ImmuCellAI: a unique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunotherapy

Miao, Ya‐Ru; Zhang, Qiong; Lei, Qian; Luo, Mei; Xie, Gui-Yan; Wang, Hongxiang; Guo, An‐Yuan

doi:10.1101/872184

Cited by 66 publications

(88 citation statements)

References 41 publications

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“…ImmuCellAI (http://bioinfo.life.hust.edu.cn/web/ImmuCellAI/) is an emerging tool to estimate the abundance of 24 immune cells based on a gene expression data set (Miao et al., 2020). The infiltrating data of TIICs corresponding to TCGA‐HCC samples were downloaded from the ImmuCellAI website.…”

Section: Methodsmentioning

confidence: 99%

Systematic summarization of the expression profiles and prognostic roles of the dishevelled gene family in hepatocellular carcinoma

Mei

Yang

Xia

et al. 2020

Molec Gen & Gen Med

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Background Dishevelled (DVL) family members are crucial to Wnt‐induced signaling transduction, and their expression is highly correlated with the progression of multiple malignant cancers. However, the expression profiles and exact prognostic values of DVLs in hepatocellular carcinoma (HCC) have not been explored until now. Methods The expression of DVL isoforms was assessed using the Oncomine, HCCDB and UALCAN databases. The prognostic roles of DVLs were further evaluated using the GEPIA database. The relationship between the expression of DVLs and immune infiltration of HCC was investigated using the Timer and ImmuCellAI tools. Furthermore, protein–protein interaction (PPI) networks were built and enrichment analyses were conducted. Results We found that the expression levels of DVL2 (OMIM accession number: 602151) and DVL3 (OMIM accession number: 601368) were upregulated in HCC tissues as revealed by the Oncomine and HCCDB databases. Additionally, the expression of DVLs tended to be associated with advanced clinical features in the UALCAN database. Prognostic analysis revealed that the expression levels of DVL1 (OMIM accession number: 601365) and DVL3 were remarkably associated with a poor prognosis in HCC patients. The results also revealed that the DVL expression level was correlated with the infiltration levels of multiple immune cells. By constructing the PPI network and enrichment analyses, the DVL1‐3 gene was identified to interact with 20 key genes and participate in several pathways. Conclusion In summary, DVL2 and DVL3 are highly expressed in HCC, and DVL1 and DVL3 are related to a poor prognosis, which might be used as candidate targets for targeted therapy and reliable prognostic biomarkers in HCC.

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Section: Methodsmentioning

confidence: 99%

Systematic summarization of the expression profiles and prognostic roles of the dishevelled gene family in hepatocellular carcinoma

Mei

Yang

Xia

et al. 2020

Molec Gen & Gen Med

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“…After comprehensive consideration of TIMER database (26) and CIBERSORT algorithm(27), we further conducted immune cell infiltration analysis in ImmuneCellAI (28), which demonstrated powerful and unique function in tumor immune infiltration estimation and immunotherapy response prediction (http://bioinfo.life.hust.edu.cn/ImmuCellAI/). Transcriptome data from both groups were submitted to ImmuneCellAI, and all original matrices containing infiltrating immune cells information were downloaded.…”

Section: Immunecellai and Prognostic Analysis Of Immune Cellsmentioning

confidence: 99%

A novel panel based on Immune infiltration and tumor mutational burden for prognostic prediction in hepatocellular carcinoma

