Circadian rhythm-related genes index: A predictor for HNSCC prognosis, immunotherapy efficacy, and chemosensitivity

Chi, Hao; Yang, Jinyan; Peng, Gaoge; Zhang, Jinhao; Song, Guobin; Xie, Xixi; Xia, Zhijia; Liu, Jinhui; Tian, Gang

doi:10.3389/fimmu.2023.1091218

Cited by 57 publications

(55 citation statements)

References 87 publications

(54 reference statements)

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“…Considering the demonstrated potential value of multi-gene risk models in predicting prognosis and treatment response in HNSCC, [6,7,36] this study constructed a prognostic risk score model for HNSCC using DEGs between molecular subtypes derived from TMG. The model includes 9 independent prognostic genes, some of which have been shown to be important in the occurrence and development of tumors.…”

Section: Discussionmentioning

confidence: 99%

“…[4] Presently, there has been a development of multi-gene risk signatures utilizing specific gene sets, which significantly contribute to the understanding of heterogeneity, prognosis, and treatment response in patients diagnosed with HNSCC. [5][6][7] Therefore, it is crucial to find new prognostic biomarkers and therapeutic targets to overcome the low survival rate of HNSCC.…”

Section: Introductionmentioning

confidence: 99%

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Telomere maintenance genes-derived prognosis signature characterizes immune landscape and predicts prognosis of head and neck squamous cell carcinoma

et al. 2023

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Telomere dysfunction has been identified as a biological marker of cancer progression in several types of cancer, including Head and Neck Squamous Cell Carcinoma (HNSCC). This study aimed to characterize the telomere maintenance genes (TMG)-related signature in prognosis and treatment response in HNSCC. The transcriptome and clinical data of HNSCC were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases, respectively. Non-negative matrix factorization (NMF) was used to identify molecular subtypes derived from TMG. Gene set enrichment analysis (GSEA) was performed to analyze the differentially expressed pathways between subtypes, and a risk score model derived from TMG was established. Kaplan-Meier survival analysis was used to evaluate inter-group prognostic features, and the correlation between TMG-derived molecular subtypes and risk score model with immune infiltration, immunotherapy, and chemosensitivity was assessed. Two HNSCC subtypes were identified based on 59 TMG-related genes, which exhibit significant heterogeneity in prognosis, immune cell infiltration, and treatment response. Additionally, a TMG-derived risk signature containing 9 genes was developed to assess the prognosis of HNSCC patients. The signature had significant predictive ability for HNSCC prognosis and was significantly correlated with immune cell infiltration and immunotherapy response. A nomogram integrating the risk signature, N stage and radiotherapy was constructed to predict 1-, 3-, and 5-year overall survival (OS) of HNSCC patients, which had better performance than other prognostic models and included TMG-derived risk score, radiotherapy, and N stage. This study identified TMG-derived molecular subtypes in HNSCC and developed a novel prognostic score model, highlighting the potential value of TMG in HNSCC prognosis and immunotherapy.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Telomere maintenance genes-derived prognosis signature characterizes immune landscape and predicts prognosis of head and neck squamous cell carcinoma

et al. 2023

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“…[28,30] A signature score was also alculated based on all fibroblast marker genes using gene set variation analysis. [31] We used the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm to assess the correlation of 22 immune cells with risk scores, selected genes, and the signature of all CAF marker genes. [32]…”

Section: Methodsmentioning

confidence: 99%

Single-cell and bulk RNA sequencing reveal cancer-associated fibroblast heterogeneity and a prognostic signature in prostate cancer

