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Tumor Microenvironment Characterization in Gastric Cancer Identifies Prognostic and Immunotherapeutically Relevant Gene Signatures
Published version of a preprint
Abstract
Tumor microenvironment (TME) cells constitute a vital element of tumor tissue. Increasing evidence has elucidated their clinicopathologic significance in predicting outcomes and therapeutic efficacy. Nonetheless, no studies have reported a systematic analysis of cellular interactions in the TME. In this study, we comprehensively estimated the TME infiltration patterns of 1,524 gastric cancer patients and systematically correlated the TME phenotypes with genomic characteristics and clinicopathologic features of gastric cancer using two proposed computational algorithms. Three TME phenotypes were defined, and the TMEscore was constructed using principal component analysis algorithms. The high TMEscore subtype was characterized by immune activation and response to virus and IFNγ. Activation of transforming growth factor β, epithelial–mesenchymal transition, and angiogenesis pathways were observed in the low TMEscore subtype, which are considered T-cell suppressive and may be responsible for significantly worse prognosis in gastric cancer [hazard ratio (HR), 0.42; 95% confidence interval (CI), 0.33–0.54; P < 0.001]. Multivariate analysis revealed that the TMEscore was an independent prognostic biomarker, and its value in predicting immunotherapeutic outcomes was also confirmed (IMvigor210 cohort: HR, 0.63; 95% CI, 0.46–0.89; P = 0.008; GSE78220 cohort: HR, 0.25; 95% CI, 0.07–0.89; P = 0.021). Depicting a comprehensive landscape of the TME characteristics of gastric cancer may, therefore, help to interpret the responses of gastric tumors to immunotherapies and provide new strategies for the treatment of cancers.
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“Recent studies reported that alteration of tumour immune microenvironment in gastric cancer is a pivotal strategy for predicting the immunotherapeutic responses and prognosis, which might provide new treatment strategies for patients [26, 27].”
From Phosphoserine phosphatase as a prognostic biomarker in patients with gastric cancer and its potential association with immune cells (2022) · cites this paper as [27]
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“To investigate the relationship between SLC2A1 expression and immunotherapy, we extracted eight immune checkpoint-related genes (Ravi et al., 2018; Wang et al., 2019; Zeng et al., 2019; Yi et al., 2020) and evaluated their association with SLC2A1.”
MethodAn Update of G-Protein-Coupled Receptor Signaling and Its Deregulation in Gastric Carcinogenesis
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“Then, ssGSEA algorithm was utilized to calculate the enrichment scores of stromal activation relevant signatures, including EMT1, EMT2, EMT3, Pan_F_TBRS, wnt target, and angiogenesis (Zeng et al. 2019).”
An Integrated Multi-Omics Analysis Identifying Immune Subtypes of Pancreatic Cancer
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“To better predict the immunotherapeutic effect of tumors, previous studies classified most human tumors into three subtypes based on the characteristics of the TME as follows: immune-desert, immune-excluded, and immune-inflamed subtypes [28,58].”
BackgroundLiu, S.-S., Wan, Q.-S., Lv, C., Wang, J., Jiang, S., Cai, D., Liu, M., Wang, T., & Zhang, K.-H. (2024) · BMC Cancer · doi:10.1186/s12885-024-12175-z · Cited by 13
“…the transcriptional levels of genes associated with immune checkpoints between the high and low mRNA level groups of these potential biomarkers [22, 23], including TIGIT (T-cell immunoglobulin and ITIM domain), SIGLEC15 (Sialic acid-binding immunoglobulin-like lectin 15), HAVCR2 (T-cell…”
BackgroundSkubleny, D., Purich, K., McLean, D. R., Martins-Filho, S. N., Buttenschoen, K., Haase, E., McCall, M., Ghosh, S., Spratlin, J. L., Schiller, D., et al. (2024) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-23-3523 · Cited by 15
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“These strategies should aim not only to improve treatment efficacy across GC’s varied landscape but also to minimize collateral damage to the patient’s overall health [7, 8].”
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The Clinical Significance of DNA Damage Repair Signatures in Clear Cell Renal Cell Carcinoma
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“A formula similar to that used in previous studies was adopted to quantify the m6Ascore [28, 29].”
