1
|
Silva-Ferreira M, Carvalho JA, Salta S, Henriques TS, Pereira Rodrigues P, Monteiro-Reis S, Henrique R, Jerónimo C. Diagnostic Test Accuracy of Urinary DNA Methylation-based Biomarkers for the Detection of Primary and Recurrent Bladder Cancer: A Systematic Review and Meta-analysis. Eur Urol Focus 2024:S2405-4569(24)00088-9. [PMID: 38897871 DOI: 10.1016/j.euf.2024.05.024] [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: 03/21/2024] [Revised: 05/13/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND AND OBJECTIVE Diagnosis of primary and relapsed bladder carcinomas is accomplished by urethrocystoscopy, an invasive procedure, combined with urinary cytology, with limited sensitivity, resulting in a substantial burden. Thus, noninvasive biomarkers have been investigated, among which DNA methylation has shown promise. This systematic review and meta-analysis sought to assess the diagnostic accuracy of DNA methylation biomarkers reported in the literature for bladder cancer detection, pinpointing the most informative one. METHODS The search for this systematic review and meta-analysis was conducted on PubMed, Scopus, and Cochrane Library for relevant studies published until December 31, 2022. A meta-analysis was performed using a random-effect model, to compute the pooled sensitivity and specificity of the markers. PROSPERO's registration ID for the study is CRD42023397703. KEY FINDINGS AND LIMITATIONS Out of the 2297 studies retrieved, 68 were included in the final analysis, despite considerable heterogeneity. These involved 12 696 participants, of whom 5557 were diagnosed with bladder cancer. Using diagnostic odds ratio (DOR) as a comparative measure, the five most promising markers (pooled sensitivity, specificity, and DOR) were SALL3 (61%, 97%, and 55.67, respectively), PENK (77%, 93%, and 47.90, respectively), ZNF154 (87%, 90%, and 45.07, respectively), VIM (82%, 90%, and 44.81, respectively), and POU4F2 (81%, 89%, and 34.89, respectively). Urinary cytology identified bladder cancer with 55% sensitivity, 92% specificity, and 14.37 DOR. CONCLUSIONS AND CLINICAL IMPLICATIONS DNA methylation biomarkers disclose high accuracy for bladder cancer detection in urine. Nonetheless, validation studies in different clinical settings are scarce, hampering clinical use. The identified biomarkers should be prioritized in future validation studies. PATIENT SUMMARY In this meta-analysis, we include previously published studies that used urine samples of bladder cancer patients' from all around the globe. We were able to compare the diagnostic accuracy of noninvasive markers across different populations. We were able to conclude on the most promising DNA methylation markers to detect bladder cancer using urine.
Collapse
Affiliation(s)
- Mariana Silva-Ferreira
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Master Program in Oncology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - João A Carvalho
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Doctoral Program in Medical Science, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Department of Urology & Urology Clinics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Doctoral Program in Pathology and Molecular Genetics, ICBAS - School of Medicine and Biomedical Sciences - University of Porto, Porto, Portugal
| | - Teresa S Henriques
- CINTESIS@RISE - Health Research Network & MEDCIDS, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Pedro Pereira Rodrigues
- CINTESIS@RISE - Health Research Network & MEDCIDS, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Sara Monteiro-Reis
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Institute of Science and Innovation in Mechanical and Industrial Engineering (INEGI), Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal; Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, IPO Porto Research Center of IPO Porto (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center - Raquel Seruca (Porto.CCC) & CI-IPOP@RISE (Health Research Network), Porto, Portugal; Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
| |
Collapse
|
2
|
Shenoy US, Adiga D, Alhedyan F, Kabekkodu SP, Radhakrishnan R. HOXA9 transcription factor is a double-edged sword: from development to cancer progression. Cancer Metastasis Rev 2024; 43:709-728. [PMID: 38062297 PMCID: PMC11156722 DOI: 10.1007/s10555-023-10159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 04/02/2024]
Abstract
The HOXA9 transcription factor serves as a molecular orchestrator in cancer stemness, epithelial-mesenchymal transition (EMT), metastasis, and generation of the tumor microenvironment in hematological and solid malignancies. However, the multiple modes of regulation, multifaceted functions, and context-dependent interactions responsible for the dual role of HOXA9 as an oncogene or tumor suppressor in cancer remain obscure. Hence, unravelling its molecular complexities, binding partners, and interacting signaling molecules enables us to comprehend HOXA9-mediated transcriptional programs and molecular crosstalk. However, it is imperative to understand its central role in fundamental biological processes such as embryogenesis, foetus implantation, hematopoiesis, endothelial cell proliferation, and tissue homeostasis before designing targeted therapies. Indeed, it presents an enormous challenge for clinicians to selectively target its oncogenic functions or restore tumor-suppressive role without altering normal cellular functions. In addition to its implications in cancer, the present review also focuses on the clinical applications of HOXA9 in recurrence and drug resistance, which may provide a broader understanding beyond oncology, open new avenues for clinicians for accurate diagnoses, and develop personalized treatment strategies. Furthermore, we have also discussed the existing therapeutic options and accompanying challenges in HOXA9-targeted therapies in different cancer types.
Collapse
Affiliation(s)
- U Sangeetha Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Faisal Alhedyan
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield, United Kingdom
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield, United Kingdom.
| |
Collapse
|
3
|
Loza M, Vandenbon A, Nakai K. Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression. Nucleic Acids Res 2024; 52:1107-1119. [PMID: 38084904 PMCID: PMC10853790 DOI: 10.1093/nar/gkad1164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 02/10/2024] Open
Abstract
In this research, we elucidate the presence of around 11,000 housekeeping cis-regulatory elements (HK-CREs) and describe their main characteristics. Besides the trivial promoters of housekeeping genes, most HK-CREs reside in promoter regions and are involved in a broader role beyond housekeeping gene regulation. HK-CREs are conserved regions rich in unmethylated CpG sites. Their distribution highly correlates with that of protein-coding genes, and they interact with many genes over long distances. We observed reduced activity of a subset of HK-CREs in diverse cancer subtypes due to aberrant methylation, particularly those located in chromosome 19 and associated with zinc finger genes. Further analysis of samples from 17 cancer subtypes showed a significantly increased survival probability of patients with higher expression of these genes, suggesting them as housekeeping tumor suppressor genes. Overall, our work unravels the presence of housekeeping CREs indispensable for the maintenance and stability of cells.
Collapse
Affiliation(s)
- Martin Loza
- The Institute of Medical Science, The University of Tokyo, Japan
| | - Alexis Vandenbon
- Institute for Life and Medical Sciences, Kyoto University, Japan
| | - Kenta Nakai
- The Institute of Medical Science, The University of Tokyo, Japan
| |
Collapse
|
4
|
Chin FW, Chan SC, Veerakumarasivam A. Homeobox Gene Expression Dysregulation as Potential Diagnostic and Prognostic Biomarkers in Bladder Cancer. Diagnostics (Basel) 2023; 13:2641. [PMID: 37627900 PMCID: PMC10453580 DOI: 10.3390/diagnostics13162641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/27/2023] Open
Abstract
Homeobox genes serve as master regulatory transcription factors that regulate gene expression during embryogenesis. A homeobox gene may have either tumor-promoting or tumor-suppressive properties depending on the specific organ or cell lineage where it is expressed. The dysregulation of homeobox genes has been reported in various human cancers, including bladder cancer. The dysregulated expression of homeobox genes has been associated with bladder cancer clinical outcomes. Although bladder cancer has high risk of tumor recurrence and progression, it is highly challenging for clinicians to accurately predict the risk of tumor recurrence and progression at the initial point of diagnosis. Cystoscopy is the routine surveillance method used to detect tumor recurrence. However, the procedure causes significant discomfort and pain that results in poor surveillance follow-up amongst patients. Therefore, the development of reliable non-invasive biomarkers for the early detection and monitoring of bladder cancer is crucial. This review provides a comprehensive overview of the diagnostic and prognostic potential of homeobox gene expression dysregulation in bladder cancer.