Zheng

Pan

et al. 2020

Preprint

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Background : Tumor mutation burden (TMB) was associated with prognosis in various malignancies, but it remains to be elucidated in hepatocellular carcinoma (HCC). We aimed to investigate the prognostic effects of TMB and its relationship with immune infiltration so as to establish a panel model capable of predicting prognosis. Methods : TMB was calculated in all 374 HCC patients from the Cancer Genome Atlas, and high TMB and low TMB groups were determined based on propensity score matching and X-tile analysis. WCGNA was utilized to screen out genes related to immune cells and TMB, followed by multivariate analysis to generated the final TMB-Infiltration (TMB-IF) panel. 453 HCC patients from ICGC-LIRI-JP, GSE76427 and GSE20017 verified the robustness and extensibility of TMB-IF. Additionally, whole-exome sequencing (WES) was performed in 8 follow-up patients to investigate the relationship between HCC recurrence and TMB. Results : Patients in high TMB group had worse prognosis than those in low TMB group, with a cutoff TMB value of 4.9. Enrichment analysis demonstrated that differentially expressed genes were mainly related to T cell activation, cell membrane localization and matrix composition. Tumor immune infiltration analysis revealed the infiltrations of Th2, Th17, and Tgd were up-regulated in high TMB group, while those of Tr1, MAIT, and DC were up-regulated in low TMB group. And TMB-IF fit well with the actual survival observation, with a C-index 0.785 (0.700-0.870), which verified in ICGC-LIRI-JP was 0.670 (0.573-0.767), and 0.774 (0.670-0.877) in GSE76427. In addition, TMB-IF showed a good performance in predicting tumor vascular invasion with a C-index of 0.847 (0.778-0.916). Conclusions : Higher TMB means worse prognosis in HCC patients. Patients with higher frequency of immune-related gene mutations and TMB are prone to relapse after radical treatment.

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“…ImmuCellAI is a newly developed algorithm used to evaluate the concentrations of in ltrating immune cells precisely [10] in decreasing order based on the SNF5 expression level and extracted the upper-third and lower-third of these samples for subsequent analysis. P < 0.05 was considered the criterion to de ne a type of lymphocytes as affected by the expression of SNF5.…”

Section: Immune In Ltration Analysis and Prediction Of Immune Checkpomentioning

confidence: 99%

The associations of SNF5 with prognosis and immune responses in bladder cancer

Hua

Zhang

et al. 2020

Preprint

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Background Bladder cancer (BC) is the second most common malignancy in the urinary system. Improving survival has been hampered by high heterogeneity and drug resistance. SNF5, a subunit of the SWI/SNF chromatin-remodeling complex, is commonly lost or inactivated in multiple malignancies. The role of SNF5 in bladder cancer has not yet been elucidated. This is the first exploration into the associations of SNF5 with prognosis and its functions in BC. Methods Using datasets from The Cancer Genome Atlas projects and our institution, we investigated the predictive value of SNF5 in bladder cancer, as well as the relationships with clinical characteristics. The differential genes expression analysis, gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene set enrichment analyses (GSEA) were performed to investigate the functions of SNF5. The Immune Cell Abundance Identifier (ImmuCellAI) algorithm was used to infer the fractions of tumor-infiltrating lymphocytes (TILs). Next, we conducted gene set variation analysis (GSVA) and Tumor Immune Dysfunction and Exclusion (TIDE) algorithm to assess the effects of SNF5 on antitumor response and sensitivity to immune checkpoint blockade (ICB). Results SNF5 had the potential to predict bladder cancer and a negative correlation with survival. SNF5 was involved in immune response. Low expression of SNF5 promoted infiltration of immune cells into tumor, enhanced the abilities to process and present antigens by activating the MHC-T cell receptor activation pathway. Moreover, decreased SNF5 activated CTLA-4 pathway, upregulating CTLA-4 expression, but SNF5 did not modify the expression of PD-1 or PD-L1. A higher TIDE score was generated in the low-expression group, which indicated that patients with low expression might derive greater benefit from ICB. Conclusions Our findings indicated that SNF5 was not only a good biomarker for diagnosis and prognosis of BC, but a potential new target in the immunotherapy for BC.

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ImmuCellAI: a unique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunotherapy

Cited by 66 publications

References 41 publications

Systematic summarization of the expression profiles and prognostic roles of the dishevelled gene family in hepatocellular carcinoma

Systematic summarization of the expression profiles and prognostic roles of the dishevelled gene family in hepatocellular carcinoma

A novel panel based on Immune infiltration and tumor mutational burden for prognostic prediction in hepatocellular carcinoma

The associations of SNF5 with prognosis and immune responses in bladder cancer

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