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“The Correlation of the KIF2C Expression With TME and Tumor Cell Infiltration TME metagenes construction and gene signature scoring were carried out in accordance with previous literature (23).”
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Tumor vessel normalization and immunotherapy in gastric cancer
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“Therefore, TISIDB, TIMER databases and xCell algorithm were utilized to estimate ACAP1-related immune cells infiltration in LUAD.”
BackgroundInfluentialXiang, L., Piao, L., Wang, D., & Qi, L. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.974241 · Cited by 13
Meijing, Z., Tianhang, L., & Biao, Y. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.913307 · Cited by 13
“The m6A score was calculated using the following formula (Sotiriou et al., 2006; Zeng et al., 2019): m6Ascore = ∑(PC1i + PC2 i), where i represents the expression of m6A-related genes.”
MethodDong, M., Chen, J., Lu, N., Wang, S., Wei, W., Wang, Z., Wang, J., Zhang, J., Han, X., Wang, F., et al. (2025) · Breast Cancer Research · doi:10.1186/s13058-025-02026-5 · Cited by 12
“TME scoring was estimated using principal component analysis based on gene expressions associated with different TME phenotypes using the R package “TMEscore” (https:// github. com/ Dongq iangZ eng08 08/ TMEsc ore) [24–26].”
Self-citationPrognosis of Tumor Microenvironment in Luminal B-Type Breast Cancer
Lv, J., Ren, J. L., Zheng, J., Zhang, F.-L., & Han, M. (2022) · Disease Markers · doi:10.1155/2022/5621441 · Cited by 12
“Multiple algorithms developed for estimating the abundance of immune cells along with other cell types in TME [17–19] were previously applied to explore the association between TME infiltration and cancer progression [20, 21].”
MethodPrognostic and Immunological Role of PPP1R14A as a Pan-Cancer Analysis Candidate
Wang, Z., Huang, R., Wang, H., Peng, Y., Fan, Y., Feng, Z., Zeng, Z., Ji, Y., Wang, Y., & Lu, J. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.842975 · Cited by 12
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“54 Therefore, we investigated the important biological pathways in TME, including epithelial-mesenchymal transition (EMT), angiogenesis, Wnt signaling pathway, and CD8 T effector, DNA damage repair, and nucleotide excision related pathways from previous research.”
Xia, X., Xu, F., Dai, D., Xiong, A., Sun, R., Ling, Y., Qiu, L., Wang, R., Ding, Y., Lin, M., et al. (2024) · Bioscience Reports · doi:10.1042/bsr20231845 · Cited by 12
“The TME related pathway score was established by the principal component analysis algorithms [37].”
MethodChen, D., Xiong, L., Zhang, L., Yu, H., Xu, Y., Wang, M., Jiang, X., & Xiong, Z. (2021) · Pharmacogenomics and Personalized Medicine · doi:10.2147/pgpm.s301303 · Cited by 12
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BOP1 Used as a Novel Prognostic Marker and Correlated with Tumor Microenvironment in Pan-Cancer
Li, W., Song, P., Zhao, M., Gao, L., Xie, J., & You, C. (2021) · Journal of Oncology · doi:10.1155/2021/3603030 · Cited by 12
Zhan, L., Zhang, J., Zhu, S., Liu, X., Zhang, J., Wang, W., Fan, Y., Sun, S., Wei, B., & Cao, Y. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.736298 · Cited by 12
“m6A RNA modification patterns are quantified as m6Ascore by a specific procedure (Zeng et al., 2019).”
MethodSelf-citationm6A-Mediated Tumor Invasion and Methylation Modification in Breast Cancer Microenvironment
Liu, F., Yu, X., & He, G. (2021) · Journal of Oncology · doi:10.1155/2021/9987376 · Cited by 12
Huang, Z.-D., Liu, Z., Liu, Y.-Y., Fu, Y.-C., Lin, L., Hu, C., Gu, H.-Y., & Wei, R. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.791621 · Cited by 12
“A recent study has shown that molecular subtypes based on TME recognition have provided new insights for customizing immunotherapy regimens for individual cancer patients (10).”