Collapse
Affiliation(s)
- Fee-Wai Chin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Soon-Choy Chan
- School of Liberal Arts, Science and Technology, Perdana University, Kuala Lumpur 50490, Malaysia
| | - Abhi Veerakumarasivam
- School of Medical and Life Sciences, Sunway University, Bandar Sunway 47500, Selangor, Malaysia
| |
Collapse
|
5
|
Matar M, Prince G, Hamati I, Baalbaky M, Fares J, Aoude M, Matar C, Kourie HR. Implication of KDM6A in bladder cancer. Pharmacogenomics 2023; 24:509-522. [PMID: 37458596 DOI: 10.2217/pgs-2023-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Abstract
Background: Bladder cancer is a common urogenital malignancy characterized by frequent genetic alterations. Histone demethylase gene KDM6A is commonly mutated in bladder cancer. Aim: To review the characteristics of KDM6A and its mutation consequences, and to introduce a potential KDM6A-targeted treatment. Methods: We conducted a comprehensive literature search using two electronic databases, MEDLINE and Cochrane Library, to retrieve topic-related articles from July 2013 to July 2022 using keywords 'KDM6A', 'bladder cancer', 'UTX', 'treatment' and 'mutation'. Five reviewers independently screened literature search results and abstracted data from included studies. Descriptive analysis was conducted and 30 articles were retained. Main Results: A total of 30 articles were retrieved. Experimental and clinical data were collected and grouped by theme. Therapeutic strategies are depicted and organized by tables for a better understanding. Conclusion: This review demonstrates that KDM6A has crucial implications in bladder cancer pathogenesis and treatment.
Collapse
Affiliation(s)
- Marianne Matar
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Gilles Prince
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Ibrahim Hamati
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Maria Baalbaky
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Jonas Fares
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Marc Aoude
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Charbel Matar
- Division of Hematology-Oncology, Internal Medicine Department, George Washington University Hospital, 20037, Washington DC, USA
| | - Hampig Raphael Kourie
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| |
Collapse
|
6
|
Liu X, Chen J, Li J, Zeng Z, Jiang X, Gao Y, Huang Z, Wu Q, Gong Y, Xie C. Integrated analysis reveals common DNA methylation patterns of alcohol-associated cancers: A pan-cancer analysis. Front Genet 2023; 14:1032683. [PMID: 36861126 PMCID: PMC9968750 DOI: 10.3389/fgene.2023.1032683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Background: The role of alcohol in carcinogenesis has received increasing attention in recent years. Evidence shows its impacts on various aspects, including epigenetics alteration. The DNA methylation patterns underlying alcohol-associated cancers are not fully understood. Methods: We investigated the aberrant DNA methylation patterns in four alcohol-associated cancers based on the Illumina HumanMethylation450 BeadChip. Pearson coefficient correlations were identified between differential methylated CpG probes and annotated genes. Transcriptional factor motifs were enriched and clustered using MEME Suite, and a regulatory network was constructed. Results: In each cancer, differential methylated probes (DMPs) were identified, and 172 hypermethylated and 21 hypomethylated pan-cancer DMPs (PDMPs) were examined further. Annotated genes significantly regulated by PDMPs were investigated and enriched in transcriptional misregulation in cancers. The CpG island chr19:58220189-58220517 was hypermethylated in all four cancers and silenced in the transcription factor ZNF154. Various biological effects were exerted by 33 hypermethylated and seven hypomethylated transcriptional factor motifs grouped into five clusters. Eleven pan-cancer DMPs were identified to be associated with clinical outcomes in the four alcohol-associated cancers, which might provide a potential point of view for clinical outcome prediction. Conclusion: This study provides an integrated insight into DNA methylation patterns in alcohol-associated cancers and reveals the corresponding features, influences, and potential mechanisms.
Collapse
Affiliation(s)
- Xingyu Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiarui Chen
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengrong Huang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China,*Correspondence: Yan Gong, ; Conghua Xie,
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China,*Correspondence: Yan Gong, ; Conghua Xie,
| |
Collapse
|
7
|
Harsanyi S, Novakova ZV, Bevizova K, Danisovic L, Ziaran S. Biomarkers of Bladder Cancer: Cell-Free DNA, Epigenetic Modifications and Non-Coding RNAs. Int J Mol Sci 2022; 23:13206. [PMID: 36361996 PMCID: PMC9653602 DOI: 10.3390/ijms232113206] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 11/29/2022] Open
Abstract
Bladder cancer (BC) is the 10th most frequent cancer in the world. The initial diagnosis and surveillance of BC require a combination of invasive and non-invasive methods, which are costly and suffer from several limitations. Cystoscopy with urine cytology and histological examination presents the standard diagnostic approach. Various biomarkers (e.g., proteins, genes, and RNAs) have been extensively studied in relation to BC. However, the new trend of liquid biopsy slowly proves to be almost equally effective. Cell-free DNA, non-coding RNA, and other subcellular structures are now being tested for the best predictive and diagnostic value. In this review, we focused on published gene mutations, especially in DNA fragments, but also epigenetic modifications, and non-coding RNA (ncRNA) molecules acquired by liquid biopsy. We performed an online search in PubMed/Medline, Scopus, and Web of Science databases using the terms "bladder cancer", in combination with "markers" or "biomarkers" published until August 2022. If applicable, we set the sensitivity and specificity threshold to 80%. In the era of precision medicine, the development of complex laboratory techniques fuels the search and development of more sensitive and specific biomarkers for diagnosis, follow-up, and screening of BC. Future efforts will be focused on the validation of their sensitivity, specificity, predictive value, and their utility in everyday clinical practice.
Collapse
Affiliation(s)
- Stefan Harsanyi
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Zuzana Varchulova Novakova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Katarina Bevizova
- Institute of Anatomy, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 2, 811 08 Bratislava, Slovakia
| | - Lubos Danisovic
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Stanislav Ziaran
- Department of Urology, Faculty of Medicine, Comenius University in Bratislava, Limbova 5, 833 05 Bratislava, Slovakia
| |
Collapse
|
8
|
Shalata AT, Shehata M, Van Bogaert E, Ali KM, Alksas A, Mahmoud A, El-Gendy EM, Mohamed MA, Giridharan GA, Contractor S, El-Baz A. Predicting Recurrence of Non-Muscle-Invasive Bladder Cancer: Current Techniques and Future Trends. Cancers (Basel) 2022; 14:5019. [PMID: 36291803 PMCID: PMC9599984 DOI: 10.3390/cancers14205019] [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: 08/25/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Bladder cancer (BC) is the 10th most common cancer globally and has a high mortality rate if not detected early and treated promptly. Non-muscle-invasive BC (NMIBC) is a subclassification of BC associated with high rates of recurrence and progression. Current tools for predicting recurrence and progression on NMIBC use scoring systems based on clinical and histopathological markers. These exclude other potentially useful biomarkers which could provide a more accurate personalized risk assessment. Future trends are likely to use artificial intelligence (AI) to enhance the prediction of recurrence in patients with NMIBC and decrease the use of standard clinical protocols such as cystoscopy and cytology. Here, we provide a comprehensive survey of the most recent studies from the last decade (N = 70 studies), focused on the prediction of patient outcomes in NMIBC, particularly recurrence, using biomarkers such as radiomics, histopathology, clinical, and genomics. The value of individual and combined biomarkers is discussed in detail with the goal of identifying future trends that will lead to the personalized management of NMIBC.
