Evidence map›Paper›PMID 42271498›Full record

ArticleGenome medicine2026

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics.

Izabela Plumbom, Benedikt Obermayer, Raphael Raspe, Anna Pascual-Reguant, Ilan Theurillat, Tancredi Massimo Pentimalli, Yu-Hsin Hsieh, Marine Gil, Carola Dietrich, Michaela Seeger-Zografakis and 15 more

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Article in Genome medicine, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

25 authors.

Izabela Plumbom *Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Benedikt Obermayer *Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany.
Raphael RaspeCharité - Universitätsmedizin Berlin, Berlin, Germany.
Anna Pascual-ReguantCentre Nacional d'Anàlisis Genòmica, Barcelona, Spain.
Ilan TheurillatMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Tancredi Massimo PentimalliMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Yu-Hsin HsiehMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Marine GilMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Carola DietrichMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Michaela Seeger-ZografakisMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Claudia QuedenauMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Jeannine WildeMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Caroline BraeuningMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Cornelius FischerMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Markus SchuelkeCharité - Universitätsmedizin Berlin, Berlin, Germany.
Volkhard SeitzCharité - Universitätsmedizin Berlin, Berlin, Germany.
Leif S LudwigMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Angelika EggertCharité - Universitätsmedizin Berlin, Berlin, Germany.
Nikolaus RajewskyMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Tatiana BorodinaMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Dieter BeuleBerlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany.
Janine AltmuellerMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Helena RadbruchCharité - Universitätsmedizin Berlin, Berlin, Germany.
Anja Erika HauserCharité - Universitätsmedizin Berlin, Berlin, Germany.
Thomas ConradMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. Thomas.Conrad@mdc-berlin.de.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Monitoring T cell repertoires in human tissues provides important insights into immune response mechanisms in cancer, infectious diseases, and autoimmunity. However, retrieving VDJ information from single-cell and spatial transcriptomics workflows with 3'-barcoding of cDNA remains resource-intensive or requires specialized sequencing equipment. Here, we introduce circVDJ-seq for simplified and cost-efficient T cell receptor (TCR) profiling from 3'-directed workflows like single-cell or single-nucleus RNA sequencing, ATAC + RNA multi-omics, and spatial transcriptomics. Application of circVDJ-seq to freshly resected neuroblastomas and postmortem lymph nodes affected by pneumonia or COVID-19 reveals distinct immune microenvironments and T cell clonality patterns, highlighting broad utility across diverse clinical contexts.

Indexed as

Receptors, Antigen, T-CellSingle-Cell Gene Expression AnalysisT-LymphocytesCOVID-19HumansLymph NodesMultiomicsSpatial TranscriptomicsTumor MicroenvironmentReceptors, Antigen, T-CellAdaptive immunitySingle-cell immune profilingSpatial transcriptomicsTCR sequencingTumor microenvironment

Identifiers

PMID42271498
PMCPMC13255474

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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.