Protocol for decoding immune predictors of response to immunotherapy through pan-cancer multiomics analysis.

Xinyue Jian, Xu Zheng, Kun Jiao, Weiyuan Li, Xuexin Li

Abstract read

In one paragraph

Article in STAR protocols, 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

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

5 authors.

Xinyue JianDepartment of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, Liaoning 110032, China.

Xu ZhengDepartment of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, Liaoning 110032, China.

Kun JiaoDepartment of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, Liaoning 110032, China.

Weiyuan LiHospital of Yunnan Province, Kunming, Yunnan Province 650000, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province 650000, China.

Xuexin LiDepartment of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, Liaoning 110032, China; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning 110122, China; Department of Physiology and Pharmacology, Karolinska Institutet, 171 65 Solna, Sweden. Electronic address: xuexin.li@ki.se.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Here, we present a protocol for analyzing T cell dynamics in multiple cancers through single-cell RNA sequencing (scRNA-seq), single-cell immune profiling, and mass cytometry/cytometry by time-of-flight (CyTOF). We describe steps for performing gene-regulatory network analysis to identify key transcription factors and cell-cell interaction analysis to explore immune signaling. This protocol facilitates the identification of T cell subsets associated with immune checkpoint blockade (ICB) response and the development of predictive biomarkers. For complete details on the use and execution of this protocol, please refer to Li et al.

Indexed as

ImmunotherapyNeoplasmsSingle-Cell AnalysisGene Regulatory NetworksHumansMultiomicsT-LymphocytesBioinformaticsCancerCell BiologyImmunologyMass CytometryRNA-seq

Identifiers

PMID41187056

DOI10.1016/j.xpro.2025.104183

PMCPMC12630342

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