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Gomez F, Fisk B, McMichael JF, Mosior M, Foltz JA, Skidmore ZL, Duncavage EJ, Miller CA, Abel H, Li YS, Russler-Germain DA, Krysiak K, Watkins MP, Ramirez CA, Schmidt A, Martins Rodrigues F, Trani L, Khanna A, Wagner JA, Fulton RS, Fronick CC, O'Laughlin MD, Schappe T, Cashen AF, Mehta-Shah N, Kahl BS, Walker J, Bartlett NL, Griffith M, Fehniger TA, Griffith OL. Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2312-2330. [PMID: 37910143 PMCID: PMC10648575 DOI: 10.1158/2767-9764.crc-23-0140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.
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Affiliation(s)
- Felicia Gomez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Bryan Fisk
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Joshua F. McMichael
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Matthew Mosior
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Jennifer A. Foltz
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Zachary L. Skidmore
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Christopher A. Miller
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Haley Abel
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Yi-Shan Li
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - David A. Russler-Germain
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Kilannin Krysiak
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Marcus P. Watkins
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Cody A. Ramirez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Alina Schmidt
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Fernanda Martins Rodrigues
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Lee Trani
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Ajay Khanna
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Julia A. Wagner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Robert S. Fulton
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Catrina C. Fronick
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Michelle D. O'Laughlin
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Timothy Schappe
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Amanda F. Cashen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Neha Mehta-Shah
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Brad S. Kahl
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Jason Walker
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Nancy L. Bartlett
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Malachi Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Todd A. Fehniger
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Obi L. Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
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2
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Sun Q, Wang L, Zhang C, Hong Z, Han Z. Cervical cancer heterogeneity: a constant battle against viruses and drugs. Biomark Res 2022; 10:85. [PMCID: PMC9670454 DOI: 10.1186/s40364-022-00428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Cervical cancer is the first identified human papillomavirus (HPV) associated cancer and the most promising malignancy to be eliminated. However, the ever-changing virus subtypes and acquired multiple drug resistance continue to induce failure of tumor prevention and treatment. The exploration of cervical cancer heterogeneity is the crucial way to achieve effective prevention and precise treatment. Tumor heterogeneity exists in various aspects including the immune clearance of viruses, tumorigenesis, neoplasm recurrence, metastasis and drug resistance. Tumor development and drug resistance are often driven by potential gene amplification and deletion, not only somatic genomic alterations, but also copy number amplifications, histone modification and DNA methylation. Genomic rearrangements may occur by selection effects from chemotherapy or radiotherapy which exhibits genetic intra-tumor heterogeneity in advanced cervical cancers. The combined application of cervical cancer therapeutic vaccine and immune checkpoint inhibitors has become an effective strategy to address the heterogeneity of treatment. In this review, we will integrate classic and recently updated epidemiological data on vaccination rates, screening rates, incidence and mortality of cervical cancer patients worldwide aiming to understand the current situation of disease prevention and control and identify the direction of urgent efforts. Additionally, we will focus on the tumor environment to summarize the conditions of immune clearance and gene integration after different HPV infections and to explore the genomic factors of tumor heterogeneity. Finally, we will make a thorough inquiry into completed and ongoing phase III clinical trials in cervical cancer and summarize molecular mechanisms of drug resistance among chemotherapy, radiotherapy, biotherapy, and immunotherapy.
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Affiliation(s)
- Qian Sun
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Liangliang Wang
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Cong Zhang
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Zhenya Hong
- grid.33199.310000 0004 0368 7223Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Zhiqiang Han
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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Shen M, Zhou Z, Li BB, Lv M, Feng C, Chen S, Shi S, Kang M, Zhao T. Investigation of miR-21-5p Key Target Genes and Pathways in Head and Neck Squamous Cell Carcinoma Based on TCGA Database and Bioinformatics Analysis. Technol Cancer Res Treat 2022; 21:15330338221081245. [PMID: 35235474 PMCID: PMC9114514 DOI: 10.1177/15330338221081245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: Head and neck squamous cell carcinoma (HNSCC) is the sixth most
commonly diagnosed malignancy worldwide. Overexpressed of microRNA-21-5p
(miR-21-5p) has been reported to be involved in the development of HNSCC.