Collapse
Affiliation(s)
- Aya T. Shalata
- Biomedical Engineering Department, Faculty of Engineering, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed Shehata
- Bioengineering Department, University of Louisville, Louisville, KY 40292, USA
| | - Eric Van Bogaert
- Department of Radiology, University of Louisville, Louisville, KY 40202, USA
| | - Khadiga M. Ali
- Pathology Department, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Ahmed Alksas
- Bioengineering Department, University of Louisville, Louisville, KY 40292, USA
| | - Ali Mahmoud
- Bioengineering Department, University of Louisville, Louisville, KY 40292, USA
| | - Eman M. El-Gendy
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed A. Mohamed
- Electronics and Communication Engineering Department, Faculty of Engineering, Mansoura University, Mansoura 35516, Egypt
| | | | - Sohail Contractor
- Department of Radiology, University of Louisville, Louisville, KY 40202, USA
| | - Ayman El-Baz
- Bioengineering Department, University of Louisville, Louisville, KY 40292, USA
| |
Collapse
|
9
|
Zhu R, Jiang Y, Zhou Z, Zhu S, Zhang Z, Chen Z, Chen S, Zhang Z. Prediction of the postoperative prognosis in patients with non-muscle-invasive bladder cancer based on preoperative serum surface-enhanced Raman spectroscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:4204-4221. [PMID: 36032588 PMCID: PMC9408240 DOI: 10.1364/boe.465295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 05/29/2023]
Abstract
Non-muscle-invasive bladder cancer (NMIBC) is a common urinary tumor and has a high recurrence rate due to improper or inadequate conservative treatment. The early and accurate prediction of its recurrence can be helpful to implement timely and rational treatment. In this study, we explored a preoperative serum surface-enhanced Raman spectroscopy based prognostic protocol to predict the postoperative prognosis for NMIBC patients at the time even before treatment. The biochemical analysis results suggested that biomolecules related to DNA/RNA, protein substances, trehalose and collagen are expected to be potential prognostic markers, which further compared with several routine clinically used immunohistochemistry expressions with prognostic values. In addition, high prognostic accuracies of 87.01% and 89.47% were achieved by using the proposed prognostic models to predict the future postoperative recurrence and recurrent type, respectively. Therefore, we believe that the proposed method has great potential in the early and accurate prediction of postoperative prognosis in patients with NMIBC, which is with important clinical significance to guide the treatment and further improve the recurrence rate and survival time.
Collapse
Affiliation(s)
- Ruochen Zhu
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110167, China
- Authors contributed equally
| | - Yuanjun Jiang
- Department of Urology, First Affiliated Hospital, China Medical University, Shenyang 110001, China
- Authors contributed equally
| | - Zheng Zhou
- School of Innovation and Entrepreneurship, Liaoning Institute of Science and Technology, Benxi 117004, China
| | - Shanshan Zhu
- Research Institute for Medical and Biological Engineering, Ningbo University, Ningbo 315211, China
| | - Zhuoyu Zhang
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110167, China
| | - Zhilin Chen
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110167, China
| | - Shuo Chen
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110167, China
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, China
| | - Zhe Zhang
- Department of Urology, First Affiliated Hospital, China Medical University, Shenyang 110001, China
| |
Collapse
|
10
|
Elbadawy M, Fujisaka K, Yamamoto H, Tsunedomi R, Nagano H, Ayame H, Ishihara Y, Mori T, Azakami D, Uchide T, Fukushima R, Abugomaa A, Kaneda M, Yamawaki H, Shinohara Y, Omatsu T, Mizutani T, Usui T, Sasaki K. Establishment of an experimental model of normal dog bladder organoid using a three-dimensional culture method. Biomed Pharmacother 2022; 151:113105. [PMID: 35605292 DOI: 10.1016/j.biopha.2022.113105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/30/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022] Open
Abstract
Dog bladder cancer (BC) is mostly muscle-invasive (MI) with poor prognosis, and its pathogenesis is close to human MIBC. Three-dimensional (3D) organoid culture ensures novel knowledge on cancer diseases including BC. Recently, we have established dog BC organoids (BCO) using their urine samples. BCO recapitulated the epithelial structures, characteristics, and drug sensitivity of BC-diseased dogs. However, organoids from dog normal bladder epithelium are not established yet. Therefore, the present study aimed to establish dog normal bladder organoids (NBO) for further understanding the pathogenesis of dog BC and human MIBC. The established NBO underwent various analyzes including cell marker expressions, histopathological structures, cancer-related gene expression patterns, and drug sensitivity. NBO could be produced non-invasively with a continuous culturing and recapitulated the structures and characteristics of the dog's normal bladder mucosal tissues. Different drug sensitivities were observed in each NBO. The analysis of RNA sequencing revealed that several novel genes were changed in NBO compared with BCO. NBO showed a higher expression of p53 and E-cadherin, but a lower expression of MDM2 and Twist1 compared with BCO. These results suggest that NBO could be a promising experimental 3D model for studying the developmental mechanisms of dog BC and human MIBC.
Collapse
Affiliation(s)
- Mohamed Elbadawy
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan; Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, 13736, Moshtohor, Toukh, Elqaliobiya, Egypt.
| | - Kodai Fujisaka
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Haru Yamamoto
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Ryouichi Tsunedomi
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | - Hiromi Ayame
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yusuke Ishihara
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Takashi Mori
- Laboratory of Veterinary Clinical Oncology, Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, Gifu, Gifu 501-1193, Japan
| | - Daigo Azakami
- Laboratory of Veterinary Clinical Oncology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Tsuyoshi Uchide
- Laboratory of Veterinary Surgery, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Ryuji Fukushima
- Animal Medical Center, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Amira Abugomaa
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan; Faculty of Veterinary Medicine, Mansoura University, 35516 Mansoura, Egypt
| | - Masahiro Kaneda
- Laboratory of Veterinary Anatomy, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hideyuki Yamawaki
- Laboratory of Veterinary Pharmacology, School of Veterinary Medicine, Kitasato University, 35-1, Higashi 23 ban-cho, Towada, Aomori 034-8628, Japan
| | - Yuta Shinohara
- Pet Health & Food Division, Iskara Industry CO., LTD, 1-14-2, Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Tsutomu Omatsu
- Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Tetsuya Mizutani
- Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Tatsuya Usui
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
| | - Kazuaki Sasaki
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| |
Collapse
|
11
|
Identification of an immune gene-associated prognostic signature in patients with bladder cancer. Cancer Gene Ther 2022; 29:494-504. [PMID: 35169299 DOI: 10.1038/s41417-022-00438-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/19/2021] [Accepted: 02/01/2022] [Indexed: 02/02/2023]
Abstract
A deeper understanding of the interaction between tumor cell and the immune microenvironment in bladder cancer may help select predictive and prognostic biomarkers. The current study aims to construct a prognostic signature for bladder cancer by analysis of molecular characteristics, as well as tumor-immune interactions. RNA-sequencing and clinical information from bladder cancer patients were downloaded from the TCGA database. The single sample Gene Sets Enrichment Analysis (ssGSEA) and Cell type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) were employed to separate the samples into two clusters. Lasso Cox regression was performed to construct an immune gene signature for bladder cancer. The correlation between key target genes of immune checkpoint blockade and the prognostic signature was also analyzed. Dataset from Gene Expression Omnibus (GEO) was retrieved for validation. Two immunophenotypes and immunological characteristics were identified, and a 17-immune gene signature was constructed to provide an independent prognostic signature for bladder cancer. The signature was verified through external validation and correlated with genomic characteristics and clinicopathologic features. Finally, a nomogram was generated from the clinical characteristics and immune signature. Our study reveals a tumor-immune microenvironment signature useful for prognosis in bladder cancer. The results provide information on the potential development of treatment strategies for bladder cancer patients. Prospective studies are warranted to validate the prognostic capability of this model, but these data highlight the role of the microenvironment in the clinical outcome of patients.
Collapse
|
12
|
Expression Profiles of HOXC6 Predict the Survival of Glioblastoma Patients and Correlate with Cell Cycle. JOURNAL OF ONCOLOGY 2022; 2022:8656865. [PMID: 35432534 PMCID: PMC9007636 DOI: 10.1155/2022/8656865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/14/2021] [Accepted: 03/13/2022] [Indexed: 12/05/2022]
Abstract
The goal of this study was to investigate the homeobox (HOX) gene expression status and its prognostic value in glioblastoma multiforme (GBM) and to uncover the biological processes related to its expression. The prognostic value of HOX genes in GBM was systematically investigated by a genome-wide analysis of HOX gene expression profiles in GBM patient samples in The Cancer Genome Atlas (TCGA) project (microarray dataset) and validation datasets. Using the differentially expressed gene (DEG) analysis and a Cox regression model, we discovered that the HOXC6 could stratify patients into significantly different survival (p = 0.0012, log-rank test) groups in the training cohort. TCGA RNA-seq and GSE16011 datasets were used for validation. Multivariate Cox and stratification analysis indicated that HOXC6 was an independent prognostic factor after adjusting for other clinical covariates. Bioinformatic analysis suggested that the HOXC6 might be involved in the cell cycle-related biological processes and pathways that are well established in the context of glioblastoma tumorigenesis. We further explored the bioinformatic implications by gene set enrichment analysis (GSEA). Tumor cell biology experiments verified the role of HOXC6 in proliferation and cell cycle progression. In conclusion, HOXC6 might be a candidate biomarker gene for individual treatment optimization of glioblastoma. HOXC6 expression has a significant prognostic value and is related to the cell cycle process in glioblastoma.
