ArticleNature communications2022
Prediction of biomarkers and therapeutic combinations for anti-PD-1 immunotherapy using the global gene network association.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 85 citations in OpenAlex.
- Chromosome 11q13 amplification as a decision-making biomarker for anti-PD-1 immunotherapy in recurrent or metastatic head and neck squamous cell carcinoma: a prospective cohort study.Frontiers in immunology · 2025Trial
- A bioinformatics analysis of KIF transcriptomic subtyping reveals prognostic heterogeneity and differential therapeutic responses in cervical cancer.Oncology letters · 2026Article
- Generalizable AI predicts immunotherapy outcomes across cancers and treatments.Nature medicine · 2026Article
- Candidate MicroRNA Regulatory Axes in Melanoma CD8+ T Cell Exhaustion: A Network-Based In Silico Stratification.Cureus · 2026Article
- PRECISE: A Prognostic Thyrocyte-Derived Gene Signature for Papillary Thyroid Carcinoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance.Cell reports. Medicine · 2026Article
- Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.Genome medicine · 2026Article
- Reference-guided computational framework identifies microenvironment metabolic subtypes and targets using pan-cancer single-cell datasets.Genome medicine · 2025Article
- Lymphocyte subset-based non-invasive biomarker predicts immunochemotherapy efficacy in EGFR-TKI-pretreated EGFR-mutated NSCLC.iScience · 2025Article
- The regulatory role of CDK4/6 inhibitors in tumor immunity and the potential value of tumor immunotherapy (Review).International journal of molecular medicine · 2025Review
- Predicting the Prognosis of Bladder Cancer Patients Through Integrated Multi-omics Exploration of Chemotherapy-Related Hypoxia Genes.Molecular biotechnology · 2025Article
- Comprehensive analysis of immune subtype characterization on identification of potential cells and drugs to predict response to immune checkpoint inhibitors for hepatocellular carcinoma.Genes & diseases · 2025Article
- Network-based multi-omics integrative analysis methods in drug discovery: a systematic review.BioData mining · 2025Review
- Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis.NPJ systems biology and applications · 2025Article
- Network Medicine-Based Strategy Identifies Maprotiline as a Repurposable Drug by Inhibiting PD-L1 Expression via Targeting SPOP in Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Integrating Machine Learning and Mendelian Randomization Determined a Functional Neurotrophin-Related Gene Signature in Patients with Lower-Grade Glioma.Molecular biotechnology · 2024Article
- Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- TME-NET: an interpretable deep neural network for predicting pan-cancer immune checkpoint inhibitor responses.Briefings in bioinformatics · 2024Article
- Blood-based molecular and cellular biomarkers of early response to neoadjuvant PD-1 blockade in patients with non-small cell lung cancer.Cancer cell international · 2024Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Owing to a lack of response to the anti-PD1 therapy for most cancer patients, we develop a network approach to infer genes, pathways, and potential therapeutic combinations that are associated with tumor response to anti-PD1. Here, our prediction identifies genes and pathways known to be associated with anti-PD1, and is further validated by 6 CRISPR gene sets associated with tumor resistance to cytotoxic T cells and targets of the 36 compounds that have been tested in clinical trials for combination treatments with anti-PD1. Integration of our top prediction and TCGA data identifies hundreds of genes whose expression and genetic alterations that could affect response to anti-PD1 in each TCGA cancer type, and the comparison of these genes across cancer types reveals that the tumor immunoregulation associated with response to anti-PD1 would be tissue-specific. In addition, the integration identifies the gene signature to calculate the MHC I association immunoscore (MIAS) that shows a good correlation with patient response to anti-PD1 for 411 melanoma samples complied from 6 cohorts. Furthermore, mapping drug target data to the top genes in our association prediction identifies inhibitors that could potentially enhance tumor response to anti-PD1, such as inhibitors of the encoded proteins of CDK4, GSK3B, and PTK2.
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Registered trials
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.