However, the role of miR-21-5p in HNSCC is still not fully elucidated. The
purpose of this study was to explore the underlying molecular mechanisms of
miR-21-5p in HNSCC. Methods: RT-qPCR was used to determine the
differential expression levels of miR-21-5p in tissue samples of HNSCC patients.
Meta-analysis was performed based on miRNA expression data collected from the
Gene Expression Omnibus (GEO) database, The Cancer Genome Atlas (TCGA), and
published articles to evaluate the expression of miR-21-5p in HNSCC. We
investigated the biological function of miR-21-5P by gene ontology enrichment
and target prediction analysis. Furthermore, RT-qPCR and IHC were conducted to
verify the expression of target genes. Finally, Kaplan–Meier survival analysis
was performed to assessed the prognostic value of the putative miR-21-5p target
genes. Results: MiR-21-5p was significantly overexpressed in HNSCC
compared to healthy tissues (P < .05) and showed potent
predictive power with a summary receiver operating characteristic of 0.90.
Meanwhile, the expression of miR-21-5p was significantly correlated with tumor
stage, T stage and smoking in HNSCC (P < .05). A total of 71
down-regulated genes, both HNSCC-related and miR-21-p5-related, were obtained
from the analytical integration. Two predicted genes (ADH7, RDH12) were
down-regulated in HNSCC, and significantly negatively correlated with miR-21-5p.
IHC and RT-qPCR demonstrated that the expression of ADH7 and RDH12 in HNSCC
samples was significantly lower than control. And high expression of ADH7 was
associated with better DFS of HNSCC patients. Conclusions:
miR-21-5p may target at ADH7, RDH12 and participate in regulation of retinol
metabolism, which might affect the prognosis of HNSCC. High expression of ADH7
may indicate better prognosis in HNSCC patients.
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Affiliation(s)
- Mingjun Shen
- 117742The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China.,Guangxi Tumor Radiation Therapy Clinical Medical Research Center, Nanning, Guangxi, P.R. China
| | - Ziyan Zhou
- 117742The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China.,Guangxi Tumor Radiation Therapy Clinical Medical Research Center, Nanning, Guangxi, P.R. China
| | - Bai Bei Li
- 74626Guangxi Medical University, Nanning, Guangxi, P.R. China
| | - Meixin Lv
- 74626Guangxi Medical University, Nanning, Guangxi, P.R. China
| | - Chunling Feng
- 74626Guangxi Medical University, Nanning, Guangxi, P.R. China
| | - Sixia Chen
- 117742The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China.,Guangxi Tumor Radiation Therapy Clinical Medical Research Center, Nanning, Guangxi, P.R. China
| | - Shuo Shi
- 117742The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China
| | - Min Kang
- 117742The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China.,Guangxi Tumor Radiation Therapy Clinical Medical Research Center, Nanning, Guangxi, P.R. China
| | - Tingting Zhao
- 74626Guangxi Medical University, Nanning, Guangxi, P.R. China
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4
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Ploypetch S, Roytrakul S, Jaresitthikunchai J, Phaonakrop N, Teewasutrakul P, Rungsipipat A, Suriyaphol G. Salivary proteomics in monitoring the therapeutic response of canine oral melanoma. PLoS One 2021; 16:e0256167. [PMID: 34411146 PMCID: PMC8376060 DOI: 10.1371/journal.pone.0256167] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022] Open
Abstract
Saliva biomarkers are suitable for monitoring the therapeutic response of canine oral melanoma (COM), because saliva directly contacts the tumor, and saliva collection is non-invasive, convenient and cost effective. The present study aimed to investigate novel biomarkers from the salivary proteome of COM treated with surgery and a chemotherapy drug, carboplatin, 1-6 times, using a liquid chromatography-tandem mass spectrometry approach. The expression of a potential salivary biomarker, ubiquitin D (UBD), was observed and verified by western blot analysis. A significantly increased ratio of free UBD (fUBD) to conjugated UBD (cUBD) was shown in the pre-surgery stage (PreS) in OM dogs with short-term survival (STS) (less than 12 months after surgery) compared with that with long-term survival (more than 12 months after surgery). In dogs with STS, the ratio was also shown to be augmented in PreS compared with that after surgery, followed by treatment with carboplatin twice, 4 and 5 times [After treatment (AT)2, AT4 and AT5]. In addition, the expression of fUBD was enhanced in PreS compared with that of AT2 in the STS group. In conclusion, this study revealed that a ratio of fUBD to cUBD in PreS was plausibly shown to be a potential prognostic biomarker for survival in dogs with OM.
