Evidence map›Paper›PMID 38082384›Full record

ArticleBMC immunology2023

Dissecting cellular states of infiltrating microenvironment cells in melanoma by integrating single-cell and bulk transcriptome analysis.

Aiai Shi, Min Yan, Bo Pang, Lin Pang, Yihan Wang, Yujia Lan, Xinxin Zhang, Jinyuan Xu, Yanyan Ping, Jing Hu

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC immunology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.6field-weighted citation impact, top 29% of its field
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

5 citing papers in PubMed, 4 citations in OpenAlex.

  1. Review
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  5. 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 at 3 institutions in 1 country.

Aiai Shi *School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin, 541100, Guangxi, China.
Min Yan *Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, 400010, China.
Bo Pang *College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
Lin PangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
Yihan WangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
Yujia LanCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
Xinxin ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
Jinyuan XuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. xujinyuan9013@163.com.
Yanyan PingCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. pingyanyan@hrbmu.edu.cn.
Jing HuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. hjistb@gmail.com.
Harbin Medical University · CNChongqing Medical University · CNGuilin Medical University · CN

Funding

Prolonged Exposure (PE) for PTSD: Telemedicine vs. In PersonI01HX000152 · VA · RALPH H JOHNSON VA MEDICAL CENTER · PI ACIERNO, RONALD E. · 2011 to 2015
–
HSRD VA I01 HX000152
6 · The paper itself

Abstract

backgroundCellular states of different immune cells can affect the activity of the whole immune microenvironment.

methodsHere, leveraging reference profiles of microenvironment cell states that were constructed based on single-cell RNA-seq data of melanoma, we dissected the composition of microenvironment cell states across 463 skin cutaneous melanoma (SKCM) bulk samples through CIBERSORT-based deconvolution of gene expression profiles and revealed high heterogeneity of their distribution. Correspondence analysis on the estimated cellular fractions of melanoma bulk samples was performed to identify immune phenotypes. Based on the publicly available clinical survival and therapy data, we analyzed the relationship between immune phenotypes and clinical outcomes of melanoma.

resultsBy analysis of the relationships among those cell states, we further identified three distinct tumor microenvironment immune phenotypes: "immune hot/active", "immune cold-suppressive" and "immune cold-exhausted". They were characterized by markedly different patterns of cell states: most notably the CD8 T Cytotoxic state, CD8 T Mixed state, B non-regulatory state and cancer-associated fibroblasts (CAFs), depicting distinct types of antitumor immune response (or immune activity). These phenotypes had prognostic significance for progression-free survival and implications in response to immune therapy in an independent cohort of anti-PD1 treated melanoma patients.

conclusionsThe proposed strategy of leveraging single-cell data to dissect the composition of microenvironment cell states in individual bulk tumors can also extend to other cancer types, and our results highlight the importance of microenvironment cell states for the understanding of tumor immunity.

Indexed as

MelanomaSkin NeoplasmsGene Expression ProfilingHumansImmunosuppression TherapyPhenotypePrognosisTranscriptomeTumor MicroenvironmentCell statesImmune phenotypeImmunotherapyMelanomaMicroenvironment

Identifiers

PMID38082384
PMCPMC10714533
OpenAlexW4389579468

What OpenQuestion 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 OpenQuestion graph.