleDepartment of Pathology, Stanford University, Stanford, CA, USA.
Jianwen QueDepartment of Medicine, Columbia University, New York, NY, USA.
Joshua M StuartDepartment of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Hongxu DingDepartment of Pharmacy Practice and Science, University of Arizona, Tucson, AZ, USA. Electronic address: hongxuding@arizona.edu.
Anthony E OroProgram in Epithelial Biology and Center for Definitive and Curative Medicine, Stanford University, Stanford, CA, USA. Electronic address: oro@stanford.edu.

Funding

LABORATORY OF DEVELOPMENTAL BIOLOGYR24HD000836 · NICHD · UNIVERSITY OF WASHINGTON · PI Ian Amos Glass · 1995 to 2026
$16.9M
Gastroesophageal junction stem cells as the origin of Barretts esophagus and cancerR01CA272901 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI QUE, JIANWEN, WANG, TIMOTHY CRAGIN · 2022 to 2025
$4.9M
Chromatin Dynamics During Epithelial CommitmentR01AR073170 · NIAMS · STANFORD UNIVERSITY · PI Anthony E Oro · 2019 to 2026
$4.4M
Cell Fate Regulation in Esophageal Progenitor CellsR01DK132251 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI LU, CHAO, QUE, JIANWEN · 2022 to 2025
$2.3M
UCSC-Buck Specialized Genomic Data Analysis Center for the Genomic Data Analysis NetworkU24CA210990 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI STUART, JOSHUA MICHAEL · 2016 to 2020
$2.2M
VEGF/KDR Signaling in Airway Epithelial Regeneration and DiseaseR01HL152293 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI QUE, JIANWEN · 2021 to 2024
$2.0M
UCSC-Buck Genome Data Analysis Center for the Genomic Data Analysis Network v2.0U24CA264009 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI BENZ, CHRISTOPHER, STUART, JOSHUA MICHAEL · 2021 to 2025
$1.9M
Ultra high throughput sequencer for sustaining and enhancing multi-scale genomic studiesS10OD025212 · OD · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2018 to 2018
$600k
Computer ClusterS10OD021763 · OD · STANFORD UNIVERSITY · PI JI, HANLEE P · 2016 to 2016
$481k
Nikon A1Rsi resonant spectral confocal microscopeS10OD010580 · OD · STANFORD UNIVERSITY · PI FULLER, MARGARET T · 2013 to 2013
$377k
NCI NIH HHS R01 CA272901NCI NIH HHS U24 CA210990NCI NIH HHS U24 CA264009NHLBI NIH HHS R01 HL152293NIAMS NIH HHS R01 AR073170NICHD NIH HHS R24 HD000836NIDDK NIH HHS R01 DK132251NIH HHS S10 OD010580NIH HHS S10 OD021763NIH HHS S10 OD025212
6 · The paper itself

Abstract

Human pluripotent stem cell-derived tissue engineering offers great promise for designer cell-based personalized therapeutics, but harnessing such potential requires a deeper understanding of tissue-level interactions. We previously developed a cell replacement manufacturing method for ectoderm-derived skin epithelium. However, it remains challenging to manufacture the endoderm-derived esophageal epithelium despite possessing a similar stratified epithelial structure. Here, we employ single-cell and spatial technologies to generate a spatiotemporal multi-omics cell census for human esophageal development. We identify the cellular diversity, dynamics, and signal communications for the developing esophageal epithelium and stroma. Using Manatee, a machine-learning algorithm, we prioritize the combinations of candidate human developmental signals for in vitro derivation of esophageal basal cells. Functional validation of Manatee predictions leads to a clinically compatible system for manufacturing human esophageal mucosa.

Indexed as

Esophageal MucosaEsophagusMachine LearningPluripotent Stem CellsTissue EngineeringCell DifferentiationHumansepidermolysis bullosaesophagusgastrointestinal developmenthuman pluripotent cellmachine learningsingle-cell transcriptomicsspatial transcriptomicsstratified squamous epitheliumtissue engineering

Identifiers

PMID39798574
PMCPMC12055484

What Socratic holds

Textmetadata
LicenceTDM
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.