BackgroundGao, J.-P., Huo, S., Zhang, Y., Zhao, Z., Pan, H., & Liu, X.-W. (2022) · Cancer Medicine · doi:10.1002/cam4.4857 · Cited by 6
Wang, Y., Wen, H., & Sun, D. (2022) · Annals of Translational Medicine · doi:10.21037/atm-22-1430 · Cited by 12
“SIGLEC15, TIGIT, CD274, HAVCR2, PDCD1, CTLA4, LAG3, and PDCD1LG2 are immune checkpoint-related transcripts (24-27).”
ResultWang, D., Gu, Y., Huo, C., Zhao, Y., Teng, M., & Li, Y. (2022) · Gene · doi:10.1016/j.gene.2022.146760 · Cited by 12
Guan, H., Zhong, M., Ma, K., Tang, C., Wang, X., Ouyang, M., Qin, R., Chen, J., Zhu, E., Zhu, T., et al. (2023) · Journal of Inflammation Research · doi:10.2147/jir.s386898 · Cited by 14
“Analysis of Tumor Microenvironment (TME) The correlation between HMGB1 and TME was analyzed according to the method described by Liao et al.(26) R package “ESTIMATE” was used to analyze the correlation between HMGB1 expression and TME scores in different tumors, including stromal score, immune score, ESTIMATE score (e…”
MethodXu, H., Huang, K., Lin, Y., Gong, H., Ma, X., & Zhang, D. (2023) · BMC Medical Genomics · doi:10.1186/s12920-023-01559-y · Cited by 12
“High TMB with more neoantigens may indicate an improved response to treatment with immune checkpoint blockade [34].”
BackgroundZhu, X., Xie, X., Zhao, Q., Zhang, L., Li, C., & Zhao, D. (2020) · BioMed Research International · doi:10.1155/2020/4673153 · Cited by 12
Hu, Y., Sun, H., Zhang, H., & Wang, X. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.01189 · Cited by 12
“1), as described in previous studies (12, 13).”
MethodSelf-citationChen, D., Wang, Y., Zhang, X., Ding, Q., Wang, X., Xue, Y., Wang, W., Mao, Y., Chen, C., & Chen, Y. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.581030 · Cited by 12
“The raw data in TCGA dataset generated from Illumina were processed using the lumi software package according to a previous study (8).”
MethodInfluentialLong Noncoding RNA: Shining Stars in the Immune Microenvironment of Gastric Cancer
Xiao, X. M., Cheng, W., Zhang, G., Wang, C., Sun, B., Zha, C., Kong, F., & Jia, Y. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.862337 · Cited by 12
“An analysis of the relationship between cell expression profile and clinicopathological features in TIME of 1524 patients with GC showed that the higher the number of CAFs infiltrates in TIME, the worse clinical prognosis (114).”
BackgroundMechanisms, advances, and challenges of immunotherapy in gastric cancer
Wang, Z., & Wang, T. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1639487 · Cited by 11
Spagnol, L. W., Polettini, J., Silveira, D., Wegner, G. R. M., & Paiva, D. F. F. (2022) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2022.103843 · Cited by 11
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Yu, J., Lai, M., Zhou, Z., Zhou, J., Hu, Q., Li, J., Li, H., Chen, L., Wen, L., Zhou, M., et al. (2023) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2023.578034 · Cited by 11
Chen, Y., Xia, S., Zhang, L., Qin, X., Zhu, Z., Ma, T., Lu, S., Chen, J., Shi, X., & Ren, H. (2023) · Journal of Clinical Medicine · doi:10.3390/jcm12051830 · Cited by 12
“In addition, the signature scores of the MAM–TME subgroups were calculated as previously described to evaluate the differences in the distribution of microenvironment-related signatures of different groups [25].”
MethodLi, D., Su, L., Xue, S., Li, Y., Yu, D., Tang, X., & Huang, Y. (2023) · Journal of Cancer · doi:10.7150/jca.84654 · Cited by 11
“The Sanguini diagram was used to display the distribution of ESM1 expression in CSCC in terms of age, pathological TNM stage (pTNM), vascular invasion, lymph node metastasis and survival status[26].”
MethodChen, J., Wang, W. J., Zhang, Y., Wang, C., Wang, W., & Zheng, A. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1221445 · Cited by 11
Yu, D., Yang, J., Wang, B., Li, Z., Wang, K., Li, J., & Zhu, C. (2024) · Cancer Immunology Immunotherapy · doi:10.1007/s00262-024-03684-8 · Cited by 11
“Enhanced infiltration of immune cells within the tumors of patients categorized as high risk illuminates the intricate interplay between immune responses and the pathogenesis of gastric cancer [53].”