Collapse
|
13
|
Shukla SP, Zhang H, Fang B, Minna JD, Gomika Udugamasooriya D. Unbiased peptoid cell screen identifies a peptoid targeting newly appeared cell surface vimentin on tumor transformed early lung cancer cells. Bioorg Med Chem 2022; 58:116673. [PMID: 35189561 PMCID: PMC9040685 DOI: 10.1016/j.bmc.2022.116673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/30/2022] [Accepted: 02/13/2022] [Indexed: 11/16/2022]
Abstract
To identify potential new reagents and biomarkers for early lung cancer detection we combined the use of a novel preclinical isogenic model of human lung epithelial cells comparing non-malignant cells with those transformed to full malignancy using defined oncogenic changes and our on-bead two color (red and green stained cells) (OBTC) peptoid combinatorial screening methodology. The preclinical model used normal parent lung epithelial cells (HBEC3-KT, labeled with green dye) and isogenic fully malignant transformed derivatives (labeled with a red dye) via the sequential introduction of key genetic alterations of p53 knockdown, oncogenic KRAS and overexpression of cMYC (HBEC3p53, KRAS, cMYC). Using the unbiased OBTC screening approach, we tested 100,000 different peptoids and identified only one (named JM3A) that bound to the surface of the HBEC3p53, KRAS, cMYC cells (red cells) but not HBEC3-KT cells (green cells). Using the JM3A peptoid and proteomics, we identified the protein bound as vimentin using multiple validation approaches. These all confirmed the cell surface expression of vimentin (CSV) on transformed (HBEC3p53, KRAS, cMYC) but not on untransformed (HBEC3-KT) cells. JM3A coupled with fluorophores was able to detect and stain cell surface vimentin on very early stage lung cancers but not normal lung epithelial cells in a fashion comparable to that using anti-vimentin antibodies. We conclude: using a combined isogenic preclinical model of lung cancer and two color screening of a large peptoid library, we have identified differential expression of cell surface vimentin (CSV) after malignant transformation of lung epithelial cells, and developed a new peptoid reagent (JM3A) for detection of CSV which works well in staining of early stage NSCLCs. This new, highly specific, easy to prepare, CSV detecting JM3A peptoid provides an important new reagent for identifying cancer cells in early stage tumors as well as a resource for detection and isolating of CSV expressing circulating tumor cells.
Collapse
Affiliation(s)
- Satya Prakash Shukla
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | - Haowen Zhang
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | - Bingliang Fang
- Department of Thoracic and Cardiovascular Surgery - Research, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D Gomika Udugamasooriya
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, Houston, TX, USA; Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX , USA.
| |
Collapse
|
14
|
He J, Huang J, Tang G, Wang P, He M, Wei S. Low Expression of ZNF154 is Related to Poor Prognosis in Gastric Cancer. Cancer Manag Res 2022; 14:659-672. [PMID: 35210862 PMCID: PMC8860727 DOI: 10.2147/cmar.s340053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/03/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction Zinc finger protein 154 (ZNF154) has been identified as a tumor suppressor gene in multiple carcinomas. Lymph node (LN) metastasis is one of the most intensively negative factor of gastric cancer (GC) prognosis. However, the potential mechanisms of ZNF154-mediated LN metastasis are not elucidated. This study aimed to investigate the role of ZNF154 in LN metastasis of GC and their underlying mechanisms through in vitro and in vivo experiments. Methods Antitumor effect was measured by growth inhibition by cell counting kit-8 (CCK-8) and colony formation assay. Cell cycle distribution and apoptosis were evaluated by flow cytometry. Cell migration and invasion were measured by wound healing and transwell invasion assays, respectively. The expression levels of proteins were analyzed by Western blot. Xenograft models were used for validation in vivo. Results Our research showed that ZNF154 was down-regulated in 81.43% (57 of 70) of GC tissues compared with 58.6% of paired non-tumor tissues from patients, ZNF154 was down-regulated in 100% (7 of 7) of GC cell lines, up-regulated expression of ZNF154 in MGC-803 GC cells reduced cell proliferation, viability, migration and invasion, and enhanced cell apoptosis and arrested cell cycle in G2 phase, and suppressed tumorigenicity of MGC-803 cells in mice. Furthermore, up-regulated expression of ZNF154 mRNA reduced the expression of B-cell lymphoma-2 (Bcl-2), matrix metalloproteinase 2 (MMP-1), hepatocyte growth factor (HGF), vascular endothelial growth factor-A/C (VEGF-A/C). Conclusion ZNF154 inhibited LN metastasis of GC cells by suppressing several biological events of GC cells. ZNF154 was a tumor suppressor gene that is a promising target for blocking nodal involvement in GC.
Collapse
Affiliation(s)
- Jinsong He
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Jing Huang
- Lung Cancer Institute, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Guo Tang
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Pan Wang
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Ming He
- Graduate School of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Shoujiang Wei
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Correspondence: Shoujiang Wei, Email
| |
Collapse
|
15
|
Yu H, Li E, Liu S, Wu Z, Gao F. Identification of Signature Genes in the PD-1 Relative Gastric Cancer Using a Combined Analysis of Gene Expression and Methylation Data. JOURNAL OF ONCOLOGY 2022; 2022:4994815. [PMID: 36568638 PMCID: PMC9780002 DOI: 10.1155/2022/4994815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/03/2022] [Accepted: 08/06/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND The morbidity and mortality rates for gastric cancer (GC) rank second among all cancers, indicating the serious threat it poses to human health, as well as human life. This study aims to identify the pathways and genes as well as investigate the molecular mechanisms of tumor-related genes in gastric cancer (GC). METHOD We compared differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in gastric cancer and normal tissue samples using The Cancer Genome Atlas (TCGA) data. The Kyoto Encyclopedia of Gene and Genome (KEGG) and the Gene Ontology (GO) enrichment analysis' pathway annotations were conducted on DMGs and DEGs using a clusterProfiler R package to identify the important functions, as well as the biological processes and pathways involved. The intersection of the two was chosen and defined as differentially methylated and expressed genes (DMEGs). For DMEGs, we used the principal component analysis (PCA) to differentiate gastric cancer from adjacent samples. The linear discriminant analysis method was applied to categorize the samples using DMEGs methylation data and DMEGs expression profiles data and was validated using the leave-one-out cross-validation (LOOCV) method. We plotted the ROC curve for the classification and calculated the AUC (area under the ROC curve) value for a more intuitive view of the classification effect. We also used the NetworkAnalyst 3.0 tool to analyze DMEGs, using DrugBank to acquire information on protein-drug interactions and generate a network map of gene-drug interactions. RESULTS We identified a total of 971 DMGs in 188 PD-1 negative and 187 PD-1 positive gastric cancer samples obtained from TCGA. The KEGG and GO enrichment analysis showed the involvement of the regulation of ion transmembrane transport, collagen-containing extracellular matrix, cell-cell junction, and peptidase regulator activity. We simultaneously obtained 1,189 DEGs, out of which 986 were downregulated, while 203 were upregulated in tumors. The enriched analysis of the GO's and KEGG's pathways indicated that the most significant pathways included an intestinal immune network for IgA production, Staphylococcus aureus infection, cytokine-cytokine receptor interaction, and viral protein interaction with cytokine and cytokine receptor, which have previously been linked with gastric cancer. The compound DB01830 can bind well to the active site of the LCK protein and shows good stability, thus making it a potential inhibitor of the LCK protein. To observe the relationship between DMEGs' expression and prognosis, we observed 10 genes, among which were TRIM29, TSPAN8, EOMES, PPP1R16B, SELL, PCED1B, IYD, JPH1, CEACAM5, and RP11-44K6.2. Their high expressions were related to high risks. Besides, those genes were validated in different internal and external validation sets. CONCLUSION These results may provide potential molecular biological therapy for PD-1 negative gastric cancer.
