Evidence map›Paper›PMID 42067542›Full record

ArticleNature communications2026

Spatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT.

Haikuo Li, Bo Tao, Archibald Enninful, Dingyao Zhang, Yi Dai, Fiona Oh, Negin Farzad, Keyi Li, Zhiliang Bai, Xiaoyu Qin and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Spatial biology in cancer epigenetics.Molecular oncology · 2026
    Review
  3. Article
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

18 authors.

Haikuo Li *Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
Bo Tao *Department of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-5490-4668
Archibald EnninfulDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.
Dingyao ZhangDepartment of Genetics, Yale University School of Medicine, New Haven, CT, USA.
Yi DaiDepartment of Computer Science, University of California, Irvine, CA, USA.ORCID http://orcid.org/0009-0004-1018-5931
Fiona OhArc Institute, Palo Alto, CA, USA.
Negin FarzadDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0009-0002-5391-9363
Keyi LiDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-7421-0121
Zhiliang BaiDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-3977-3057
Xiaoyu QinDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.
Mingyu YangDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-0986-3825
Emily J HwangDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0009-0006-3207-9755
Jing ZhangDepartment of Computer Science, University of California, Irvine, CA, USA.
Jun LuDepartment of Genetics, Yale University School of Medicine, New Haven, CT, USA.
Mark GersteinProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
Jingtian ZhouArc Institute, Palo Alto, CA, USA. jingtian.zhou@arcinstitute.org.ORCID http://orcid.org/0000-0003-2060-1922
Mina L XuDepartment of Pathology, Yale University School of Medicine, New Haven, CT, USA. mina.xu@yale.edu.ORCID http://orcid.org/0000-0001-9513-245X
Rong FanDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA. rong.fan@yale.edu.ORCID http://orcid.org/0000-0001-7805-8059

Funding

Spatiotemporal Tumor Analytics for Guiding Sequential Targeted-Inhibitor: Immunotherapy Combinations (ST-Analytics)U54CA274509 · NCI · INSTITUTE FOR SYSTEMS BIOLOGY · PI Rong Fan · 2022 to 2026
$15.6M
Tech Core 2U54CA268083 · NCI · JOHNS HOPKINS UNIVERSITY · PI Pei-Hsun wu · 2022 to 2026
$10.2M
Yale TMC for Cellular Senescence in Lymphoid OrgansU54AG076043 · NIA · YALE UNIVERSITY · PI FAN, RONG, HALENE, STEPHANIE · 2021 to 2025
$7.0M
Yale Murine-TMC on Immune Cell Senescence Derived InflammationU54AG079759 · NIA · YALE UNIVERSITY · PI DIXIT, VISHWA DEEP, MONTGOMERY, RUTH R · 2022 to 2025
$6.5M
Center for Human Lymphoma Spatiotemporal Atlas (HuLymSTA)U01CA294514 · NCI · YALE UNIVERSITY · PI FAN, RONG, HALENE, STEPHANIE · 2024 to 2025
$5.1M
Highly scalable and sensitive spatial transcriptomic and epigenomic sequencing of brain tissues from human and non-human primateRF1MH128876 · NIMH · YALE UNIVERSITY · PI FAN, RONG, SESTAN, NENAD · 2021 to 2021
$2.9M
Ex vivo analysis of human brain tumor cells in a microvascular niche modelR01CA245313 · NCI · YALE UNIVERSITY · PI FAN, RONG, ZHOU, JIANGBING · 2020 to 2024
$2.6M
High-spatial-resolution ECM-inclusive multi-omics sequencing of human PFA and FFPE tissue slidesUH3CA257393 · NCI · YALE UNIVERSITY · PI FAN, RONG · 2022 to 2023
$1.2M
High-spatial-resolution ECM-inclusive multi-omics sequencing of human PFA and FFPE tissue slidesUG3CA257393 · NCI · YALE UNIVERSITY · PI FAN, RONG · 2020 to 2021
$800k
U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01CA245313U.S. Department of Health & Human Services | National Institutes of Health (NIH) RF1MH128876U.S. Department of Health & Human Services | National Institutes of Health (NIH) U01CA294514U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54AG076043U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54AG079759U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54CA268083U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54CA274509U.S. Department of Health & Human Services | National Institutes of Health (NIH) UG3CA257393U.S. Department of Health & Human Services | National Institutes of Health (NIH) UH3CA257393
6 · The paper itself

Abstract

While formalin-fixed paraffin-embedded (FFPE) samples are invaluable for human non-Hodgkin B-cell lymphoma translational research, effective methods for spatial profiling of chromatin accessibility and histone modifications in these tissues remain limited. Here, we introduce epi-Patho-DBiT, a platform that combines reverse crosslinking of FFPE tissues with spatially resolved assays for transposase-accessible chromatin using sequencing (spatial-FFPE-ATAC) or cleavage under targets and tagmentation (spatial-FFPE-CUT&Tag). Using spatial-FFPE-ATAC, we map epigenetic landscapes in mucosa-associated lymphoid tissue and follicular lymphoma, identifying chromatin variants linked to B-cell malignancy and resolving tumor karyotypes. Mitotic age inference reveals spatial tumor dynamics and uncovers cholesterol-mediated cell proliferation. Furthermore, spatial-FFPE-CUT&Tag elucidates genomic alterations during transformation of follicular lymphoma into diffuse large B-cell lymphoma and identifies DIP2C with dysregulated H3K4me3 and H3K27me3 levels. Unexpectedly, we observe elevated H3K27me3 occupancy at a chromosome 2 locus containing tumor-promoting genes, attributed to copy number amplification and thereby upregulation in transformed diffuse large B-cell lymphoma.

Indexed as

Epigenesis, GeneticLymphomaLymphoma, FollicularLymphoma, Large B-Cell, DiffuseChromatinFormaldehydeGene Expression Regulation, NeoplasticGenotypeHistonesHumansParaffin EmbeddingTissue FixationChromatinFormaldehydeHistones

Identifiers

PMID42067542
PMCPMC13338050

What OpenQuestion holds

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LicenceCC BY-NC-ND
Read underepoch 390

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.