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Affiliation(s)
- Sekkarin Ploypetch
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Companion Animal Cancer Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Patharakrit Teewasutrakul
- Companion Animal Cancer Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Oncology Clinic, Faculty of Veterinary Science, Small Animal Teaching Hospital, Chulalongkorn University, Bangkok, Thailand
| | - Anudep Rungsipipat
- Companion Animal Cancer Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Companion Animal Cancer Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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5
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Li C, Yu H, Sun Y, Zeng X, Zhang W. Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis. PeerJ 2021; 9:e10682. [PMID: 33717664 PMCID: PMC7938783 DOI: 10.7717/peerj.10682] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/09/2020] [Indexed: 02/05/2023] Open
Abstract
Background Gastric cancer is one of the most lethal tumors and is characterized by poor prognosis and lack of effective diagnostic or therapeutic biomarkers. The aim of this study was to find hub genes serving as biomarkers in gastric cancer diagnosis and therapy. Methods GSE66229 from Gene Expression Omnibus (GEO) was used as training set. Genes bearing the top 25% standard deviations among all the samples in training set were performed to systematic weighted gene co-expression network analysis (WGCNA) to find candidate genes. Then, hub genes were further screened by using the “least absolute shrinkage and selection operator” (LASSO) logistic regression. Finally, hub genes were validated in the GSE54129 dataset from GEO by supervised learning method artificial neural network (ANN) algorithm. Results Twelve modules with strong preservation were identified by using WGCNA methods in training set. Of which, five modules significantly related to gastric cancer were selected as clinically significant modules, and 713 candidate genes were identified from these five modules. Then, ADIPOQ, ARHGAP39, ATAD3A, C1orf95, CWH43, GRIK3, INHBA, RDH12, SCNN1G, SIGLEC11 and LYVE1 were screened as the hub genes. These hub genes successfully differentiated the tumor samples from the healthy tissues in an independent testing set through artificial neural network algorithm with the area under the receiver operating characteristic curve at 0.946. Conclusions These hub genes bearing diagnostic and therapeutic values, and our results may provide a novel prospect for the diagnosis and treatment of gastric cancer in the future.
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Affiliation(s)
- Chunyang Li
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Cheng, China.,Medical Big Data Center, Sichuan University, Chengdu, China
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Cheng, China.,Medical Big Data Center, Sichuan University, Chengdu, China
| | - Yajing Sun
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Cheng, China.,Medical Big Data Center, Sichuan University, Chengdu, China
| | - Xiaoxi Zeng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Cheng, China.,Medical Big Data Center, Sichuan University, Chengdu, China
| | - Wei Zhang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Cheng, China.,Medical Big Data Center, Sichuan University, Chengdu, China
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6
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Wen F, Huang J, Lu X, Huang W, Wang Y, Bai Y, Ruan S, Gu S, Chen X, Shu P. Identification and prognostic value of metabolism-related genes in gastric cancer. Aging (Albany NY) 2020; 12:17647-17661. [PMID: 32920549 PMCID: PMC7521523 DOI: 10.18632/aging.103838] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is one of the most commonly occurring cancers, and metabolism-related genes (MRGs) are associated with its development. Transcriptome data and the relevant clinical data were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases, and we identified 194 MRGs differentially expressed between GC and adjacent nontumor tissues. Through univariate Cox and lasso regression analyses we identified 13 potential prognostic differentially expressed MRGs (PDEMRGs). These PDEMRGs (CKMT2, ME1, GSTA2, ASAH1, GGT5, RDH12, NNMT, POLR1A, ACYP1, GLA, OPLAH, DCK, and POLD3) were used to build a Cox regression risk model to predict the prognosis of GC patients. Further univariate and multivariate Cox regression analyses showed that this model could serve as an independent prognostic parameter. Gene Set Enrichment Analysis showed significant enrichment pathways that could potentially contribute to pathogenesis. This model also revealed the probability of genetic alterations of PDEMRGs. We have thus identified a valuable metabolic model for predicting the prognosis of GC patients. The PDEMRGs in this model reflect the dysregulated metabolic microenvironment of GC and provide useful noninvasive biomarkers.
