Evidence map›Paper›PMID 42242233›Full record

ArticleCancer cell2026

Clonal lineage tracing of innate immune cells in human cancer.

Vincent Liu, Katalin Sandor, Patrick K Yan, Zhuang Miao, Yajie Yin, Robert R Stickels, Andy Y Chen, Kamir Hiam-Galvez, Jacob Gutierrez, Wenxi Zhang and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cancer cell, 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. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Vincent LiuDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA. Electronic address: liuv@stanford.edu.
Katalin SandorDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA.
Patrick K YanDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA.
Zhuang MiaoDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA.
Yajie YinDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA.
Robert R StickelsDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA.
Andy Y ChenDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Kamir Hiam-GalvezDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA.
Jacob GutierrezComputational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Wenxi ZhangDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA.
Sairaj M SajjathRobin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
Raeline ValbuenaDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Steven WangDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Bence DanielDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA.
Leif S LudwigBerlin Institute of Health at Charité - Universitätsmedizin Berlin, 10178 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany.
Brooke E HowittDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Caleb A LareauComputational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: lareauc@mskcc.org.
Ansuman T SatpathyDepartment of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Immunotherapy Design, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA. Electronic address: satpathy@stanford.edu.

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Single-cell Mapping Center for Human Regulatory Elements and Gene ActivityUM1HG012076 · NHGRI · STANFORD UNIVERSITY · PI Michael Ryan Corces, Ansuman Satpathy · 2021 to 2026
$13.8M
The Human DNA virome: from petabase scale to single-cell resolutionU01AT012984 · NCCIH · SLOAN-KETTERING INST CAN RESEARCH · PI Caleb Andrew Lareau · 2024 to 2026
$5.2M
Unraveling heterogeneity in endometrial cancer via integrated single cell genotype-phenotype mappingR37CA303960 · NCI · STANFORD UNIVERSITY · PI Brooke E Howitt · 2025 to 2026
$1.3M
Programmable nucleic acid cytometry for unraveling heterogeneity in tumors and therapiesR33CA302491 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI Ronan Chaligne, Caleb Andrew Lareau · 2025 to 2026
$836k
Charting somatic evolution via single-cell multiomicsR00HG012579 · NHGRI · SLOAN-KETTERING INST CAN RESEARCH · PI LAREAU, CALEB ANDREW · 2023 to 2025
$747k
Long-term systemic consequences of type 2 skin inflammation on epithelial stem cellsF31AR083275 · NIAMS · ROCKEFELLER UNIVERSITY · PI Sairaj M Sajjath · 2024 to 2026
$124k
NCCIH NIH HHS U01 AT012984NCI NIH HHS P30 CA008748NCI NIH HHS R33 CA302491NCI NIH HHS R37 CA303960NHGRI NIH HHS R00 HG012579NHGRI NIH HHS UM1 HG012076NIAMS NIH HHS F31 AR083275
6 · The paper itself

Abstract

Innate immune cells constitute the majority of the tumor microenvironment (TME) and mediate anti-tumor immunity and immunotherapy responses. While single-cell T and B cell receptor sequencing have revealed insights into the clonal dynamics of adaptive immunity, the lack of analogous tools has precluded similar analysis of innate immune cells. Here, we describe a method leveraging somatic mitochondrial DNA (mtDNA) mutations to reconstruct clonal lineage relationships between cells in native human tissues. By jointly profiling single-cell chromatin accessibility and mtDNA variants, we resolve clonal dynamics of 218,715 cells from matched tumors, tissues, and blood from patients with lung and ovarian cancers. Clonal tracing reveals that TME-resident myeloid subsets, including macrophages and type 3 dendritic cells (DC3), are clonally related to circulating and tissue-infiltrating monocytes. We further identify distinct DC-biased and macrophage-biased clones, whose circulating monocyte precursors exhibit distinct epigenetic profiles, suggesting intratumoral myeloid differentiation fate may be peripherally programmed before TME infiltration.

Indexed as

Cell LineageImmunity, InnateLung NeoplasmsNeoplasmsOvarian NeoplasmsDendritic CellsDNA, MitochondrialFemaleHumansMacrophagesMonocytesMutationSingle-Cell AnalysisTumor MicroenvironmentDNA, Mitochondrialfate biasinnate immunitylineage tracingsingle-cell multi-omicstumor microenvironment

Identifiers

PMID42242233
PMCPMC13309241

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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 Socratic graph.