Liu

Wang

et al. 2023

Medicine

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Cancer-associated fibroblasts (CAFs), the central players in the tumor microenvironment (TME), can promote tumor progression and metastasis via various functions. However, the properties of CAFs in prostate cancer (PCa) have not been fully assessed. Therefore, we aimed to examine the CAF characteristics in PCa and construct a CAF-derived signature to predict PCa prognosis. CAFs were identified using single-cell RNA sequencing (scRNA-seq) data from 3 studies. We performed the FindAllMarkers function to extract CAF marker genes and constructed a signature to predict the biochemical relapse-free survival (bRFS) of PCa in the Cancer Genome Atlas (TCGA) cohort. Subsequently, different algorithms were applied to reveal the differences of the TME, immune infiltration, treatment responses in the high- and low-risk groups. Additionally, the CAF heterogeneity was assessed in PCa, which were confirmed by the functional enrichment analysis, gene set enrichment analysis (GSEA), and AUCell method. The scRNA-seq analysis identified a CAF cluster with 783 cells and determined 183 CAF marker genes. Cell-cell communication revealed extensive interactions between fibroblasts and immune cells. A CAF-related prognostic model, containing 7 genes (ASPN, AEBP1, ALDH1A1, BGN, COL1A1, PAGE4 and RASD1), was developed to predict bRFS and validated by 4 independent bulk RNA-seq cohorts. Moreover, the high-risk group of the signature score connected with an immunosuppressive TME, such as a higher level of M2 macrophages and lower levels of plasma cells and CD8+ T cells, and a reduced reaction rate for immunotherapy compared with low-risk group. After re-clustering CAFs via unsupervised clustering, we revealed 3 biologically distinct CAF subsets, namely myofibroblast-like CAFs (myCAFs), immune and inflammatory CAFs (iCAFs) and antigen-presenting CAFs (apCAFs). In conclusion, the CAF-derived signature, the first of its kind, can effectively predict PCa prognosis and serve as an indicator for immunotherapy. Furthermore, our study identified 3 CAF subpopulations with distinct functions in PCa.

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“…Immunization-related information, tumor-infiltrating immune cells, and variable cellular contexts were analyzed using EPIC (E), MCPCOUNT (M), QUANTISEQ (Q), TIMER (T), and XCELL (X) modes [31]. Heatmaps illustrated the differential landscape across settings.…”

Section: Bioinformatic Analysismentioning

confidence: 99%

The high expression of immune checkpoint co-stimulators predicts a favorable prognosis in head and neck carcinomas

Chang,

Chou,

et al. 2024

Preprint

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Objectives: T cells require second immune checkpoint molecules for activation and immune memory after antigen presentation. In our previous study, we found ICOS a favorable prognostic factor amongst B7 immune checkpoint co-stimulators (ICSs) families in head and neck squamous cell carcinoma (HNSCC) and oral SCC (OSCC). Materials and method: This study analyzed the expression of on-B7 TNF ligand/receptor superfamily ICSs in the Cancer Genome Atlas (TCGA) HNSCC cohort, our OSCC cohort, and pan-cancer datasets. The correlation in expression, prognosis, and immune status was assessed. Results: The higher expression of CD27, CD30, CD40L, DR3, and OX40, presumably on the T cell surface, defined better overall survival of HNSCC patients. Besides, CD27, CD30, CD40L, and OX40 were highly correlated with ICOS expression in tumors. CD27, CD40L, and DR3 expression are higher in HPV+ HNSCC tumors than in HPV- tumors. The combined expression level of CD27/OX40 or CD27/CD40L/OX40 enables the potent survival prediction of small, less nodal involvement, early stage, and HPV+ tumor subsets. In both HNSCC and our OSCC cohorts, tumors expressing high CD27, CD30, CD40L, ICOS, and OX40 exhibited enhanced immune cell infiltration. The high correlation in the expression of these ICSs is also noted in the vast majority of tumor types in addition to HNSCC in TCGA datasets. Conclusion: The findings suggest that the concordant stimulation of CD27, CD30, CD40L, ICOS, and OX40 could be a crucial strategy in cancer immunotherapy.

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Circadian rhythm-related genes index: A predictor for HNSCC prognosis, immunotherapy efficacy, and chemosensitivity

Cited by 57 publications

References 87 publications

Telomere maintenance genes-derived prognosis signature characterizes immune landscape and predicts prognosis of head and neck squamous cell carcinoma

Telomere maintenance genes-derived prognosis signature characterizes immune landscape and predicts prognosis of head and neck squamous cell carcinoma

Single-cell and bulk RNA sequencing reveal cancer-associated fibroblast heterogeneity and a prognostic signature in prostate cancer

The high expression of immune checkpoint co-stimulators predicts a favorable prognosis in head and neck carcinomas

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