Evidence map›Paper›PMID 42263684›Full record

ArticleCell stem cell2026

SPACE-seq integrates spatial transcriptomics and lineage tracing in native tissues.

Yuemeng Jia, Dawei Sun, Jackson A Weir, Xugeng Liu, Andrew J C Russell, YeEun Kim, Nicholas Thom, Giovanni Marrero, Vipin Kumar, Fei Chen and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell stem 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

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

11 authors.

Yuemeng JiaStem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Dawei SunDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Jackson A WeirBroad Institute of Harvard and MIT, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA.
Xugeng LiuStem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Andrew J C RussellDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
YeEun KimStem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Nicholas ThomBroad Institute of Harvard and MIT, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA.
Giovanni MarreroBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Vipin KumarBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Fei ChenDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA. Electronic address: chenf@broadinstitute.org.
Fernando D CamargoStem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. Electronic address: fernando.camargo@childrens.harvard.edu.

Funding

VectorP30CA006516 · NCI · DANA-FARBER CANCER INSTITUTE · PI Irene M. Ghobrial · 1985 to 2026
$330.6M
COVID19 Slide-seqR01HG010647 · NHGRI · BROAD INSTITUTE, INC. · PI Fei Chen, Evan Z Macosko · 2019 to 2026
$6.0M
Molecular regulation of native hematopoiesisR01HL128850 · NHLBI · BOSTON CHILDREN'S HOSPITAL · PI CAMARGO, FERNANDO · 2016 to 2024
$4.9M
Generation of a temporal, spatial, and molecular map of in situ hematopoiesisRC2DK131963 · NIDDK · BOSTON CHILDREN'S HOSPITAL · PI Fernando Camargo, Charles P. Lin · 2022 to 2026
$4.8M
High resolution lineage tracing of developmental hematopoiesisR01HL158192 · NHLBI · BOSTON CHILDREN'S HOSPITAL · PI Fernando Camargo, Sahand Hormoz · 2023 to 2026
$3.0M
Characterizing glioma heterogeneity with novel multiplexed nanoscale imaging technologiesDP5OD024583 · OD · BROAD INSTITUTE, INC. · PI CHEN, FEI · 2017 to 2021
$2.2M
Investigating Histone Acetylation Modulator Function in Alveolar Regeneration and Disease PathogenesisK99HL181185 · NHLBI · BROAD INSTITUTE, INC. · PI Dawei Sun · 2025 to 2026
$261k
NCI NIH HHS P30 CA006516NHGRI NIH HHS R01 HG010647NHLBI NIH HHS K99 HL181185NHLBI NIH HHS R01 HL128850NHLBI NIH HHS R01 HL158192NIDDK NIH HHS RC2 DK131963NIH HHS DP5 OD024583
6 · The paper itself

Abstract

Understanding how cells change state, interact with their neighbors, and organize into tissues requires recording of cellular lineage history in native spatial context. Here, we present SPACE-seq (spatial tracing enabled by CRISPR-based barcodes and slide-seq), a versatile platform that integrates CRISPR-based lineage recording with spatial transcriptomics to jointly resolve lineage, cell state, and tissue architecture at near-cellular resolution in situ. Using SPACE-seq, we uncovered intratumor transcriptional diversification among clonally related cells and identified tumor-stroma crosstalk that reciprocally reshapes behaviors of both malignant and stromal populations, which we further experimentally validated. Beyond disease, SPACE-seq revealed a narrow developmental window in which hepatoblast dispersion contributes to spatially confined lineage compartments that prefigure liver lobar architecture. Together, these results highlight the broad applicability and adaptability of SPACE-seq to uncover previously inaccessible principles of cellular organization, lineage dynamics, and tissue patterning.

Indexed as

Cell LineageTranscriptomeAnimalsHumansLiverLiver NeoplasmsSpatial Transcriptomicsbrain developmentcellular barcodinglineage tracingliver cancerliver developmentspatial transcriptomics

Identifiers

PMID42263684
PMCPMC13401910

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.