BackgroundPoniewierska-Baran, A., Sobolak, K., Niedźwiedzka‐Rystwej, P., Plewa, P., & Pawlik, A. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25126471 · Cited by 11
“Early results from the use of ramucirumab in combination with anti-PD-1/PD-L1 therapy are promising options for improving patient survival [66,67].”
BackgroundCapuano, A., Vescovo, M., Canesi, S., Pivetta, E., Doliana, R., Nadin, M. G., Yamamoto, M., Tsukamoto, T., Nomura, S., Pilozzi, E., et al. (2024) · Gastric Cancer · doi:10.1007/s10120-024-01528-z · Cited by 11
“Successful treatment of GC still represents a challenge in therapy and this is in part due to the poor understanding of the intricate players within the tumor micro-environment [29].”
BackgroundRamesh, P., Nisar, M., Neha, Ammankallu, S., Babu, S., Nandakumar, R., Abhinand, C. S., Prasad, T. S. K., Codi, J. A. K., & Raju, R. (2024) · Journal of Proteomics · doi:10.1016/j.jprot.2024.105262 · Cited by 11
Shi, M., Zeng, D., Luo, H., Xiao, J., Li, Y., Yuan, X., Huang, N., Wu, J., Zheng, S., Wu, J., et al. (2024) · Med · doi:10.1016/j.medj.2024.07.006 · Cited by 12
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“The package ‘ggalluvial’ of R software (version 4.2.1) was used to build Sankey diagram (17).”
MethodInfluentialZhang, E., Ding, X., Zhang, J., Liu, W., Liu, G., Li, M., Liu, X., Wang, Y., Zhang, F., Li, B., et al. (2025) · Cancer Letters · doi:10.1016/j.canlet.2025.217887 · Cited by 11
Self-citationDai, D., Zhao, X., Li, X., Shu, Y., Shen, B., Chen, X., Chen, D., & Wang, D. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2019.01452 · Cited by 11
“gov/) and the NCBI Gene Expression Omnibus (GEO; GSE62254 for ACRG) and processed as previously described (21).”
MethodImmune Escape in Prostate Cancer
Reva, B. A., Omelchenko, T., Nair, S. S., & Tewari, A. K. (2020) · Urologic Clinics of North America · doi:10.1016/j.ucl.2020.10.004 · Cited by 11
Chen, Z., Wang, Y., Fong, W. P., Hu, M.-T., Liang, J., Wang, L., & Li, Y. (2021) · International Immunopharmacology · doi:10.1016/j.intimp.2021.107890 · Cited by 11
Yuan, D.-D., Wei, Z., Wang, Y., Cheng, F., Zeng, Y.-J., Yang, L., Zhang, S., Li, J.-B., & Tang, R. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.734873 · Cited by 7
“We constructed the DMS using an algorithm similar to the GGI: DMS = S(PC1i + PC2 i), where i stood for the relevant gene expression of the selected set (22, 23).”
MethodLi, C., Pan, J., Jiang, Y., Yu, Y., Jin, Z., & Chen, X. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2021.793628 · Cited by 11
“TME analysis revealed higher stromal and immune scores were found in ICI cluster C than other two clusters, indicating anti-tumor immune response was significantly activated in ICI cluster C of GC (Zeng et al., 2019).”
BackgroundPrediction of Two Molecular Subtypes of Gastric Cancer Based on Immune Signature
Wu, D., Feng, M., Shen, H., Shen, X., Hu, J., Liu, J., Yang, Y., Li, Y., Yang, M., Wang, W., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2021.793494 · Cited by 11
Analysis of m6A Methylation Modification Patterns and Tumor Immune Microenvironment in Breast Cancer
Dong, M., Shen, W., Yang, G., Zhifang, Y., & Li, X. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.785058 · Cited by 12
Fan, T., Wan, Y., Niu, D., Wang, B., Zhang, B., Zhang, Z., Zhang, Y., Gong, Z., & Zhang, L. (2022) · Discover Oncology · doi:10.1007/s12672-022-00474-5 · Cited by 11
“PSscore was defined by using a method was analogous to GGI [30, 31]: where “i” was the expression of pyroptosis-related genes.”
