Whole exome sequencing approach to analysis of the origin of cancer stem cells in patients with head and neck squamous cell carcinoma

Salazar-García, Lorena; Pérez‐Sayáns, Mario; García‐García, Abel; Carracedo, Ángel; Cruz, Raquel; Lozano, Antonio; Barros, Francisco

doi:10.1111/jop.12771

Cited by 6 publications

(2 citation statements)

References 24 publications

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“…High-throughput RNA sequencing (RNA-Seq) has been widely used to analyze transcriptomic changes across the whole genome (Ozsolak and Milos, 2011;Raz et al, 2011). Due to the outstanding advantages of sensitive, efficient, and accurate detection of digital method of all expressed genes, RNA-Seq has been widely used to identify the potential transcriptional mechanisms and components of oral cancers; for example, it has been used to analyze the initiation of cancer stem cells in patients with head and neck squamous cell carcinoma, and for identifying specific global gene expression signatures of tongue squamous cell carcinoma (Salazar-Garcia et al, 2018;Zhang et al, 2018). In the present study, we used time-course RNA-Seq transcriptomic analysis to identify the tumor-associated gene (TAG) and core dynamic differentially expressed gene (DEG) signatures affected by timeseries F. nucleatum stimulation.…”

Section: Introductionmentioning

confidence: 99%

Time-Course Transcriptome Analysis of Gingiva-Derived Mesenchymal Stem Cells Reveals That Fusobacterium nucleatum Triggers Oncogene Expression in the Process of Cell Differentiation

Kang

Sun

Tang

et al. 2020

Front. Cell Dev. Biol.

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Fusobacterium nucleatum has pathogenic effects on oral squamous cell carcinoma and colon cancer, while the effects of continuously altered gene expression in normal human cells, as induced by persistent exposure to F. nucleatum, remain unclear. In this study, a microarray Significant Profiles (maSigPro) analysis was used to obtain the transcriptome profile of gingiva-derived mesenchymal stem cells (GMSCs) stimulated by F. nucleatum for 3, 7, 14, and 21 day, and the results revealed 790 (nine clusters) differentially expressed genes (DEGs), which were significantly enriched in cell adherens junctions and cancer-related pathways. On the basis of a short time-series expression miner (STEM) analysis, all the expressed genes in the GMSCs were grouped into 50 clusters according to dynamic gene expression patterns, and the expression levels of three gene clusters in the F. nucleatum-treated GMSCs were significantly different than the predicted values. Among the 790 DEGs, 50 tumor-associated genes (TAGs; such as L3MBTL4, CD163, CCCND2, CADM1, BCL7A, and IGF1) and five core dynamic DEGs (PLCG2, CHI3L2, L3MBTL4, SH2D2A, and NLRP3) were identified during F. nucleatum stimulation. Results from a GeneMANIA database analysis showed that PLCG2, CHI3L2, SH2D2A, and NLRP3 and 20 other proteins formed a complex network of which 12 genes were enriched in cancer-related pathways. Based on the five core dynamic DEGs, the related microRNAs (miRNAs) and transcription factors (TFs) were obtained from public resources, and an integrated network composed of the related TFs, miRNAs, and mRNAs was constructed. The results indicated that these genes were regulated by several miRNAs, such as miR-372-3p, miR-603, and miR-495-3p, and several TFs, including CREB3, GATA2, and SOX4. Our study suggests that long-term stimulation by F. nucleatum may trigger the expression of cancer-related genes in normal gingiva-derived stem cells.

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Section: Introductionmentioning

confidence: 99%

Time-Course Transcriptome Analysis of Gingiva-Derived Mesenchymal Stem Cells Reveals That Fusobacterium nucleatum Triggers Oncogene Expression in the Process of Cell Differentiation

Kang

Sun

Tang

et al. 2020

Front. Cell Dev. Biol.

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“…Consequently, the process of sequence assembly becomes necessary in order to derive meaningful and conclusive outcomes from the data. Researchers with an interest in performing Whole Exome Sequencing (WES) analysis for the purpose of variant calling and investigating genetic diseases can effectively employ the following pipeline [64].…”

Section: Discussionmentioning

confidence: 99%

Integrated Whole Exome and Transcriptome Sequencing in Cholesterol Metabolism in Melanoma: Systematic Review

Mahmoud Nour Eldin,

Ahmed Nasif,

Ahmed Nasif

et al. 2024

Sudan JMS

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Background: Melanoma is a highly malignant form of skin cancer that exhibits remarkable metabolic adaptability. Melanoma cells exhibit the capacity to adapt to specific conditions of the tumor microenvironment through the utilization of diverse energy sources, thereby facilitating the growth and advancement of the tumor. One of the notable characteristics of metabolic reprogramming is the heightened rate of lipid synthesis. This review was conducted to illustrate how the integration of whole exom and transcriptome sequencing will enhance the detection of the effect of cholesterol metabolism in melanoma. Methods: The Cochrane database, Embase, PubMed, SCOPUS, Google Scholar, Ovid, and other databases were thoroughly searched for works addressing integrated whole exome and transcriptome sequencing in cholesterol metabolism in melanoma. Skin malignancy, melanoma progression, transcriptome sequencing, whole exome sequencing, transcriptome sequencing by RNA sequencing, and integrated transcriptome and whole exome sequencing were the key phrases employed. This article underwent a phased search for pertinent literature using a staged literature search methodology. Each section’s relevant papers were identified and summarized independently. The results have been condensed and narratively given in the pertinent sections of this thorough assessment. Results: DNA-based analysis has proven to be ineffective in identifying numerous mutations that have an impact on splicing or gene expression. RNA-Sequencing, when combined with suitable bioinformatics, offers a reliable method for detecting supplementary mutations that aid in the genetic diagnosis of geno-dermatoses. Therefore, clinical RNA-Sequencing expands the scope of molecular diagnostics for rare genodermatoses, and it has the potential to serve as a dependable initial diagnostic method for expanding mutation databases in individuals with inheritable skin conditions. Conclusion: The integration of patient-specific tumor RNA-sequencing and tumor DNA whole-exome sequencing (WES) would potentially enhance mutation detection capabilities compared to relying solely on DNA-WES.

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Heterogeneity of Head and Neck Squamous Cell Carcinoma Stem Cells

Qian

Nie

Wollenberg

et al. 2019

Stem Cells Heterogeneity in Cancer

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Whole exome sequencing approach to analysis of the origin of cancer stem cells in patients with head and neck squamous cell carcinoma

Abstract: These findings support the idea that it is possible to identify in each individual patient if the CS are of tumour origin or vice versa, thus being possible a more personalized treatment.

Cited by 6 publications

References 24 publications

Time-Course Transcriptome Analysis of Gingiva-Derived Mesenchymal Stem Cells Reveals That Fusobacterium nucleatum Triggers Oncogene Expression in the Process of Cell Differentiation

Time-Course Transcriptome Analysis of Gingiva-Derived Mesenchymal Stem Cells Reveals That Fusobacterium nucleatum Triggers Oncogene Expression in the Process of Cell Differentiation

Integrated Whole Exome and Transcriptome Sequencing in Cholesterol Metabolism in Melanoma: Systematic Review

Heterogeneity of Head and Neck Squamous Cell Carcinoma Stem Cells

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