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Affiliation(s)
- Fang Wen
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China,Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Jiani Huang
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,College of Traditional Chinese Medicine, College of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaona Lu
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China,Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Wenjie Huang
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China,Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Yulan Wang
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,Department of Hematology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Yingfeng Bai
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,College of Traditional Chinese Medicine, College of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shuai Ruan
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China,Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Suping Gu
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China,Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Xiaoxue Chen
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China,Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Peng Shu
- Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China,Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China,Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
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7
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RNA-based high-risk HPV genotyping and identification of high-risk HPV transcriptional activity in cervical tissues. Mod Pathol 2020; 33:748-757. [PMID: 31537894 DOI: 10.1038/s41379-019-0369-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 01/09/2023]
Abstract
Nearly all cervical cancers are initiated by a persistent infection with one of the high-risk human papillomaviruses (high-risk HPV). High-risk HPV DNA testing is highly sensitive but cannot distinguish between active, productive infections and dormant infections or merely deposited virus. A solution for this shortcoming may be the detection of transcriptional activity of viral oncogenes instead of mere presence of high-risk HPVs. In this study, fresh-frozen cervical tissues (n = 22) were subjected to high-risk HPV DNA detection using the line probe assay and to targeted RNA next-generation sequencing using single-molecule molecular inversion probes. Targeted RNA sequencing was applied for (1) RNA-based genotyping of high-risk HPV, giving information on specific HPV-subtype (2) discrimination of E2, E6, and E7 transcripts and (3) discovery of possible non-HPV cancer biomarkers. Data were analyzed using computational biology. Targeted RNA sequencing enabled reliable genotyping of high-risk HPV subtypes and allowed quantitative detection of E2, E6, and E7 viral gene expression, thereby discriminating cervical lesions from normal cervical tissues. Moreover, targeted RNA sequencing identified possible cervical cancer biomarkers other than high-risk HPV. Interestingly, targeted RNA sequencing also provided high-quality transcription profiles from cervical scrape samples, even after 1 week of dry storage or storage in Preservcyt fixative. This proof of concept study shows that targeted RNA sequencing can be used for high-risk HPV genotyping and simultaneous detection of high-risk HPV gene activity. Future studies are warranted to investigate the potential of targeted RNA sequencing for risk assessment for the development of cervical lesions, based on molecular analysis of cervical scrapes.
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8
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Wu Y, Zhao J, Dong S, Wang Y, Li A, Jiang Y, Chen Z, Li C, Wang W, Zhang Z. Whole-exome and RNA sequencing reveal novel insights into the pathogenesis of HPV associated cervical cancer. Cancer Biomark 2020; 25:341-350. [PMID: 31306105 DOI: 10.3233/cbm-190055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Worldwide, cervical cancer is the fouth leading cause of deaths in gynecological oncology. Although the causes of cervical cancer have been extensively investigated, understanding of its exact pathogenesis remains incomplete. OBJECTIVE This study aimed to identify alterations of genome and transcriptome of HPV associated cervical cancer pathogenesis using multi-omics approaches. METHODS Cervical cancer and matched adjacent non-tumor specimens of one HPV16+ and two HPV- patients were sampled for whole-exome sequencing (WES) and RNA sequencing to characterize DNA mutations and gene expression profiles. WES and Affymetrix SNP 6.0 arrays data were analyzed from 6 HPV- and 93 HPV16+ cervical cancer patients in the cancer genome atlas (TCGA) database, as an independent validation group. RESULTS WES identified 64 somatic mutation genes in tumors of 3 patients. HPV16+ tumor got fewer somatic mutated genes than HPV- tumors, which was validated by TCGA results. In this study, somatic mutated profile, CNV and gene expression heat map presented that HPV16+ tumors was distinct with HPV- tumors. The most significant altered pathways and GO terms were both related with cell cycle. Integrated analysis of multi-omics showed positive correlation between gene expression level and copy numbers. CONCLUSIONS The results of this study provided novel insights into the pathogenesis of HPV associated cervical cancer.
