Evidence map›Paper›PMID 40816280›Full record

ArticleCell genomics2025

Urine cf-nucleosomes: A non-invasive window into human physiology and disease.

Matan Lotem, Israa Sharkia, Batia Azria, Esther Harpenas, Maayan Ormianer, Hadar Rosen, Tal Falick-Michaeli, Nir Friedman

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. 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

8 authors.

Matan LotemThe Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, the Hebrew University of Jerusalem, Jerusalem, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem, Israel; The Hebrew University Computational Medicine Center, the Hebrew University of Jerusalem, Jerusalem, Israel.
Israa SharkiaThe Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, the Hebrew University of Jerusalem, Jerusalem, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem, Israel.
Batia AzriaDepartment of Developmental Biology and Cancer Research Institute for Medical Research Israel-Canada, Hebrew University Medical School, the Hebrew University of Jerusalem, Jerusalem, Israel.
Esther HarpenasThe Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, the Hebrew University of Jerusalem, Jerusalem, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem, Israel.
Maayan OrmianerDepartment of Obstetrics and Gynecology, Hadassah Hebrew University Medical Center, Ein-Kerem, Jerusalem, Israel.
Hadar RosenDepartment of Obstetrics and Gynecology, Hadassah Hebrew University Medical Center, Ein-Kerem, Jerusalem, Israel.
Tal Falick-MichaeliDepartment of Developmental Biology and Cancer Research Institute for Medical Research Israel-Canada, Hebrew University Medical School, the Hebrew University of Jerusalem, Jerusalem, Israel; Department of Radiation and Medical Oncology, Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel.
Nir FriedmanThe Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, the Hebrew University of Jerusalem, Jerusalem, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem, Israel; The Hebrew University Computational Medicine Center, the Hebrew University of Jerusalem, Jerusalem, Israel. Electronic address: nir.friedman@mail.huji.ac.il.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Urine contains fragments of cell-free DNA (cfDNA) that offer molecular insights into processes within the urinary system and the body. It remains unclear whether these fragments exist as chromatin and retain chromatin modifications from their cells of origin. Here, we employ cell-free chromatin immunoprecipitation followed by sequencing (cfChIP-seq) on human urine to address this issue. We show that cf-nucleosomes can be captured from urine and preserve histone modifications associated with gene activation and repression. Analysis in healthy individuals reveals distinct tissue contributions to urine cf-nucleosomes, including a kidney-derived population not detected in matched exfoliated cells or plasma. This suggests that kidney filtration largely excludes plasma cf-nucleosomes. In patients with bladder cancer, urine cf-nucleosomes reflect tumor-associated transcriptional programs and immune responses. These findings highlight the utility of urine cf-nucleosomes as accessible, non-invasive biomarkers for studying renal physiology and monitoring urinary pathologies.

Indexed as

Cell-Free Nucleic AcidsNucleosomesUrinary Bladder NeoplasmsBiomarkersChromatinChromatin ImmunoprecipitationFemaleHumansMaleBiomarkersCell-Free Nucleic AcidsChromatinNucleosomesbladder cancerChIP-seqchromatin immunoprecipitation followed by sequencingepigenomicsglomerular filtrationhistone post-translational modificationsnon-invasive molecular assaysurinary cell-free DNA

Identifiers

PMID40816280
PMCPMC12790998

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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.