Evidence map›Paper›PMID 41256395›Full record

ArticlebioRxiv : the preprint server for biology2025

High-Dimensional Spatiotemporal Single-Cell and 3D Atlas of the Bone Marrow Microenvironment during Leukemic Progression.

Lanzhu Li, Isabelle Rottmann, Geoff Ivison, Huan Wei, Jan C Schroeder, Gina Dunkel, Yury Goltsev, Garry P Nolan, Aaron T Mayer, Borhan R Saeed and 2 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

12 authors.

Lanzhu LiDepartment of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.ORCID 0009-0004-5394-2285
Isabelle RottmannCluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Germany.
Geoff IvisonEnable Medicine Inc., Menlo Park, CA, USA.
Huan WeiDepartment of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Germany.
Jan C SchroederDepartment of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.
Gina DunkelCluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Germany.
Yury GoltsevDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-4079-7969
Garry P NolanDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-8862-9043
Aaron T MayerEnable Medicine Inc., Menlo Park, CA, USA.
Borhan R SaeedDepartment of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.
Bettina WeigelinCluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Germany.ORCID 0000-0003-4460-3113
Christian M SchürchDepartment of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.ORCID 0000-0002-1792-1768

Funding

Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5M
Systems Biology CoreU19AI100627 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI NOLAN, GARRY P · 2012 to 2021
$49.1M
Technology CoreU19AI135976 · NIAID · SEATTLE CHILDREN'S HOSPITAL · PI ADEREM, ALAN A · 2018 to 2022
$17.0M
The Cellular Geography of Therapeutic Resistance in CancerU2CCA233195 · NCI · DANA-FARBER CANCER INST · PI JOHNSON, BRUCE E. · 2018 to 2023
$13.7M
Project 3: Identifying plasma biomarkers predicting time to HIV rebound after treatment interruptionP01AI131374 · NIAID · J. DAVID GLADSTONE INSTITUTES · PI PILLAI, SATISH KUMAR · 2017 to 2021
$8.5M
The Lung PCA: A Multi-Dimensional Atlas of Pulmonary PremalignancyU2CCA233238 · NCI · BOSTON UNIVERSITY MEDICAL CAMPUS · PI DUBINETT, STEVEN M., SPIRA, AVRUM E · 2018 to 2021
$7.0M
Stanford Tissue Mapping CenterU54HG010426 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2018 to 2021
$5.1M
Tissue Cytokine Sequestration and Immune Regulation in AutoimmunityU01AI101984 · NIAID · STANFORD UNIVERSITY · PI BOLLYKY, PAUL L · 2012 to 2021
$5.0M
Multiscale Modeling of Myelodysplastic SyndromesR01HL128173 · NHLBI · VIRGINIA COMMONWEALTH UNIVERSITY · PI COREY, SETH JOEL, KIMMEL, MAREK · 2015 to 2019
$3.8M
Balanced signaling cues to guide cell transitions in the blood lineage continuumR01HL120724 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHAKRABORTY, ARUP K., NOLAN, GARRY P · 2015 to 2019
$3.7M
T Cell Reagent Research for Monitoring T Cell in Food AllergyU01AI140498 · NIAID · STANFORD UNIVERSITY · PI NADEAU, KARI C. · 2018 to 2022
$1.8M
Integrating mass cytometric and transcriptomic profiles of solid tumorsR33CA183692 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WEISS, WILLIAM A · 2014 to 2016
$1.2M
NCI NIH HHS F32 CA233203NCI NIH HHS F99 CA212231NCI NIH HHS R33 CA183692NCI NIH HHS U2C CA233195NCI NIH HHS U2C CA233238NHGRI NIH HHS U54 HG010426NHLBI NIH HHS R01 HL120724NHLBI NIH HHS R01 HL128173NIAID NIH HHS P01 AI131374NIAID NIH HHS U01 AI101984NIAID NIH HHS U01 AI140498NIAID NIH HHS U19 AI057229NIAID NIH HHS U19 AI100627NIAID NIH HHS U19 AI135976NIDDK NIH HHS UG3 DK114937
6 · The paper itself

Abstract

The bone marrow microenvironment (BMME) is essential for hematopoiesis and immunity, yet spatiotemporal single-cell analysis during leukemogenesis remains challenging. We characterized the BMME in femurs from wild-type and chronic myeloid leukemia (CML) mice at 7, 14 and 21 days post-induction by highly multiplexed and 3D microscopy. Using a 54-marker CODEX panel, we profiled 2,033,725 cells in 55 tissue regions of interest and identified 41 cell types through unsupervised clustering and supervised annotation. During leukemic progression, we observed an expansion of myeloid and progenitor cell populations, increased PD-L1

Indexed as

3D light sheet microscopyBone marrow microenvironmentChronic myeloid leukemiaCODEXImmature vesselsImmunosuppressiveLeukemic progressionMegakaryocyte dysplasiaVascularized bone marrow

Identifiers

PMID41256395
PMCPMC12621829

What OpenQuestion holds

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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.