Evidence map›Paper›PMID 40480216›Full record

ArticleCell genomics2025

SpaLinker identifies phenotype-associated spatial tumor microenvironment features by integrating bulk and spatial sequencing data.

Xiaojie Cheng, Chen Tang, Kejing Dong, Yuzhou You, Xueying Zhao, Bin Duan, Shaoqi Chen, Guohui Chuai, Zhenbo Zhang, Qi Liu

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 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. Review
  3. Review
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

10 authors.

Xiaojie ChengDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Reproductive Medicine Center, Department of Obstetrics and Gynecology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
Chen TangDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Kejing DongDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Yuzhou YouDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Xueying ZhaoDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Bin DuanDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Shaoqi ChenDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Guohui ChuaiDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China. Electronic address: 18alexanderm117@tongji.edu.cn.
Zhenbo ZhangReproductive Medicine Center, Department of Obstetrics and Gynecology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China. Electronic address: zhangzhenbozzb@tongji.edu.cn.
Qi LiuDepartment of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China. Electronic address: qiliu@tongji.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The emergence of spatial transcriptomics (ST) technology offers unprecedented opportunities to elucidate the complexity and heterogeneity of the tumor microenvironment (TME). However, quantitatively linking spatially resolved features with clinical phenotypes remains challenging due to the scarcity of clinical annotations of spatial sequencing samples. Herein, we introduce SpaLinker, an innovative integrated framework that utilizes ST data to decipher spatially resolved TMEs at molecular, cellular, and tissue structure levels. Specifically, it assesses the prognostic significance of spatially defined features by integrating well-accumulated bulk RNA sequencing (RNA-seq) data, using a phenotype-driven computational framework. Applying SpaLinker to diverse tumor ST datasets demonstrated its utility and effectiveness in recognizing spatial architectures, including tertiary lymphoid structures and tumor-normal interfaces, and in establishing links to distinct clinical outcomes. Overall, this study presents a valuable and comprehensive pan-cancer analytical platform to de novo identify phenotype-associated spatial TME features, significantly enhancing the clinical utility of spatial sequencing technology.

Indexed as

NeoplasmsTumor MicroenvironmentComputational BiologyGene Expression ProfilingHumansPhenotypePrognosisSequence Analysis, RNATranscriptomeclinical phenotypeSpaLinkerspatial transcriptomicstertiary lymphoid structuretumor microenvironmenttumor-normal interface

Identifiers

PMID40480216
PMCPMC12278630

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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.