Collapse
Affiliation(s)
- Han Yu
- Department of Gastrointestinal Surgery, Meizhou People's Hospital, Huangtang Road, Meijiang District, Meizhou 514031, Guangdong Province, China
| | - En Li
- Department of Gastrointestinal Surgery, Meizhou People's Hospital, Huangtang Road, Meijiang District, Meizhou 514031, Guangdong Province, China
| | - Sha Liu
- Department of Gastrointestinal Surgery, Meizhou People's Hospital, Huangtang Road, Meijiang District, Meizhou 514031, Guangdong Province, China
| | - ZuGuang Wu
- Department of Gastrointestinal Surgery, Meizhou People's Hospital, Huangtang Road, Meijiang District, Meizhou 514031, Guangdong Province, China
| | - FenFei Gao
- Department of Pharmacology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong Province, China
| |
Collapse
|
16
|
El Azzouzi M, El Ahanidi H, Hafidi Alaoui C, Chaoui I, Benbacer L, Tetou M, Hassan I, Bensaid M, Oukabli M, Ameur A, Al Bouzidi A, El Mzibri M, Attaleb M. Evaluation of DNA methylation in promoter regions of hTERT, TWIST1, VIM and NID2 genes in Moroccan bladder cancer patients. Cancer Genet 2021; 260-261:41-45. [PMID: 34922269 DOI: 10.1016/j.cancergen.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/08/2021] [Accepted: 12/05/2021] [Indexed: 12/11/2022]
Abstract
Promoter hypermethylation have been reported to play a key role in bladder cancer development and progression. The aim of this study is to evaluate the methylation status of hTERT, TWIST1, VIM and NID2 genes in bladder cancer. The methylation status was evaluated using the Methylation-Specific PCR (MSP) approach on 70 tumour biopsies from Moroccan bladder cancer patients. Overall, methylation frequencies of hTERT, TWIST1, VIM and NID2 genes, were 90%, 85.71%, 67.14% and 67.14%, respectively. Hypermethylation of all studied genes was found in all pathological grades and stages of bladder cancer. Nevertheless, statistical analysis showed no significant association between promoter methylation of hTERT, TWIST1, VIM and NID2 genes and tumours stage/grade (p value >0.05). Moreover, we have investigated the association between the methylation pattern of selected genes and the treatment outcome in a sub-group of non-muscle-invasive bladder cancer cases (52/70). Hypermethylation of hTERT, TWIST1, VIM and NID2 was detected in 83.34%; 66.67%; 83.34% and 58.34% of recurrent cases, respectively, and in 80%; 80%; 80% and 60% of progressive cases, respectively. Statistical analysis highlighted a significant association between TWIST1 hypermethylation and tumour recurrence (p = 0.041<0.05). Our results indicate that hypermethylation of hTERT, TWIST1, VIM and NID2 genes is a frequent epigenetic event in bladder cancer and could be a promising therapeutic target to prevent bladder cancer progression and metastasis.
Collapse
Affiliation(s)
- Meryem El Azzouzi
- Biology and Medical Research Unit, CNESTEN, Rabat, Morocco; Faculty of Medicine and Pharmacy of Rabat. Mohammed V University in Rabat, Rabat, Morocco
| | - Hajar El Ahanidi
- Biology and Medical Research Unit, CNESTEN, Rabat, Morocco; Faculty of Medicine and Pharmacy of Rabat. Mohammed V University in Rabat, Rabat, Morocco
| | - Chaimae Hafidi Alaoui
- Biology and Medical Research Unit, CNESTEN, Rabat, Morocco; Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Imane Chaoui
- Biology and Medical Research Unit, CNESTEN, Rabat, Morocco
| | - Laila Benbacer
- Biology and Medical Research Unit, CNESTEN, Rabat, Morocco
| | | | | | | | - Mohamed Oukabli
- Faculty of Medicine and Pharmacy of Rabat. Mohammed V University in Rabat, Rabat, Morocco; Mohammed V Military Hospital, Rabat, Morocco
| | - Ahmed Ameur
- Faculty of Medicine and Pharmacy of Rabat. Mohammed V University in Rabat, Rabat, Morocco; Mohammed V Military Hospital, Rabat, Morocco
| | | | | | | |
Collapse
|
17
|
Singh A, Gupta S, Sachan M. Evaluation of the Diagnostic Potential of Candidate Hypermethylated Genes in Epithelial Ovarian Cancer in North Indian Population. Front Mol Biosci 2021; 8:719056. [PMID: 34778370 PMCID: PMC8581490 DOI: 10.3389/fmolb.2021.719056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/12/2021] [Indexed: 01/22/2023] Open
Abstract
Most ovarian cancers, despite improvement in management of cancer, are still diagnosed at an advanced stage. Early detection plays an essential role in reducing ovarian cancer mortality and, therefore, is critically needed. Liquid biopsies-based approaches hold significant promise for cancer detection. The present study investigates a panel of epigenetic biomarkers for the detection of epithelial ovarian cancer. A qPCR assay has been developed based on the assessment of DNA methylation markers in circulating cell-free DNA as a minimally invasive tool. Herein, the promoter methylation of seven ovarian cancer-specific genes (RASSF1A, DAPK1, SOX1, HOXA9, HIC1, SPARC, and SFRP1) was analyzed quantitatively in 120 tissue samples by MethyLight assay. The best-performing genes were further evaluated for their methylation status in 70 matched serum cell-free DNA of cancerous and non-cancerous samples. Additionally, DNA methylation patterns of these best-performing genes were validated by clonal bisulfite sequencing. The ROC (Receiver-operator characteristic) curves were constructed to evaluate the diagnostic performances of both individual and combined gene panels. The seven candidate genes displayed a methylation frequency of 61.0-88.0% in tissue samples. The promoter methylation frequencies for all the seven candidate genes were significantly higher in cancer samples than in normal matched controls. In tissue samples, the multiplex MethyLight assay for HOXA9, HIC1, and SOX1 were the best performing gene panels in terms of sensitivity and specificity. The three best-performing genes exhibited individual frequencies of 53.0-71.0% in serum CFDNA, and the multiplex assay for these genes were identified to discriminate serum from cancer patients and healthy individuals (area under the curve: HOXA9+HIC1 = 0.95, HIC1+SOX1 = 0.93 and HOXA9+SOX1 = 0.85). The results of MethyLight showed high concordance with clonal bisulfite sequencing results. Individual genes and combined panel exhibited better discriminatory efficiencies to identify ovarian cancer at various stages of disease when analyzed in tissue and serum cell-free DNA. We report a qPCR-based non-invasive epigenetic biomarker assay with high sensitivity and specificity for OC screening. Our findings also reveal the potential utility of methylation-based detection of circulating cell-free tumor DNA in the clinical management of ovarian cancer.