MethodZhu, C., Wu, Q., Yang, N., Zheng, Z., Zhou, F., & Zhou, Y. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.848841 · Cited by 11
“We presented the expression profile of TCGA cohort similar with the results from the GSE65858 cohort and GSE41613 cohort, so that the data were comparable among samples (Wagner et al., 2012; Zeng et al., 2019).”
MethodWu, G., Chen, M., Ren, H., Sha, X., He, M., Ren, K., Qi, J., & Lin, F. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.930933 · Cited by 11
“The TME-related pathways were obtained and pathway scores were calculated according to the published paper (Zeng et al., 2019).”
MethodWu, Q., Tian, R., Tan, H. L. E., Liu, J., Ou, C., Li, Y., & Fu, X. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.1048356 · Cited by 11
“The TME context correlated with the immune response and benefit of chemotherapy, and different dominant cell populations within the TME could result in distinct clinical outcomes of cancers (Zeng et al., 2019).”
BackgroundWang, X.-X., Deng, S., Wu, L., Liu, Q.-Q., Zheng, G., Du, K., Dou, Q.-Y., Zheng, J., & Zhang, H. (2023) · ACS Omega · doi:10.1021/acsomega.2c07052 · Cited by 11
Cuproptosis‐related miRNAs signature and immune infiltration characteristics in colorectal cancer
Zhu, Z., Guo, T., Weng, J., Li, S., Zhu, C., Zhao, Q., & Xu, Y. (2023) · Cancer Medicine · doi:10.1002/cam4.6270 · Cited by 10
Liu, J., Dou, M., Liu, X., Lu, Y., & Lu, W. (2023) · Journal of Cancer Research and Clinical Oncology · doi:10.1007/s00432-023-05033-1 · Cited by 11
Targeting the immune milieu in gastrointestinal cancers
Turkes, F., Mencel, J., & Starling, N. (2020) · Journal of Gastroenterology · doi:10.1007/s00535-020-01710-x · Cited by 11
Prognostic signature of ovarian cancer based on 14 tumor microenvironment-related genes
Nie, X., Song, L., Li, X., Wang, Y., & Qu, B. (2021) · Medicine · doi:10.1097/md.0000000000026574 · Cited by 11
Zhang, C., Ding, J., Xu, X., Liu, Y., Huang, W., Da, L., Ma, Q., & Chen, S. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.645024 · Cited by 11
“Many studies have proved that it has clinical significance in predicting prognosis and treatment (Zeng et al., 2019; Zhang et al., 2020).”
BackgroundLv, X., & Xu, G. (2021) · World Journal of Gastrointestinal Oncology · doi:10.4251/wjgo.v13.i11.1648 · Cited by 11
Chu, G., Shan, W., Ji, X., Wang, Y., & Niu, H. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.764125 · Cited by 11
“Therefore, the different states of macrophages between the high- and low-score groups worth investigating further and may contribute to the accurate application of treatments (Li et al., 2019b; Tang et al., 2013).”
BackgroundPeng, J., Zou, D., Han, L., Yin, Z., & Hu, X. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.778276 · Cited by 12
“In addition to clinical factors and radiological response, detailed knowledge of the patient’s immune status of peripheral blood is needed to evaluate the efficacy of combination anti-PD-1/ PD-L1 treatment, and tumor immunogenicity score is evaluated as a predictor of immune checkpoint inhibitor response (31, 32).”
BackgroundZhong, W., Wu, Y., Zhu, M., Zhong, H., Huang, C., Lin, Y., & Huang, J. (2022) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2022.01.014 · Cited by 11
“As previously reported, the formula was employed to define the AS or APA score: AS or APA score = P (PC1i + PC2i), where i represented the PDUI or PSI value of the selected AS or APA event.(42,43)”
MethodISYNA1: An Immunomodulatory-Related Prognostic Biomarker in Colon Adenocarcinoma and Pan-Cancer
Jia, Z., & Wan, X. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.792564 · Cited by 11
Pyroptosis patterns and immune infiltrates characterization in head and neck squamous cell carcinoma
Deng, H.-X., Wei, Z.-Y., Qiu, S.-J., Ye, D., Gu, S., Shen, Y., Shen, Z.-S., Jin, Y., & Zhou, C. (2022) · Journal of clinical laboratory analysis (Print) · doi:10.1002/jcla.24292 · Cited by 10
Feng, C., Li, T., Xiao, J., Wang, J., Meng, X., Niu, H., Jiang, B., Huang, L., Deng, X., Yan, X., et al. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.814836 · Cited by 11
Fu, R., Shao, Q., Yang, B., Chen, Y., Ye, Q., Chen, X., & Zhu, J. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.903484 · Cited by 11
“However, because of the small sample size of genome-wide association studies related to pancreatic cancer, compared with, for example, breast and colorectal cancer, there are fewer associated genes and fewer variant sites in pancreatic cancer (8).”