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Affiliation(s)
- Yibo Wu
- Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362002, China.,Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362002, China
| | - Jiangman Zhao
- Biotecan Medical Diagnostics Co., Ltd, Shanghai 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai 201204, China.,Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362002, China
| | - Shu Dong
- Biotecan Medical Diagnostics Co., Ltd, Shanghai 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai 201204, China
| | - Yu Wang
- Biotecan Medical Diagnostics Co., Ltd, Shanghai 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai 201204, China
| | - Ailu Li
- Department of Gynecology and Obstetrics, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362002, China
| | - Yancheng Jiang
- Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362002, China
| | - Zixuan Chen
- Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362002, China
| | - Chunxiao Li
- Department of Gynecology and Obstetrics, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362002, China
| | - Wei Wang
- School of Public Health, Fujian Medical University, Fuzhou, Fujian 350004, China.,Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Public Health Research Center of Jiangnan University, Wuxi, Jiangsu 214064, China
| | - Zhishan Zhang
- Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362002, China
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9
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Chong GO, Han HS, Lee SD, Lee YH. Improvement in RNA quantity and quality in cervico-vaginal cytology. Virol J 2020; 17:8. [PMID: 31959186 PMCID: PMC6971917 DOI: 10.1186/s12985-020-1282-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/15/2020] [Indexed: 11/25/2022] Open
Abstract
The separation of exfoliated cells from the brushes used during cervico-vaginal smears is difficult, a problem which may affect the quality of ribonucleic acid (RNA) extracted. We compared the results of RNA extraction from cervico-vaginal cytology samples according to the type of tubes, preservative solutions, and storage temperature. The samples included exfoliated cervico-vaginal cytological specimens from patients with human papilloma virus 16, positive for cervical intraepithelial neoplasia or cervical cancer. Exfoliated cells were obtained by shaking a brush in a conventional rigid vial tube or squeezing the brush in a soft vial tube. RNA quantity and quality were compared between the two tubes. The concentration and purity of RNA (A260/A280 and A260/A230 ratios) was compared amongst five groups: Group 1, standard frozen storage; Group 2–4, RNA stabilization reagents with room temperature [RNAlater RNA Stabilization Reagent, RNAprotect cell Reagent and AllProtect Tissue Reagent]; and Group 5, Surepath Preservative fluid. To demonstrate the utility of the extracted RNA for PCR-based cDNA synthesis, GAPDH and E6 were targeted and gel band densities of GAPDH and E6 were measured. The median RNA concentration was significantly higher in the soft tubes compared with the rigid tubes (100.2 vs. 7.1 ng/μL, p = 0.0209). The purity of the RNA was higher in soft vial tubes than in rigid vials, as measured by A260/280 and A260/230 ratios. The RNA concentration, purity, and GAPDH density of groups 1, 2 and 3 were significantly higher than those of groups 4 and 5. Moreover, E6 density of group 1 and 2 was significantly higher than that of group 3, 4 and 5. The use of soft tubes enhanced the mRNA quantity and quality in cervico-vaginal cytology. The products of mRNA extraction using RNAlater RNA Stabilization Reagent and RNAprotect Cell Reagent at room temperature were comparable to those obtained by conventional frozen storage. Our protocol improved the yield and quality of RNA and might produce better results for molecular analysis in cervico-vaginal cytology.
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Affiliation(s)
- Gun Oh Chong
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea.,Molecular Diagnostics and Imaging Center, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyung Soo Han
- Molecular Diagnostics and Imaging Center, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. .,Department of Physiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
| | - Seon Duk Lee
- Molecular Diagnostics and Imaging Center, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yoon Hee Lee
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea.,Molecular Diagnostics and Imaging Center, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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10
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Lin M, Ye M, Zhou J, Wang ZP, Zhu X. Recent Advances on the Molecular Mechanism of Cervical Carcinogenesis Based on Systems Biology Technologies. Comput Struct Biotechnol J 2019; 17:241-250. [PMID: 30847042 PMCID: PMC6389684 DOI: 10.1016/j.csbj.2019.02.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 02/06/2023] Open
Abstract
Cervical cancer is one of the common malignancies in women worldwide. Exploration of pathogenesis and molecular mechanism of cervical cancer is pivotal for development of effective treatment for this disease. Recently, systems biology approaches based on high-throughput technologies have been carried out to investigate the expression of some genes and proteins in genomics, transcriptomics, proteomics, and metabonomics of cervical cancer. Compared with traditional methods,systems biology technology has been shown to provide large of information regarding prognostic biomarkers and therapeutic targets for cervical cancer. These molecular signatures from system biology technology could be useful to understand the molecular mechanisms of cervical cancer development and progression, and help physicians to design targeted therapeutic strategies for patients with cervical cancer.