Collapse
Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| |
Collapse
|
18
|
Tawk B, Wirkner U, Schwager C, Rein K, Zaoui K, Federspil PA, Adeberg S, Linge A, Ganswindt U, Hess J, Unger K, Tinhofer I, Budach V, Lohaus F, Krause M, Guberina M, Stuschke M, Balermpas P, Rödel C, Grosu AL, Schäfer H, Zips D, Combs SE, Pigorsch S, Zitzelsberger H, Baumeister P, Kirchner T, Bewerunge-Hudler M, Weichert W, Hess J, Herpel E, Belka C, Baumann M, Debus J, Abdollahi A. Tumor DNA-methylome derived epigenetic fingerprint identifies HPV-negative head and neck patients at risk for locoregional recurrence after postoperative radiochemotherapy. Int J Cancer 2021; 150:603-616. [PMID: 34648658 DOI: 10.1002/ijc.33842] [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: 06/25/2021] [Revised: 08/18/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022]
Abstract
Biomarkers with relevance for loco-regional therapy are needed in human papillomavirus negative aka HPV(-) head and neck squamous cell carcinoma (HNSCC). Based on the premise that DNA methylation pattern is highly conserved, we sought to develop a reliable and robust methylome-based classifier identifying HPV(-) HNSCC patients at risk for loco-regional recurrence (LR) and all-event progression after postoperative radiochemotherapy (PORT-C). The training cohort consisted of HPV-DNA negative HNSCC patients (n = 128) homogeneously treated with PORT-C in frame of the German Cancer Consortium-Radiation Oncology Group (DKTK-ROG) multicenter biomarker trial. DNA Methylation analysis was performed using Illumina 450 K and 850 K-EPIC microarray technology. The performance of the classifier was integrated with a series of biomarkers studied in the training set namely hypoxia-, 5-microRNA (5-miR), stem-cell gene-expression signatures and immunohistochemistry (IHC)-based immunological characterization of tumors (CD3/CD8/PD-L1/PD1). Validation occurred in an independent cohort of HPV(-) HNSCC patients, pooled from two German centers (n = 125). We identified a 38-methylation probe-based HPV(-) Independent Classifier of disease Recurrence (HICR) with high prognostic value for LR, distant metastasis and overall survival (P < 10-9 ). HICR remained significant after multivariate analysis adjusting for anatomical site, lymph node extracapsular extension (ECE) and size (T-stage). HICR high-risk tumors were enriched for younger patients with hypoxic tumors (15-gene signature) and elevated 5-miR score. After adjustment for hypoxia and 5-miR covariates, HICR maintained predicting all endpoints. HICR provides a novel mean for assessing the risk of LR in HPV(-) HNSCC patients treated with PORT-C and opens a new opportunity for biomarker-assisted stratification and therapy adaptation in these patients.
Collapse
Affiliation(s)
- Bouchra Tawk
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University, Heidelberg, Germany
| | - Ute Wirkner
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University, Heidelberg, Germany
| | - Christian Schwager
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University, Heidelberg, Germany
| | - Katrin Rein
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University, Heidelberg, Germany
| | - Karim Zaoui
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Philippe A Federspil
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Sebastian Adeberg
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,Department of Radiation Oncology, University Hospital Heidelberg, Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg, Germany
| | - Annett Linge
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, Dresden, Germany.,Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Helmholtz Association/Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Ute Ganswindt
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Department of Radiation Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Julia Hess
- Department of Radiation Oncology, University Hospital Ludwig-Maximilians-University of Munich, Munich, Germany.,Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Kristian Unger
- Department of Radiation Oncology, University Hospital Ludwig-Maximilians-University of Munich, Munich, Germany.,Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.,Department of Radiooncology and Radiotherapy, Charité University Hospital, Berlin, Germany
| | - Volker Budach
- German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.,Department of Radiooncology and Radiotherapy, Charité University Hospital, Berlin, Germany
| | - Fabian Lohaus
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, Dresden, Germany.,Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Helmholtz Association/Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Mechthild Krause
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, Dresden, Germany.,Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Helmholtz Association/Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Maja Guberina
- German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany.,Department of Radiotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Martin Stuschke
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Radiotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Panagiotis Balermpas
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany.,Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Claus Rödel
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany.,Department of Radiotherapy and Oncology, Goethe-University Frankfurt, Frankfurt, Germany
| | - Anca L Grosu
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany.,Department of Radiation Oncology, Clinical Study Section, University of Freiburg, Freiburg, Germany.,Department of Radiation Oncology, University of Freiburg, Freiburg, Germany
| | - Henning Schäfer
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany.,Department of Radiation Oncology, Clinical Study Section, University of Freiburg, Freiburg, Germany
| | - Daniel Zips
- German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,Department of Radiation Oncology, Faculty of Medicine and University Hospital Tübingen, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Stephanie E Combs
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Department of Radiation Oncology, Technische Universität München, Munich, Germany
| | - Steffi Pigorsch
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Department of Radiation Oncology, Technische Universität München, Munich, Germany
| | - Horst Zitzelsberger
- Department of Radiation Oncology, University Hospital Ludwig-Maximilians-University of Munich, Munich, Germany.,Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Philipp Baumeister
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Thomas Kirchner
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Munich, Germany
| | | | - Wilko Weichert
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Institute of Pathology, Technische Universität München, Munich, Germany
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Department of Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center, Heidelberg, Germany
| | - Esther Herpel
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Claus Belka
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Department of Radiation Oncology, University Hospital Ludwig-Maximilians-University of Munich, Munich, Germany.,Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Michael Baumann
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, Dresden, Germany.,Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jürgen Debus
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University, Heidelberg, Germany
| | | |
Collapse
|
19
|
Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
Collapse
Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
| |
Collapse
|
20
|
Humayun-Zakaria N, Ward DG, Arnold R, Bryan RT. Trends in urine biomarker discovery for urothelial bladder cancer: DNA, RNA, or protein? Transl Androl Urol 2021; 10:2787-2808. [PMID: 34295762 PMCID: PMC8261432 DOI: 10.21037/tau-20-1327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 04/23/2021] [Indexed: 02/01/2023] Open
Abstract
Urothelial bladder cancer is a complex disease displaying a landscape of heterogenous molecular subtypes, mutation profiles and clinical presentations. Diagnosis and surveillance rely on flexible cystoscopy which has high accuracy, albeit accompanied by a high-cost burden for healthcare providers and discomfort for patients. Advances in "omic" technologies and computational biology have provided insights into the molecular pathogenesis of bladder cancer and provided powerful tools to identify markers for disease detection, risk stratification, and predicting responses to therapy. To date, numerous attempts have been made to discover and validate diagnostic biomarkers that could be deployed as an adjunct to the cystoscopic diagnosis and long-term surveillance of bladder cancer. We report a comprehensive literature analysis using PubMed to assess the changing trends in investigating DNA, RNA, or proteins as diagnostic urinary biomarkers over a period of 5 decades: 1970-2020. A gradual shift has been observed in research away from protein biomarkers to nucleic acids including different classes of RNA, and DNA methylation and mutation markers. Until 2000, publications involving protein biomarker discovery constituted 87% of the total number of research articles with DNA comprising 6% and RNA 7%. Since 2000 the proportion of protein biomarker articles has fallen to 40%, and DNA and RNA studies increased to 32% and 28%, respectively. Clearly research focus, perhaps driven by technological innovation, has shifted from proteins to nucleic acids. We optimistically hypothesise that, following thorough validation, a clinically useful detection test for bladder cancer based on a panel of DNA or RNA markers could become reality within 5-10 years.
Collapse
Affiliation(s)
- Nada Humayun-Zakaria
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
21
|
Charpentier M, Gutierrez C, Guillaudeux T, Verhoest G, Pedeux R. Noninvasive Urine-Based Tests to Diagnose or Detect Recurrence of Bladder Cancer. Cancers (Basel) 2021; 13:cancers13071650. [PMID: 33916038 PMCID: PMC8036846 DOI: 10.3390/cancers13071650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/10/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022] Open
Abstract
Liquid biopsies are increasingly used for the diagnosis and follow-up of cancer patients. Urine is a body fluid that can be used to detect cancers and others diseases. It is noninvasive and easy to collect. To detect Bladder Cancer (BC), cytology is the first assay used. It is an effective way to detect high grade BC but has a high rate of equivocal results, especially for low grade BC. Furthermore, cystoscopy is used to confirm cytology results and to determine cancer status. Cystoscopy is also effective but highly invasive, and not well accepted by patients, especially for BC follow-up. In this review we survey the numerous assays recently developed in order to diagnose BC at an early stage, and to facilitate the follow-up of patients. We discuss their effectiveness, ease of use, and applications. Finally, we discuss assays that, in the future, could improve the diagnosis and management of BC patients.