BackgroundChen, C., Chen, L., Zhang, J., & Xu, H. (2022) · Current Oncology · doi:10.3390/curroncol30010044 · Cited by 10
Self-citationZhang, Q., Deng, Z., & Yang, Y. (2023) · Molecular Biotechnology · doi:10.1007/s12033-023-00681-7 · Cited by 11
Li, X., Xiong, F., Hu, Z., Qing, T., Yang, Y., Qiao, X., Peng, C., Jiang, Y., Han, M., Dong, K., et al. (2024) · Journal of Translational Medicine · doi:10.1186/s12967-024-04859-8 · Cited by 10
Tan, Z., Li, H., Huang, Y., Fu, S., Wang, H., & Wang, J. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e26804 · Cited by 10
“…the correlation between the arginine biosynthesis score and tumor immune microenvironment by referring to the method described by Zeng et al. [15], and the arginine biosynthesis score was negatively related to immune-related pathways (Antigen_processing_machinery, Immune_Checkpoint,…”
MethodLian, C., Li, F., Xie, Y., Zhang, L., Chen, H., Wang, Z., Pan, X., Wang, X., & Zhang, J. (2024) · Journal of Cancer · doi:10.7150/jca.92839 · Cited by 10
“We collected three GEO immunotherapy cohorts (GSE78220[30] GSE35640[31] and GSE100797[32]), along with the IMvigor210 cohort, to investigate the relationship between TEX characteristics and immunotherapy.”
MethodSelf-citationWang, Y., Mou, Y.-K., Liu, W.-C., Wang, H., Song, X., Yang, T., Ren, C., & Song, X. (2024) · Scientific Reports · doi:10.1038/s41598-024-70430-6 · Cited by 10
Wang, W., Wu, Q., Wang, Z., Ren, S., Shen, H., Shi, W., & Xu, Y. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.647273 · Cited by 10
“Many previous study have applied the algorithm to various types of cancer, such as breast cancer (11), colon cancer (12), gastric cancer (13) and brain cancer (14).”
MethodProfiles of immune infiltration in the tumor microenvironment of hepatocellular carcinoma
Meng, L., Ma, R., Yan, R., Yuan, D., Li, Y., Shi, L., & Li, K. (2021) · Journal of Gastrointestinal Oncology · doi:10.21037/jgo-21-291 · Cited by 10
“Previous studies have shown TME score to be a prognostic biomarker that could predict immunotherapeutic efficacy (23).”
Association of Angiogenesis Gene Expression With Cancer Prognosis and Immunotherapy Efficacy
Li, X., Ma, W., Su, L., Shen, Y., Zhang, L., Shao, Y.-H., Wang, D., Wang, Z., Wen, M., & Yang, X. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.805507 · Cited by 10
Li, C., Tian, C., Zeng, Y.-L., Liang, J.-Y., Yang, Q.-F., Gu, F., Hu, Y., & Liu, L. (2022) · BMC Medical Genomics · doi:10.1186/s12920-022-01184-1 · Cited by 10
“The abundance of LM22 (22 immune cell types) was calculated using CIBERSORT algorithm [16] (model = relative, permutation = 1000, disable quantile normalization = True, https:// ciber sort. stanf ord. edu/).”
MethodInfluentialIdentification of lncRNAs based on different patterns of immune infiltration in gastric cancer
Chen, S., Ben, X., Guo, L., & Li, X. (2022) · Journal of Gastrointestinal Oncology · doi:10.21037/jgo-21-833 · Cited by 10
“Studies have shown that different immune subtypes result in different prognoses (28).”
