Evidence map›Paper›PMID 39896575›Full record

ArticlebioRxiv : the preprint server for biology2025

Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors.

Vignesh Shanmugam, Neriman Tokcan, Daniel Chafamo, Sean Sullivan, Mehdi Borji, Haley Martin, Gail Newton, Naeem Nadaf, Saoirse Hanbury, Irving Barrera and 11 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

21 authors.

Vignesh ShanmugamBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-2005-9080
Neriman TokcanBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-7676-5534
Daniel ChafamoKlarman Cell Observatory, Broad Institute, Cambridge, MA, USA.ORCID 0009-0001-8877-5913
Sean SullivanBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Mehdi BorjiBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0009-0002-7023-434X
Haley MartinDepartment of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Gail NewtonDepartment of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Naeem NadafBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-7805-8523
Saoirse HanburyBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Irving BarreraHarvard Medical School, Boston, MA, USA.ORCID 0000-0001-6099-4316
Dylan CableDepartment of Biostatistics, University of Michigan, Ann Arbor, MI, USA.ORCID 0000-0001-7042-2960
Jackson WeirBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-8741-1344
Orr AshenbergKlarman Cell Observatory, Broad Institute, Cambridge, MA, USA.ORCID 0000-0002-7802-8834
Geraldine PinkusDepartment of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
Scott RodigDepartment of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
Caroline UhlerBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-7008-0216
Evan MacoskoBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-2794-5165
Margaret ShippBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-3949-6897
Abner LouissaintBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Fei ChenBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-2308-3649
Todd GolubBroad Institute of MIT and Harvard, Cambridge, MA, USA.

Funding

Making cancer precision medicine real: bottlenecks and opportunitiesR35CA242457 · NCI · BROAD INSTITUTE, INC. · PI GOLUB, TODD R. · 2019 to 2025
$6.9M
NCI NIH HHS R35 CA242457
6 · The paper itself

Abstract

A key challenge in cancer research is to identify the secreted factors that contribute to tumor cell survival. Nowhere is this more evident than in Hodgkin lymphoma, where malignant Hodgkin Reed Sternberg (HRS) cells comprise only 1-5% of the tumor mass, the remainder being infiltrating immune cells that presumably are required for the survival of the HRS cells. Until now, there has been no way to characterize the complex Hodgkin lymphoma tumor microenvironment at genome scale. Here, we performed genome-wide transcriptional profiling with spatial and single-cell resolution. We show that the neighborhood surrounding HRS cells forms a distinct niche involving 31 immune and stromal cell types and is enriched in CD4+ T cells, myeloid and follicular dendritic cells, while being depleted of plasma cells. Moreover, we used machine learning to nominate ligand-receptor pairs enriched in the HRS cell niche. Specifically, we identified IL13 as a candidate survival factor. In support of this hypothesis, recombinant IL13 augmented the proliferation of HRS cells

Identifiers

PMID39896575
PMCPMC11785141

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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.