Collapse
Affiliation(s)
- Marine Charpentier
- COSS (Chemistry Oncogenesis Stress Signaling)—UMR_S 1242, University of Rennes, INSERM, CLCC Eugène Marquis, F-35000 Rennes, France; (M.C.); (C.G.); (T.G.)
| | - Charly Gutierrez
- COSS (Chemistry Oncogenesis Stress Signaling)—UMR_S 1242, University of Rennes, INSERM, CLCC Eugène Marquis, F-35000 Rennes, France; (M.C.); (C.G.); (T.G.)
| | - Thierry Guillaudeux
- COSS (Chemistry Oncogenesis Stress Signaling)—UMR_S 1242, University of Rennes, INSERM, CLCC Eugène Marquis, F-35000 Rennes, France; (M.C.); (C.G.); (T.G.)
| | - Grégory Verhoest
- Department of Urology, CHU RENNES, Rue Henri le Guilloux, 35033 Rennes, France;
| | - Rémy Pedeux
- COSS (Chemistry Oncogenesis Stress Signaling)—UMR_S 1242, University of Rennes, INSERM, CLCC Eugène Marquis, F-35000 Rennes, France; (M.C.); (C.G.); (T.G.)
- Correspondence: ; Tel.: +33-223-234-702
| |
Collapse
|
22
|
Chen Z, Liu G, Liu G, Bolkov MA, Shinwari K, Tuzankina IA, Chereshnev VA, Wang Z. Defining muscle-invasive bladder cancer immunotypes by introducing tumor mutation burden, CD8+ T cells, and molecular subtypes. Hereditas 2021; 158:1. [PMID: 33388091 PMCID: PMC7778803 DOI: 10.1186/s41065-020-00165-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
Immunotherapy, especially anti-PD-1, is becoming a pillar of modern muscle-invasive bladder cancer (MIBC) treatment. However, the objective response rates (ORR) are relatively low due to the lack of precise biomarkers to select patients. Herein, the molecular subtype, tumor mutation burden (TMB), and CD8+ T cells were calculated by the gene expression and mutation profiles of MIBC patients. MIBC immunotypes were constructed using clustering analysis based on tumor mutation burden, CD8+ T cells, and molecular subtypes. Mutated genes, enriched functional KEGG pathways and GO terms, and co-expressed network-specific hub genes have been identified. We demonstrated that ORR of immunotype A patients identified by molecular subtype, CD8+ T cells, and TMB is about 36% predictable. PIK3CA, RB1, FGFR3, KMT2C, MACF1, RYR2, and EP300 are differentially mutated among three immunotypes. Pathways such as ECM-receptor interaction, PI3K-Akt signaling pathway, and TGF-beta signaling pathway are top-ranked in enrichment analysis. Low expression of ACTA2 was associated with the MIBC survival benefit. The current study constructs a model that could identify suitable MIBC patients for immunotherapy, and it is an important step forward to the personalized treatment of bladder cancers.
Collapse
Affiliation(s)
- Zihao Chen
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Guojun Liu
- Department of Medical Biochemistry and Biophysics, Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg, 620000, Russia.
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
| | - Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Mikhail A Bolkov
- Department of immunochemistry, Institute of Chemical Engineering, Ural Federal University, Ekaterinburg, 620000, Russia
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620000, Russia
| | - Khyber Shinwari
- Department of immunochemistry, Institute of Chemical Engineering, Ural Federal University, Ekaterinburg, 620000, Russia
| | - Irina A Tuzankina
- Department of immunochemistry, Institute of Chemical Engineering, Ural Federal University, Ekaterinburg, 620000, Russia
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620000, Russia
| | - Valery A Chereshnev
- Department of immunochemistry, Institute of Chemical Engineering, Ural Federal University, Ekaterinburg, 620000, Russia
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620000, Russia
| | - Zhifeng Wang
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou, 450003, China
| |
Collapse
|
23
|
Lian J, Liu S, Yue Y, Yang Q, Zhang Z, Yang S, Zhang Y. Eomes promotes esophageal carcinoma progression by recruiting Treg cells through the CCL20-CCR6 pathway. Cancer Sci 2020; 112:144-154. [PMID: 33113266 PMCID: PMC7780006 DOI: 10.1111/cas.14712] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/13/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
Eomesodermin (Eomes) is a T‐box transcription factor that drives the differentiation and function of cytotoxic lymphocytes. However, the underlying function and mechanism of Eomes in tumor cells remains elusive. Here, we studied the role of Eomes in human esophageal squamous cell carcinoma (ESCC). Using 2 human ESCC cell lines, we found that Eomes knockdown reduced esophageal cancer cell proliferation and that the esophageal cancer cell cycle was blocked in the G2/M phase. Mechanistically, we identified CCL20 as the main downstream target of Eomes. Furthermore, we found that CCL20 could chemoregulate regulatory T cells (Tregs) through their specific receptor CCR6, then promoting the proliferation of esophageal cancer cells. Eomes knockdown also delayed the growth of human ESCC xenografts in BALB/c nude mice. Importantly, in 133 human ESCC tissues, high Eomes levels were associated with poor clinical prognosis. Overall, our findings suggested that the Eomes‐CCL20‐CCR6 pathway plays a vital role in human ESCC progress. Therefore, targeting this pathway may represent a promising strategy for controlling human ESCC.
Collapse
Affiliation(s)
- Jingyao Lian
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| | - Saisai Liu
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| | - Ying Yue
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Clinical Laboratory, Henan Medical College Hospital Workers, Zhengzhou, China
| | - Qingshan Yang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| | - Zhen Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| | - Shengli Yang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| |
Collapse
|
24
|
Miller BF, Pisanic Ii TR, Margolin G, Petrykowska HM, Athamanolap P, Goncearenco A, Osei-Tutu A, Annunziata CM, Wang TH, Elnitski L. Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers. Clin Epigenetics 2020; 12:154. [PMID: 33081832 PMCID: PMC7574234 DOI: 10.1186/s13148-020-00939-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based cancer testing. Here, we describe development and validation of a methylation density binary classification method called EpiClass (available for download at https://github.com/Elnitskilab/EpiClass ) that can be used to predict and optimize the performance of methylation biomarkers, particularly in challenging, heterogeneous samples such as liquid biopsies. This approach is based upon leveraging statistical differences in single-molecule sample methylation density distributions to identify ideal thresholds for sample classification. RESULTS We developed and tested the classifier using reduced representation bisulfite sequencing (RRBS) data derived from ovarian carcinoma tissue DNA and controls. We used these data to perform in silico simulations using methylation density profiles from individual epiallelic copies of ZNF154, a genomic locus known to be recurrently methylated in numerous cancer types. From these profiles, we predicted the performance of the classifier in liquid biopsies for the detection of epithelial ovarian carcinomas (EOC). In silico analysis indicated that EpiClass could be leveraged to better identify cancer-positive liquid biopsy samples by implementing precise thresholds with respect to methylation density profiles derived from circulating cell-free DNA (cfDNA) analysis. These predictions were confirmed experimentally using DREAMing to perform digital methylation density analysis on a cohort of low volume (1-ml) plasma samples obtained from 26 EOC-positive and 41 cancer-free women. EpiClass performance was then validated in an independent cohort of 24 plasma specimens, derived from a longitudinal study of 8 EOC-positive women, and 12 plasma specimens derived from 12 healthy women, respectively, attaining a sensitivity/specificity of 91.7%/100.0%. Direct comparison of CA-125 measurements with EpiClass demonstrated that EpiClass was able to better identify EOC-positive women than standard CA-125 assessment. Finally, we used independent whole genome bisulfite sequencing (WGBS) datasets to demonstrate that EpiClass can also identify other cancer types as well or better than alternative methylation-based classifiers. CONCLUSIONS Our results indicate that assessment of intramolecular methylation density distributions calculated from cfDNA facilitates the use of methylation biomarkers for diagnostic applications. Furthermore, we demonstrated that EpiClass analysis of ZNF154 methylation was able to outperform CA-125 in the detection of etiologically diverse ovarian carcinomas, indicating broad utility of ZNF154 for use as a biomarker of ovarian cancer.