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Affiliation(s)
- Min Lin
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Miaomiao Ye
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Junhan Zhou
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Z Peter Wang
- Center of Scientific Research, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.,Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xueqiong Zhu
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
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11
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Lin CY, Yang ST, Shen SC, Hsieh YC, Hsu FT, Chen CY, Chiang YH, Chuang JY, Chen KY, Hsu TI, Leong WC, Su YK, Lo WL, Yeh YS, Patria YN, Shih HM, Chang CC, Chou SY. Serum amyloid A1 in combination with integrin αVβ3 increases glioblastoma cells mobility and progression. Mol Oncol 2018; 12:756-771. [PMID: 29603594 PMCID: PMC5928363 DOI: 10.1002/1878-0261.12196] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/26/2018] [Accepted: 03/07/2018] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a highly malignant type of brain tumor found in humans. GBM cells reproduce quickly, and the median survival time for patients after therapy is approximately 1 year with a high relapse rate. Current therapies and diagnostic tools for GBM are limited; therefore, we searched for a more favorable therapeutic target or marker protein for both therapy and diagnosis. We used mass spectrometry (MS) analysis to identify GBM-associated marker proteins from human plasma and GBM cell cultures. Additional plasma and 52 brain tissues obtained from patients with gliomas were used to validate the association rate of serum amyloid A1 (SAA1) in different grades of gliomas and its distribution in tumors. Microarray database analysis further validated the coefficient of SAA1 levels in gliomas. The cellular mechanisms of SAA1 in GBM proliferation and infiltration were investigated in vitro. We analyzed the correlation between SAA1 and patients' medication requirement to demonstrate the clinical effects of SAA1 in GBM. SAA1 was identified from MS analysis, and its level was revealed to be correlated with the disease grade, clinical severity, and survival rate of patients with gliomas. In vitro cultures, including GBM cells and normal astrocytes, revealed that SAA1 promotes cell migration and invasion through integrin αVβ3 to activate the Erk signaling pathway. Magnetic resonance imaging and tumor region-specific microarray analysis identified a correlation between SAA1 and GBM cell infiltration in patients. In summary, our results demonstrate that SAA1 in combination with integrin αV and β3 can serve as an indicator of high glioblastoma risk. We also identified the cellular mechanisms of SAA1 contributing to GBM progression, which can serve as the basis for future GBM therapy.
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Affiliation(s)
- Ching-Yu Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Shun-Tai Yang
- Division of Neurosurgery, Shuang Ho Hospital, Taipei Medical University, Taiwan.,Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taiwan.,Comprehensive Cancer Center of Taipei Medical University, Taiwan
| | - Shing-Chuan Shen
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taiwan
| | - Yi-Chen Hsieh
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,The PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Fei-Ting Hsu
- Department of Medical Imaging, Taipei Medical University Hospital, Taiwan.,Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, Taiwan.,Research Center of Translational Imaging (TIRC), College of Medicine, Taipei Medical University, Taiwan
| | - Cheng-Yu Chen
- Department of Medical Imaging, Taipei Medical University Hospital, Taiwan.,Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, Taiwan.,Research Center of Translational Imaging (TIRC), College of Medicine, Taipei Medical University, Taiwan
| | - Yung-Hsiao Chiang
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taiwan.,Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,The PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,Division of Neurosurgery, Department of Surgery, Taipei Medical University Hospital, Taiwan
| | - Jian-Ying Chuang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,The PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Kai-Yun Chen
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,The PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Tsung-I Hsu
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,The PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Wan-Chong Leong
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,The PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Yu-Kai Su
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taiwan
| | - Wei-Lun Lo
- Division of Neurosurgery, Shuang Ho Hospital, Taipei Medical University, Taiwan.,Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,The PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Yi-Shian Yeh
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taiwan
| | - Yudha Nur Patria
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Hsiu-Ming Shih
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Che-Chang Chang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,Neuroscience Research Center, Taipei Medical University Hospital, Taiwan
| | - Szu-Yi Chou
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan.,The PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
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12
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Karuri AR, Kashyap VK, Yallapu MM, Zafar N, Kedia SK, Jaggi M, Chauhan SC. Disparity in rates of HPV infection and cervical cancer in underserved US populations. Front Biosci (Schol Ed) 2017; 9:254-269. [PMID: 28410118 DOI: 10.2741/s486] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
There is a higher rate of HPV infection and cervical cancer incidence and mortality in underserved US population who reside in Appalachian mountain region compared to Northern Plains. Social and behavioral factors such as smoking and alcohol consumption are for such a high incidence. However, by and large, the reasons for these discrepancies lie in the reluctance of the underserved population to adopt preventive measures such as prophylactic Human papilloma virus (HPV) vaccines and Pap smear screening that have significantly reduced the incidence and mortality rate of cervical cancer in Caucasian women. Thus, it is clear that drastic change in social behavior and implementation of preventive measures is required to effectively reduce the incidence and mortality from cervical cancer in this underserved population.
