RNA-Seq analysis of peripheral blood mononuclear cells reveals unique transcriptional signatures associated with radiotherapy response of nasopharyngeal carcinoma and prognosis of head and neck cancer

Liu, Guohong; Zeng, Xiaojiao; Wu, Balu; Jin, Zhao; Pan, Yunbao

doi:10.1080/15384047.2019.1670521

Cited by 44 publications

(32 citation statements)

References 24 publications

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“…It has been reported to be related to the clinical outcomes of acute lymphoblastic leukemia patients (42). Along with CHAC2, CLEC9A, and 8 other genes, JCHAIN was also found to be associated with survival in head and neck squamous cell carcinoma (43). Moreover, You reported that JCHAIN might exert a critical influence on resistance and tumorigenesis in Marek's disease (44).…”

Section: Discussionmentioning

confidence: 96%

A signature of estimate-stromal-immune score-based genes associated with the prognosis of lung adenocarcinoma

Ma¹,

Chen²,

Xiao³

et al. 2021

Transl Lung Cancer Res

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Background: Immune and stromal component evaluation is necessary to establish accurate prognostic markers for the prediction of clinical outcomes in lung adenocarcinoma (LUAD). We aimed to develop a gene signature based on the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE)-stromal-immune score in LUAD. Methods:The transcriptomic profiles of patients with LUAD were obtained from The Cancer Genome Atlas (TCGA), and the immune and stromal scores were derived using the ESTIMATE algorithm. The prognostic signature genes were selected from the differentially expressed genes (DEGs) using the robust partial likelihood-based cox proportional hazards regression method. The negative log-likelihood and the Akaike Information Criterion (AIC) were used to identify the optimal gene signature. The validation was carried out in 2 independent datasets from the Gene Expression Omnibus (GSE68571 and GSE72094).Results: Patients with high ESTIMATE, stromal, and immune scores had better overall survivals (P=0.0035, P=0.066, and P=0.0077). The expression of thirty-seven genes was related to ESTIMATE-stromal-immune score. A risk stratification model was developed based on a gene signature containing CD74, JCHAIN, and PTGDS. The ESTIMATE-stromal-immune risk score was revealed to be a prognostic factor (P=0.009) after multivariate analysis. Four groups were classified based on this risk stratification model, yielding increasing survival outcomes (log-rank test, P=0.0051). This risk stratification model and other clinicopathological factors were combined to generate a nomogram. The calibration curves showed perfect agreement between the nomogram-predicted outcomes and those actually observed. Similar observations were made in 2 independent cohorts. Conclusions:The gene signature based on the ESTIMATE-stromal-immune score could predict the prognosis of patients with LUAD.

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Section: Discussionmentioning

confidence: 96%

A signature of estimate-stromal-immune score-based genes associated with the prognosis of lung adenocarcinoma

Ma¹,

Chen²,

Xiao³

et al. 2021

Transl Lung Cancer Res

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“…KLRB1 protein is expressed by NK cells and may be involved in the regulation of NK cell function. Previous studies shows that high expression of KLRB1 is closely related to the better prognosis of HNSCC patients [ 26 ]. CCL19, as the ligand of CCR7, induces several CCR7 activated pathways in metastatic HNSCC [ 27 – 38 ].…”

Section: Discussionmentioning

confidence: 99%

HPV infection related immune infiltration gene associated therapeutic strategy and clinical outcome in HNSCC

Zeng

Song

et al. 2020

BMC Cancer

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Background: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common tumor in human. Research has shown that HPV status HNSCC is a unique prognosis factor, which may due to its immune infiltration landscape. But the underlying mechanism is unclear. Methods: In this study, we used a combination of several bioinformatics tools, including WCGNA, ssGSEA, CIBERSORT, TIDE,etc., to explore significant genes both related to HPV infection status and immune cell infiltration in HNSCC patients. Results: Combined with several bioinformatics algorithms, eight hub genes were identified, including LTB, CD19, CD3D, SKAP1, KLRB1, CCL19, TBC1D10C and ARHGAP4. In HNSCC population, the hub genes had a stable coexpression, which was related to immune cell infiltration, especially CD8+ T cells, and the infiltrative immune cells were in a dysfunctional status. Samples with high hub genes expression presented with better response to immune check point block (ICB) therapy and sensitivity to bleomycin and methotrexate. Conclusions: The eight hub genes we found presented with a stable co-expression in immune cell infiltration of HPV + ve HNSCC population. The co-expression of hub genes related to an immune microenvironment featuring an increase in immune cells but high degree of immune dysfunction status. Patients with high hub gene expression had a better response to ICB treatment, bleomycin and methotrexate. The co-expression of hub genes may be related to immune infiltration status in patients. The concrete molecular mechanism of hub genes function demands further exploration.

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“…Additionally, miR-574-5p, miR-9 and miR92a, which modulate the expression of MHC class I and interferon-regulated genes associated with NPC metastasis, could potentially be non-invasive blood-based biomarkers for metastasis prediction [ 132 , 133 ]. RNA sequencing of NPC patients’ peripheral blood mononuclear cells (PBMC) before and after RT has revealed 11 potential mRNA prognostic biomarkers for NPC for post-RT evaluation [ 160 ]. RNA_0000285 at homeodomain interacting protein kinase 3 (HIPK3) was observed in high level radio-resistance NPC patients and low radiosensitive NPC patients, thus showing its ability to predict NPC radiosensitivity [ 136 ].…”

Section: Npc Prognosis Biomarkersmentioning

confidence: 99%

Current Status and Future Perspectives about Molecular Biomarkers of Nasopharyngeal Carcinoma

Siak

Khoo

Leong

et al. 2021

Cancers

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Nasopharyngeal carcinoma (NPC) is an epithelial malignancy that shows a remarkable ethnic and geographical distribution. It is one of the major public health problems in some countries, especially Southern China and Southeast Asia, but rare in most Western countries. Multifactorial interactions such as Epstein–Barr virus infection, individual’s genetic susceptibility, as well as environmental and dietary factors may facilitate the pathogenesis of this malignancy. Late presentation and the complex nature of the disease have led it to become a major cause of mortality. Therefore, an effective, sensitive, and specific molecular biomarker is urgently needed for early disease diagnosis, prognosis, and prediction of metastasis and recurrence after treatment. In this review, we discuss the recent research status of potential biomarker discovery and the problems that need to be explored further for better NPC management. By studying the aberrant pattern of these candidate biomarkers that promote NPC development and progression, we are able to understand the complexity of this malignancy better, hence positing our stands better towards strategies that may provide a way forward to the discovery of more reliable and specific biomarkers for diagnosis and targeted therapeutic development.

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RNA-Seq analysis of peripheral blood mononuclear cells reveals unique transcriptional signatures associated with radiotherapy response of nasopharyngeal carcinoma and prognosis of head and neck cancer

Abstract: Pan (2020) RNA-Seq analysis of peripheral blood mononuclear cells reveals unique transcriptional signatures associated with radiotherapy response of nasopharyngeal carcinoma and prognosis of head and neck cancer,

Cited by 44 publications

References 24 publications

A signature of estimate-stromal-immune score-based genes associated with the prognosis of lung adenocarcinoma

A signature of estimate-stromal-immune score-based genes associated with the prognosis of lung adenocarcinoma

HPV infection related immune infiltration gene associated therapeutic strategy and clinical outcome in HNSCC

Current Status and Future Perspectives about Molecular Biomarkers of Nasopharyngeal Carcinoma

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