BackgroundYue, Q., Zhang, Y., Wang, F., Cao, F., Bai, J. Y., & Duan, X. (2022) · Journal of Immunology Research · doi:10.1155/2022/8766735 · Cited by 10
“Next, principal component analysis (PCA) was performed for dimension reduction, and the final weight values of PC1 and PC2 were used to construct the m6Ascore model with the formula as follows [35]: m6Ascore =∑ðPC 1i + PC2iÞ, where “i” represents the expression of m6A regulator cluster-associated DEGs.”
Yin, T., Huang, M.-X., Wang, F., Jiang, Y., Long, J., Li, L., & Cao, J. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.943849 · Cited by 10
“Later, this study determined lactate score by gene expression grade index (GGI) (Sotiriou et al., 2006; Zeng et al., 2019): Lactate score ∑(PC1i + PC2i) in the formula, i stands for LRG expression levels.”
MethodGuo, L., Yan, T., Guo, W., Niu, J., Wang, W., Ren, T., Huang, Y., Xu, J., & Wang, B. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.986785 · Cited by 11
“We also defined CSC score using a similar approach from previous studies (44, 45).”
MethodXu, X., Zhou, N., Lan, H., Yang, F., Dong, B., & Zhang, X. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23179767 · Cited by 10
“As the immune checkpoint-related signatures, we chose CD274, CTLA4, LAG3, HAVCR2, IDO1, and PDCD1; as the immunological activity-related signatures, we chose CD8A, CXCL10, GZMA, CXCL9, GZMB, GZMA, IFNG, PRF1, TBX2, and TNF [42,43].”
Tu, J., Kuang, Z., Xie, X., Wu, S., Wu, T., & Chen, S. (2020) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.15851 · Cited by 10
Klein, S., & Duda, D. G. (2021) · Cancers · doi:10.3390/cancers13194919 · Cited by 10
Tian, Y., Wei, Y., Liu, H., Shang, H., Xu, Y., Wu, T., Liu, W., Huang, A., Dang, Q., & Sun, Y. (2021) · Aging · doi:10.18632/aging.203584 · Cited by 10
Cell Differentiation Trajectory-Associated Molecular Classification of Osteosarcoma
Xu, A., Qian, C., Lin, J., Yu, W., Jin, J., Liu, B., & Tao, H. (2021) · Genes · doi:10.3390/genes12111685 · Cited by 10
“gov/programs/target/projects/osteosarcoma, accessed on 9 August 2021) were also gathered, and FPKM values were transformed into transcripts per kilobase million (TPM) values and then log2(TPM+1) values, which are more comparable between samples and more similar to data from microarrays [15,16].”
Metadata
- Authors
- Zeng, D., Li, M., Zhou, R., Zhang, J., Sun, H., Shi, M., Bin, J., Liao, Y., Rao, J., & Liao, W.
- Affiliations
- Nanfang Hospital (CN)
- Southern Medical University (CN)
- ORCID
- Venue
- Cancer Immunology Research
- Published
- 2019-05-01
- Volume
- 7
- Issue
- 5
- Pages
- 737-750
- ISSN
- 2326-6066 (ISSN-L)
- 2326-6074
- OpenAlex
- W2920600229
- Semantic Scholar
- 180648d1827a7e8c086f03b00ca69831a1ca538e
- Cited by
- 986
- References
- 76
- Citations by year
- 2026: 38 · 2025: 87 · 2024: 164 · 2023: 211 · 2022: 251 · 2021: 162 · 2020: 64 · 2019: 9
- FWCI
- 53.10
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Cancer Immunology Research (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (81772580)
- Topics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Health Sciences › Medicine › Oncology › Gastric Cancer Management and Outcomes
- Life Sciences › Immunology and Microbiology › Immunology › Immune cells in cancer
- Keywords
- gastric cancer, tumor microenvironment, prognostic factors, immunotherapy response, immune cell infiltration, T cell suppression, epithelial-mesenchymal transition, angiogenesis, TGF-beta signaling, IFN-gamma response, gene expression signatures, IMvigor210
- MeSH terms
- Antineoplastic Agents, Immunological, Algorithms, Humans, Immunotherapy, Phenotype, Prognosis, Stomach Neoplasms, Gene Expression Regulation, Neoplastic, Tumor Microenvironment
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