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Affiliation(s)
- Asok Ranjan Karuri
- Department of Pharmaceutical Sciences and Cancer Research Center, University of Tennessee Health Science Center, Memphis, Tennessee, USA, 38163
| | - Vivek Kumar Kashyap
- Department of Pharmaceutical Sciences and Cancer Research Center, University of Tennessee Health Science Center, Memphis, Tennessee, USA, 38163
| | - Murali Mohan Yallapu
- Department of Pharmaceutical Sciences and Cancer Research Center, University of Tennessee Health Science Center, Memphis, Tennessee, USA, 38163
| | - Nadeem Zafar
- Department of Pathology, University of Tennessee Health Science Center, Memphis, Tennessee, USA, 38163
| | - Satish K Kedia
- Division of Social and Behavioral Sciences, School of Public Health, University of Memphis, Memphis, TN, 38152
| | - Meena Jaggi
- Department of Pharmaceutical Sciences and Cancer Research Center, University of Tennessee Health Science Center, Memphis, Tennessee, USA, 38163
| | - Subhash C Chauhan
- Department of Pharmaceutical Sciences and Cancer Research Center, University of Tennessee Health Science Center, Memphis, Tennessee, USA, 38163,
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13
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Ebisch RM, Siebers AG, Bosgraaf RP, Massuger LF, Bekkers RL, Melchers WJ. Triage of high-risk HPV positive women in cervical cancer screening. Expert Rev Anticancer Ther 2016; 16:1073-85. [PMID: 27598683 DOI: 10.1080/14737140.2016.1232166] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION High-risk human papillomavirus (hrHPV) testing is expected to replace cytology as primary screening method for cervical cancer screening in an increasing number of countries. The high sensitivity of hrHPV testing is combined with a limited specificity which makes triaging of hrHPV positive women necessary. As an ideal triage method does not yet exist, an optimal triage strategy for hrHPV positive women based on current knowledge should be obtained. The aim of this article is to present an overview of available options for triage of hrHPV positive women, with their strengths and limitations and possible future opportunities. AREAS COVERED Current knowledge on morphological biomarkers, molecular biomarkers and combined triage strategies will be discussed to give an overview of the state-of-the-art on triaging hrHPV positive women. The literature search was limited to studies on triage strategies for hrHPV positive women. Expert commentary: Experience with morphology-based biomarkers makes these a valuable triage method. However, they lack the ability of differentiating productive from transforming infections. Molecular biomarkers are objective, highly reproducible, can be used in high throughput testing, and show promising results. With more extensive knowledge on these molecular markers, cervical cancer screening may transform to a full molecular screening in the future.
