Evidence map›Paper›PMID 40501545›Full record

ArticlebioRxiv : the preprint server for biology2025

Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease.

Lingting Shi, Ajna Uzuni, Ximi K Wang, Michael Pressler, David W Harle, Shami Chakrabarti, Rodney Macedo, Kirubel Belay, Christian A Gordillo, Erik Raps and 17 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

27 authors.

Lingting ShiIrving Institute for Cancer Dynamics, Columbia University, New York, NY, 10027, USA.
Ajna UzuniColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Ximi K WangColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Michael PresslerDepartment of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
David W HarleColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Shami ChakrabartiColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Rodney MacedoColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Kirubel BelayColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Christian A GordilloColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Erik RapsColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Jia Yi Ady ZhangIrving Institute for Cancer Dynamics, Columbia University, New York, NY, 10027, USA.
Achille NazaretIrving Institute for Cancer Dynamics, Columbia University, New York, NY, 10027, USA.
Joy L FanIrving Institute for Cancer Dynamics, Columbia University, New York, NY, 10027, USA.
Yinuo JinIrving Institute for Cancer Dynamics, Columbia University, New York, NY, 10027, USA.
Xumin ShenDepartment of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
Joshua S FullerDepartment of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
Tamjeed AzadDepartment of Computer Science, Columbia University, New York, NY, 10027, USA.
Jessie HuangDepartment of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
Pranik ChainaniDepartment Statistics and Data Science, Yale University, CT, 06520, USA.
Julian A AbramsDivision of Digestive and Liver Diseases, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA.
Armando Del PortilloDepartment of Pathology and Cell Biology, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA.
Markus Y MaparaColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Mohamed AlhamarDepartment of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, MI, 48202, USA.
Megan SykesColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
José L McFaline-FigueroaIrving Institute for Cancer Dynamics, Columbia University, New York, NY, 10027, USA.
Elham AziziIrving Institute for Cancer Dynamics, Columbia University, New York, NY, 10027, USA.
Ran ReshefColumbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.ORCID 0000-0003-2185-9546

Funding

Tumor Biology and Microenvironment ProgramP30CA013696 · NCI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI Anil K Rustgi · 1985 to 2026
$115.3M
The Organoid and Cell Culture CoreP30DK132710 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Robert F. Schwabe · 2022 to 2026
$7.2M
Defining gene-by-environment interactions using multiplex single-cell genomicsR35HG011941 · NHGRI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI MCFALINE-FIGUEROA, JOSE LUIS · 2021 to 2025
$2.5M
Effector T-cell trafficking in graft-versus-host diseaseR01HL143424 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI RESHEF, RAN · 2019 to 2023
$2.0M
Machine learning methods for interpreting spatial multi-omics dataR01HG012875 · NHGRI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI Elham Azizi · 2023 to 2026
$1.7M
Integrative framework for identifying dysregulated mechanisms in the tumor-immune microenvironmentR00CA230195 · NCI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI AZIZI, ELHAM · 2020 to 2022
$652k
BD Biosciences InfluxS10OD020056 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI SNOECK, HANS-WILLEM E · 2015 to 2015
$600k
Five-laser Aurora spectral flow cytometerS10OD030282 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CREUSOT, REMI J · 2022 to 2022
$361k
Organ-specific Ugt1 profiling in detoxifying the anticancer drug CPT-11R21CA171008 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHEN, SHUJUAN · 2012 to 2013
$361k
NCI NIH HHS P30 CA013696NCI NIH HHS R00 CA230195NCI NIH HHS R21 CA171008NHGRI NIH HHS R01 HG012875NHGRI NIH HHS R35 HG011941NHLBI NIH HHS R01 HL143424NIDDK NIH HHS P30 DK132710NIH HHS S10 OD020056NIH HHS S10 OD030282
6 · The paper itself

Abstract

Allogeneic hematopoietic cell transplantation (alloHCT) is curative for various hematologic diseases but often leads to acute graft-versus-host disease (GVHD), a potentially life-threatening complication. We leverage GVHD as a uniquely tractable disease model to dissect complex T-cell-mediated pathology in 27 alloHCT recipients. We integrate pre-transplant identification of alloreactive T-cells with longitudinal tracking across blood and gut, using mixed lymphocyte reaction-based clonal "fingerprinting", TCR clonotyping, single-cell RNA/TCR sequencing, and spatial transcriptomics. Using DecompTCR, a novel computational tool for longitudinal TCR analysis, we uncover clonal expansion programs linked to GVHD severity and TCR features. Multi-omics profiling of gut biopsies reveals enrichment and clonal expansion of CD8

Indexed as

allogeneic hematopoietic cell transplantationalloreactive T cellsGraft-versus-host diseasephenotypic plasticityprobabilistic modelsingle-cell genomicsspatial transcriptomicstemporal dynamics

Identifiers

PMID40501545
PMCPMC12154625

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.