Nghiên cứu ung thư
Liquid biopsy to characterize cell-free DNA in detecting and monitoring of cancers
2019 Dec 31 JOURNAL OF RESEARCH AND DEVELOPMENT ON INFORMATION AND COMMUNICATION TECHNOLOGY, 2019
Tran N. Nguyen
Liquid biopsy, a concept introduced approximately a decade ago, refers to noninvasive approaches that have become the focus of biomedical research. In clinical oncology and research, the term liquid biopsy is used in a broad sense as the sampling and analysis of analytes including cell-free DNA from various accessible biological fluids for diagnosis, prognosis and prediction of a therapeutic response. This technology has the potential to be used in tracking the genomic evolution of tumors over time. It may also have therapeutic implications in terms of its ability to detect actionable events or resistant subclonal populations while avoiding the need...
Read more articleUnveiling Prognostics Biomarkers of Tyrosine Metabolism Reprogramming in Liver Cancer by Cross-platform Gene Expression Analyses
2020 Jun 15 PLOS ONE, 2020
Nguyen TN, Nguyen HQ, Le D-H
Tyrosine is mainly degraded in the liver by a series of enzymatic reactions. Abnormal expression of the tyrosine catabolic enzyme tyrosine aminotransferase (TAT) has been reported in patients with hepatocellular carcinoma (HCC). Despite this, aberration in tyrosine metabolism has not been investigated in cancer development. In this work, we conduct comprehensive cross-platform study to obtain foundation for discoveries of potential therapeutics and preventative biomarkers of HCC. We explore data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine and Kaplan Meier plotter (KM plotter) and performed integrated analyses to evaluate the clinical...
Read more articleMeta-analysis of computational methods for breast cancer classification
2020 Jun 26 INT. J. INTELLIGENT INFORMATION AND DATABASE SYSTEMS, 2019
Tri-Cong Pham, Chi-Mai Luong, Antoine Doucet, Van-Dung Hoang, Diem-Phuc Tran, Le Duc-Hau
Tyrosine is mainly degraded in the liver by a series of enzymatic reactions. Abnormal expression of the tyrosine catabolic enzyme tyrosine aminotransferase (TAT) has been reported in patients with hepatocellular carcinoma (HCC). Despite this, aberration in tyrosine metabolism has not been investigated in cancer development. In this work, we conduct comprehensive cross-platform study to obtain foundation for discoveries of potential therapeutics and preventative biomarkers of HCC. We explore data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine and Kaplan Meier plotter (KM plotter) and performed integrated analyses to evaluate the clinical...
Read more articleIntegrative transcriptomic analysis for linking acute stress responses to squamous cell carcinoma development
2020 Oct 14 SCIENTIFIC REPORTS 10, 17209 (2020)
Tran N. Nguyen, Kimal Rajapakshe, Courtney Nicholas, Leticia Tordesillas, Erik A. Ehli, Christel M. Davis, Cristian Coarfa, Elsa R. Flores, Sally E. Dickinson, Clara Curiel-Lewandrowski, Kenneth Y. Tsai
Cutaneous squamous cell carcinoma (cuSCC) is the second most common skin cancer and commonly arises in chronically UV-exposed skin or chronic wounds. Since UV exposure and chronic wounds are the two most prominent environmental factors that lead to cuSCC initiation, we undertook this study to test whether more acute molecular responses to UV and wounding overlapped with molecular signatures of cuSCC. We reasoned that transcriptional signatures in common between acutely UV-exposed skin, wounded skin, and cuSCC tumors, might enable us to identify important pathways contributing to cuSCC. We performed transcriptomic analysis on acutely UV-exposed human skin and integrated those findings...
Read more articleIntegrative Transcriptomic Analysis Identifies Drivers of Squamous Cell Carcinoma Development
2020 Oct 14 SCIENTIFIC REPORTS, 2020
Tran N. Nguyen, Kimal Rajapakshe, Courtney Nicholas, Leticia Tordesillas, Cristian Coarfa, Elsa R. Flores, Sally Dickinson, Clara Curiel-Lewandrowski, Kenneth Y. Tsai
Cutaneous squamous cell carcinoma (cuSCC) is the second most common skin cancer and commonly arises in chronically UV-exposed skin or chronic wounds. Since UV exposure and chronic wounds are the two most prominent environmental factors that lead to cuSCC initiation, we undertook this study to test whether more acute molecular responses to UV and wounding overlapped with molecular signatures of cuSCC. We reasoned that transcriptional signatures in common between acutely UV-exposed skin, wounded skin, and cuSCC tumors, might enable us to identify important pathways contributing to cuSCC. We performed transcriptomic analysis on acutely UV-exposed human skin and integrated those findings...
