Evidence map›Paper›PMID 40667258›Full record

ArticlebioRxiv : the preprint server for biology2025

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics.

Inbal Avraham-Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada, Matan Hofree, Evan Murray, Jonathan Chen, Karin Pelka, Arnav Mehta 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.

Inbal Avraham-DavidiKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Simon MagesKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Johanna KlughammerKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Noa MorielSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
Shinya ImadaDepartmen of Biology at MIT, Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
Matan HofreeKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Evan MurrayBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Jonathan ChenBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Karin PelkaBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Arnav MehtaBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Genevieve M BolandBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Toni DeloreyKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Leah CaplanKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Danielle DionneKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Robert StrasserGene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
Jana Lalakova10xGenomics, Solnavägen 3H, Stockholm, Sweden.
Anezka Niesnerova10xGenomics, Solnavägen 3H, Stockholm, Sweden.
Hao Xu10xGenomics, Solnavägen 3H, Stockholm, Sweden.
Morgane Rouault10xGenomics, Solnavägen 3H, Stockholm, Sweden.
Itay TiroshDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
Nir HacohenBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
Fei ChenBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.ORCID 0000-0003-2308-3649
Omer YilmazDepartmen of Biology at MIT, Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
Jatin RoperDepartmen of Biology at MIT, Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
Orit Rozenblatt-RosenKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Mor NitzanSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
Aviv RegevKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Funding

Tool and Technology Development CoreU19MH114821 · NIMH · COLD SPRING HARBOR LABORATORY · PI MITRA, PARTHA PRATIM · 2017 to 2021
$64.5M
Center for Cell CircuitsRM1HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI BLAINEY, PAUL CLARK, HACOHEN, NIR · 2016 to 2020
$14.9M
Systematic dissection of gut cellular circuits [at single cell resolution]RC2DK114784 · NIDDK · BROAD INSTITUTE, INC. · PI ASHENBERG, ORR, GRAHAM, DANIEL BARTHOLOMEW · 2017 to 2021
$9.0M
Trinity: Transcriptome assembly for genetic and functional analysis of cancerU24CA180922 · NCI · BROAD INSTITUTE, INC. · PI HAAS, BRIAN · 2013 to 2022
$7.5M
Effects of inflammaging on intestinal epithelial cells and aspirin chemoprevention.R01CA257523 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI CHAN, ANDREW T, STAPPENBECK, THADDEUS S · 2021 to 2025
$3.7M
Adipose tissue-colorectal tumor cross-talk: new targets for breaking the obesity-cancer linkR01CA254108 · NCI · UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH · PI HURSTING, STEPHEN D, ULRICH, CORNELIA M · 2021 to 2025
$3.2M
Targeting plasma membrane spatial dynamics to suppress aberrant Wnt signalingR01CA244359 · NCI · TEXAS A&M AGRILIFE RESEARCH · PI CHAPKIN, ROBERT STEPHEN, KARPAC, JASON S · 2020 to 2024
$2.7M
(PQ3) The role of damaged DNA in inter-individual variation of tumor immunityR01CA208756 · NCI · BROAD INSTITUTE, INC. · PI HACOHEN, NIR · 2016 to 2020
$2.6M
Role of immune regulation in colorectal cancer chemotherapeutic responseR01CA256530 · NCI · YALE UNIVERSITY · PI LU, JUN · 2021 to 2025
$2.4M
Wnt signaling in obesity-associated colorectal cancerR37CA259363 · NCI · DUKE UNIVERSITY · PI Jatin Roper · 2022 to 2026
$1.8M
Malignant Cell Engagement in Immune Circuits of Human Microsatellite-stable and Microsatellite-instable Colorectal CancerR00CA259511 · NCI · J. DAVID GLADSTONE INSTITUTES · PI PELKA, KARIN · 2021 to 2023
$747k
Ultra-bright fluorescent nanoparticles for colorectal adenoma detectionR21DK125911 · NIDDK · DUKE UNIVERSITY · PI ROPER, JATIN, SOKOLOV, IGOR · 2021 to 2022
$461k
NCI NIH HHS R00 CA259511NCI NIH HHS R01 CA208756NCI NIH HHS R01 CA244359NCI NIH HHS R01 CA254108NCI NIH HHS R01 CA256530NCI NIH HHS R01 CA257523NCI NIH HHS R21 CA256414NCI NIH HHS R37 CA259363NCI NIH HHS U24 CA180922NHGRI NIH HHS RM1 HG006193NIBIB NIH HHS R41 EB032693NIDDK NIH HHS R21 DK125911NIDDK NIH HHS RC2 DK114784NIMH NIH HHS U19 MH114821
6 · The paper itself

Abstract

While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide-seq, and

Identifiers

PMID40667258
PMCPMC12262820

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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.