Evidence map›Paper›PMID 42385701›Full record

ArticleCell2026

Four-dimensional molecular mapping from a spatial snapshot reveals the dynamics of hair follicle organogenesis.

Soichiro Asami, Chenshuo Yin, Jean Fan, Luis A Garza, Reza Kalhor

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Soichiro AsamiDepartment of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Chenshuo YinDepartment of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Jean FanDepartment of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Computational Biology, The Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA.
Luis A GarzaDepartment of Dermatology, Department of Cell Biology, and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Reza KalhorDepartment of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Department of Neuroscience, Department of Genetic Medicine, Department of Molecular Biology & Genetics, and Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. Electronic address: kalhor@jhu.edu.

Funding

Dynamics of lineage-specific genome reorganization in gastrulation and their response to disease-associated epigenetic perturbationsU01HL156056 · NHLBI · JOHNS HOPKINS UNIVERSITY · PI KALHOR, REZA · 2020 to 2024
$3.1M
Mapping the dynamics of mouse neurogenesis in autism models using high-resolution genomic barcoding technologiesR01HG012357 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI KALHOR, REZA · 2022 to 2025
$2.1M
NHGRI NIH HHS R01 HG012357NHLBI NIH HHS U01 HL156056
6 · The paper itself

Abstract

Understanding organ formation requires capturing molecular information simultaneously in three-dimensional (3D) space and across developmental time. To this end, we developed 3D DNase-Enhanced Expression Profiling (3DEEP), a tissue-clearing approach that removes genomic DNA to extend spatial transcriptomic profiling hundreds of microns into intact tissues. We applied 3DEEP to neonatal mouse skin, capturing hundreds of developing hair follicles across their organogenesis trajectory. Ordering follicles by molecularly inferred developmental age transformed this single spatial snapshot into a four-dimensional (3D + time) molecular map of organogenesis. This map revealed developmental dynamics spanning stem cell compartment stratification, emergence of new cell subtypes within the follicle, and cascading structural transformations leading to hair canal formation. Comparative analysis of Foxn1-deficient nude mice, a hairlessness model, revealed organ-wide changes in developmental dynamics, including delayed molecular progression, reduced coordination, and increased developmental instability, preceding overt structural defects. This work demonstrates how deep-tissue spatial transcriptomics can uncover hidden dynamics of organ formation.

Indexed as

Hair FollicleOrganogenesisAnimalsForkhead Transcription FactorsGene Expression ProfilingGene Expression Regulation, DevelopmentalMiceMice, NudeSpatial TranscriptomicsForkhead Transcription FactorsWhn protein4D mappingbirth defectdeep-tissue spatial transcriptomicsdevelopmental delaydevelopmental dynamicsdevelopmental instabilityFoxn1 deficiencyhair follicle organogenesisnude mousespatial pseudotiming

Identifiers

PMID42385701
PMCPMC13379681

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Registered trials

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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.