Read more articleMulti-Omics Analysis Detects Novel Prognostic Subgroups of Breast Cancer
2020 Oct 15 FRONT. GENET. 11:574661. (2020)
Nguyen Q-H, Nguyen H, Nguyen T, Le D-H
The unprecedented proliferation of recent large-scale and multi-omics databases of cancers has given us many new insights into genomic and epigenomic deregulation in cancer discovery in general. However, we wonder whether or not there exists a systematic connection between copy number aberrations (CNA) and methylation (MET)? If so, what is the role of this connection in breast cancer (BRCA) tumorigenesis and progression? At the same time, the PAM50 intrinsic subtypes of BRCA have gained the most attention from BRCA experts. However, this classification system manifests its weaknesses including low accuracy as well as a possible lack of association with biological...
Read more articleImproving existing analysis pipeline to identify and analyze cancer driver genes using multi-omics data
2020 Nov 25 SCIENTIFIC REPORTS, 2020
Quang-Huy Nguyen, Le Duc-Hau
The cumulative of genes carrying mutations is vital for the establishment and development of cancer. However, this driver gene exploring research line has selected and used types of tools and models of analysis unsystematically and discretely. Also, the previous studies may have neglected low-frequency drivers and seldom predicted subgroup specificities of identified driver genes. In this study, we presented an improved driver gene identification and analysis pipeline that comprises the four most widely focused analyses for driver genes: enrichment analysis, clinical feature association with expression profiles of identified driver genes as well as with their functional modules, and patient stratification...
Read more articleAn investigation of cancer cell line-based drug response prediction methods on patient data
2020 Dec 16 KSE 2020
Giang Nguyen, Hoang Le, Diep Quynh Nguyen, Tung Nguyen, Hien Dang, Le Duc-Hau
Tyrosine is mainly degraded in the liver by a series of enzymatic reactions. Abnormal expression of the tyrosine catabolic enzyme tyrosine aminotransferase (TAT) has been reported in patients with hepatocellular carcinoma (HCC). Despite this, aberration in tyrosine metabolism has not been investigated in cancer development. In this work, we conduct comprehensive cross-platform study to obtain foundation for discoveries of potential therapeutics and preventative biomarkers of HCC. We explore data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine and Kaplan Meier plotter (KM plotter) and performed integrated analyses to evaluate the clinical...
Read more articleClinical evaluation of RB1 genetic testing reveals novel mutations in Vietnamese patients with retinoblastoma
2021 Sep 1 MOLECULAR AND CLINICAL ONCOLOGY, 2021
Chinh Quoc Hoang, Hong-Quan Duong, Nguyen Thanh Nguyen, Sy Anh Hao Nguyen, Cuong Nguyen, Bo Duy Nguyen, Lan Tuyet Phung, Dung Thuy Nguyen, Chau Thi Minh Pham, Trang Le Doan, Mai Hoang Tran
Clinical evaluation of the genetic testing strategy is essential for ensuring the correct determination of mutation carriers. The current study retrospectively analyzed genetic and clinicopathological data from 62 Vietnamese patients with retinoblastoma (RB) referred to the Vinmec Hi-Tech Center for RB transcriptional corepressor 1 (RB1) genetic testing between 2017 and 2019. The present study aimed to evaluate the sensitivity of the Next Generation Sequencing (NGS) method to identify novel RB1 mutations, and to consider using age at diagnosis as a risk factor. Genomic DNA was analyzed with custom panel based targeted NGS. NGS was performed on the Beijing Genomics Institute (BGI) sequencing...
Read more articleBRCA1/2 Mutations in Vietnamese Patients with Hereditary Breast and Ovarian Cancer Syndrome
2022 Jan 29 GENES
T.-N.N. Le, V.-K. Tran, T.-T. Nguyen, N.S. Vo, T.H. Hoang, H.-L. Vo, T.-H.T. Nguyen, P.-D. Nguyen, V.-T. Nguyen, T.-V. Ta, H.-T. Tran
(1) Background: Individuals with BRCA1/2 gene mutations are at increased risk of breast and ovarian cancer. The prevalence of BRCA1/2 mutations varies by race and ethnicity, and the prevalence and the risks associated with most BRCA1/2 mutations has not been unknown in the Vietnamese population. We herein screen the entire BRCA1 and BRCA2 genes for breast and ovarian cancer patients with a family history of breast cancer and ovarian cancer, thereby, suggesting a risk score associated with carrier status and history for aiding personalized treatment; (2) Methods: Between December 2017 and December 2019, Vietnamese patients who had a pathological diagnosis of breast and epithelial ovarian cancer were followed up, prospectively,...
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