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Affiliation(s)
- Renée Mf Ebisch
- a Department of Obstetrics and Gynaecology , Radboud university medical center , Nijmegen , The Netherlands
| | - Albert G Siebers
- b Department of Pathology , Radboud university medical center , Nijmegen , The Netherlands
| | - Remko P Bosgraaf
- a Department of Obstetrics and Gynaecology , Radboud university medical center , Nijmegen , The Netherlands
| | - Leon Fag Massuger
- a Department of Obstetrics and Gynaecology , Radboud university medical center , Nijmegen , The Netherlands
| | - Ruud Lm Bekkers
- a Department of Obstetrics and Gynaecology , Radboud university medical center , Nijmegen , The Netherlands
| | - Willem Jg Melchers
- c Department of Medical Microbiology , Radboud university medical center , Nijmegen , The Netherlands
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14
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Liu Z, Gui T, Wang Z, Li H, Fu Y, Dong X, Li Y. cisASE: a likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data. Bioinformatics 2016; 32:3291-3297. [PMID: 27412088 DOI: 10.1093/bioinformatics/btw416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 06/24/2016] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Allele-specific expression (ASE) is a useful way to identify cis-acting regulatory variation, which provides opportunities to develop new therapeutic strategies that activate beneficial alleles or silence mutated alleles at specific loci. However, multiple problems hinder the identification of ASE in next-generation sequencing (NGS) data. RESULTS We developed cisASE, a likelihood-based method for detecting ASE on single nucleotide variant (SNV), exon and gene levels from sequencing data without requiring phasing or parental information. cisASE uses matched DNA-seq data to control technical bias and copy number variation (CNV) in putative cis-regulated ASE identification. Compared with state-of-the-art methods, cisASE exhibits significantly increased accuracy and speed. cisASE works moderately well for datasets without DNA-seq and thus is widely applicable. By applying cisASE to real datasets, we identified specific ASE characteristics in normal and cancer tissues, thus indicating that cisASE has potential for wide applications in cancer genomics. AVAILABILITY AND IMPLEMENTATION cisASE is freely available at http://lifecenter.sgst.cn/cisASE CONTACT: biosinodx@gmail.com or yxli@sibs.ac.cnSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhi Liu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tuantuan Gui
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunhe Fu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China School of Life Science and Technology, Shanghai Jiaotong University, Shanghai 200240, China Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai 201203, China and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, China
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15
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Shi JL, Luo W, Li Y, Yang C, Tang YP, Li KZ, Cao J. Screening differentially expressed genes in hepatocellular carcinoma by cross-species and cross-carcinogenic factors strategy based on RNA-Seq. Shijie Huaren Xiaohua Zazhi 2016; 24:1664-1675. [DOI: 10.11569/wcjd.v24.i11.1664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To identify key molecules involved in progression of hepatocellular carcinoma (HCC) by cross-species (human and tupaia) and cross-carcinogenic factors (HBV and AFB1) strategy based on RNA sequencing (RNA-Seq).
METHODS: The transcripts in human and tupaia HCC, tumor adjacent liver tissue (para-HCC) and normal liver tissue were thoroughly analyzed by RNA sequencing. Tupaia HCC was induced by HBV infection or aflatoxin B1 (AFB1). Differentially expressed genes were collected between these tissues, and common differential genes which cross human and Tupaia as well as HBV and AFB1 carcinogenic factors were identified.
RESULTS: Compared to human para-HCC and normal liver tissues, 68 differential genes were screened in human HCC, among which 14 were up-regulated and 54 down-regulated. Compared to Tupaia para-HCC and normal liver tissues, 314 differential genes were screened in HBV induced Tupaia HCC, and 20 were screened in AFB1 induced Tupaia HCC. There were 11 common differential genes between HBV and AFB1 induced Tupaia HCC, all of which were down-regulated. There were 2 common differential genes between human HCC and Tupaia HCC, and they were apolipoprotein F (APOF) and insulin-like growth factor binding protein, acid labile subunit (IGFALS), both of which were down-regulated in HCC.
CONCLUSION: The cross-species, cross-carcinogenic factors screening strategy based on RNA-Seq may promote the process of identifying key molecules for human HCC. APOF and IGFALS may be important factors for HCC.
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16
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Rice SJ, Liu X, Miller B, Joshi M, Zhu J, Caruso C, Gilbert C, Toth J, Reed M, Rassaei N, Das A, Barochia A, El-Bayoumy K, Belani CP. Proteomic profiling of human plasma identifies apolipoprotein E as being associated with smoking and a marker for squamous metaplasia of the lung. Proteomics 2015; 15:3267-77. [DOI: 10.1002/pmic.201500029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/23/2015] [Accepted: 06/04/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Shawn J. Rice
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Xin Liu
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Bruce Miller
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Monika Joshi
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Junjia Zhu
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Carla Caruso
- Department of Pathology; Penn State College of Medicine; Hershey PA USA
| | - Chris Gilbert
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Jennifer Toth
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Michael Reed
- Penn State Heart and Vascular Institute and Cardiothoracic Surgery; Penn State College of Medicine; Hershey PA USA
| | - Negar Rassaei
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Arun Das
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
| | - Amit Barochia
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Karam El-Bayoumy
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
| | - Chandra P. Belani
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
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