Collapse
Affiliation(s)
- Brendan F Miller
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas R Pisanic Ii
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Gennady Margolin
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hanna M Petrykowska
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander Goncearenco
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Akosua Osei-Tutu
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christina M Annunziata
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tza-Huei Wang
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Laura Elnitski
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
25
|
Screening and identification of potential prognostic biomarkers in bladder urothelial carcinoma: Evidence from bioinformatics analysis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
26
|
Lozano F, Raventos CX, Carrion A, Trilla E, Morote J. Current status of genetic urinary biomarkers for surveillance of non-muscle invasive bladder cancer: a systematic review. BMC Urol 2020; 20:99. [PMID: 32664878 PMCID: PMC7362437 DOI: 10.1186/s12894-020-00670-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/08/2020] [Indexed: 01/22/2023] Open
Abstract
Background Genetic biomarkers are a promising and growing field in the management of bladder cancer in all stages. The aim of this paper is to understand the role of genetic urinary biomarkers in the follow up of patients with non muscle invasive bladder cancer where there is increasing evidence that they can play a role in avoiding invasive techniques. Methods Following PRISMA criteria, we have performed a systematic review. The search yielded 164 unique articles, of which 21 articles were included involving a total of 7261 patients. Sixteen of the articles were DNA based biomarkers, analyzing different methylations, microsatellite aberrations and gene mutations. Five articles studied the role of RNA based biomarkers, based on measuring levels of different combinations of mRNA. QUADAS2 critical evaluation of each paper has been reported. Results There are not randomized control trials comparing any biomarker with the gold standard follow-up, and the level of evidence is 2B in almost all the studies. Negative predictive value varies between 55 and 98.5%, being superior in RNA based biomarkers. Conclusions Although cystoscopy and cytology are the gold standard for non muscle invasive bladder cancer surveillance, genetic urinary biomarkers are a promising tool to avoid invasive explorations to the patients with a safe profile of similar sensitivity and negative predictive value. The accuracy that genetic biomarkers can offer should be taken into account to modify the paradigm of surveillance in non muscle invasive bladder cancer patients, especially in high-risk ones where many invasive explorations are recommended and biomarkers experiment better results.
Collapse
Affiliation(s)
- F Lozano
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain. .,Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - C X Raventos
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - A Carrion
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - E Trilla
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - J Morote
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
27
|
Makabe T, Arai E, Hirano T, Ito N, Fukamachi Y, Takahashi Y, Hirasawa A, Yamagami W, Susumu N, Aoki D, Kanai Y. Genome-wide DNA methylation profile of early-onset endometrial cancer: its correlation with genetic aberrations and comparison with late-onset endometrial cancer. Carcinogenesis 2020; 40:611-623. [PMID: 30850842 PMCID: PMC6610171 DOI: 10.1093/carcin/bgz046] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 01/28/2019] [Accepted: 03/03/2019] [Indexed: 12/20/2022] Open
Abstract
The present study was performed to clarify the significance of DNA methylation alterations during endometrial carcinogenesis. Genome-wide DNA methylation analysis and targeted sequencing of tumor-related genes were performed using the Infinium MethylationEPIC BeadChip and the Ion AmpliSeq Cancer Hotspot Panel v2, respectively, for 31 samples of normal control endometrial tissue from patients without endometrial cancer and 81 samples of endometrial cancer tissue. Principal component analysis revealed that tumor samples had a DNA methylation profile distinct from that of control samples. Gene Ontology enrichment analysis revealed significant differences of DNA methylation at 1034 CpG sites between early-onset endometrioid endometrial cancer (EE) tissue (patients aged ≤40 years) and late-onset endometrioid endometrial cancer (LE) tissue, which were accumulated among 'transcriptional factors'. Mutations of the CTNNB1 gene or DNA methylation alterations of genes participating in Wnt signaling were frequent in EEs, whereas genetic and epigenetic alterations of fibroblast growth factor signaling genes were observed in LEs. Unsupervised hierarchical clustering grouped EE samples in Cluster EA (n = 22) and samples in Cluster EB (n = 12). Clinicopathologically less aggressive tumors tended to be accumulated in Cluster EB, and DNA methylation levels of 18 genes including HOXA9, HOXD10 and SOX11 were associated with differences in such aggressiveness between the two clusters. We identified 11 marker CpG sites that discriminated EB samples from EA samples with 100% sensitivity and specificity. These data indicate that genetically and epigenetically different pathways may participate in the development of EEs and LEs, and that DNA methylation profiling may help predict tumors that are less aggressive and amenable to fertility preservation treatment.
Collapse
Affiliation(s)
- Takeshi Makabe
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan.,Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Takuro Hirano
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan.,Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Nanako Ito
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | | | - Yoriko Takahashi
- Bioscience Department, Mitsui Knowledge Industry Co, Ltd, Tokyo, Japan
| | - Akira Hirasawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Wataru Yamagami
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Nobuyuki Susumu
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan.,Department of Obstetrics and Gynecology, International University of Health and Welfare School of Medicine, Chiba, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| |
Collapse
|
28
|
Abstract
PURPOSE OF REVIEW To provide a current comprehensive review of the available urinary biomarkers for the detection and surveillance of bladder cancer. RECENT FINDINGS The limitations of urine cytology and invasive nature of cystoscopic evaluation have led to a growing search for an ideal, cost-effective biomarker with acceptable sensitivity and specificity. Current FDA approved biomarkers such as UroVysion fluorescent in situ hybridization, Immunocyt, and nuclear matrix protein 22 do not have the specificity, and thus positive predictive value to warrant their cost as a routine adjunct or replacement for cystoscopy. Several promising commercially available assays such as Cxbladder, Assure MDx, and Xpert BC may perform better than cytology in select populations. Novel genomic, epigenetic, inflammatory, and metabolomic-based assays are being analyzed as potential urinary biomarkers. SUMMARY Urinary biomarkers with high sensitivity and specificity are an unmet need in bladder cancer. Several new assays may meet these criteria and future research may justify use in clinical practice.
Collapse
|
29
|
Kim J, Kim WT, Kim WJ. Advances in urinary biomarker discovery in urological research. Investig Clin Urol 2019; 61:S8-S22. [PMID: 32055750 PMCID: PMC7004831 DOI: 10.4111/icu.2020.61.s1.s8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/22/2019] [Indexed: 12/27/2022] Open
Abstract
A disease-specific biomarker (or biomarkers) is a characteristic reflecting a pathological condition in human body, which can be used as a diagnostic or prognostic tool for the clinical management. A urine-based biomarker(s) may provide a clinical value as attractive tools for clinicians to utilize in the clinical setting in particular to bladder diseases including bladder cancer and other bladder benign dysfunctions. Urine can be easily obtained by patients with no preparation or painful procedures required from patients' side. Currently advanced omics technologies and computational power identified potential omics-based novel biomarkers. An unbiased profiling based on transcriptomics, proteomics, epigenetics, metabolomics approaches et al. found that expression at RNA, protein, and metabolite levels are linked with specific bladder diseases and outcomes. In this review, we will discuss about the urine-based biomarkers reported by many investigators including us and how these biomarkers can be applied as a diagnostic and prognostic tool in clinical trials and patient care to promote bladder health. Furthermore, we will discuss how these promising biomarkers can be developed into a smart medical device and what we should be cautious about toward being used in real clinical setting.
Collapse
Affiliation(s)
- Jayoung Kim
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, University of California Los Angeles, CA, USA
| | - Won Tae Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea.,Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| | - Wun-Jae Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea.,Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| |
Collapse
|
30
|
Furuya H, Chan OT, Hokutan K, Tsukikawa Y, Chee K, Kozai L, Chan KS, Dai Y, Wong RS, Rosser CJ. Prognostic Significance of Lymphocyte Infiltration and a Stromal Immunostaining of a Bladder Cancer Associated Diagnostic Panel in Urothelial Carcinoma. Diagnostics (Basel) 2019; 10:diagnostics10010014. [PMID: 31905599 PMCID: PMC7168167 DOI: 10.3390/diagnostics10010014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 01/08/2023] Open
Abstract
We set out to expand on our previous work in which we reported the epithelial expression pattern of a urine-based bladder cancer-associated diagnostic panel (A1AT, ANG, APOE, CA9, IL8, MMP9, MMP10, PAI1, SDC1, and VEGFA). Since many of the analytes in the bladder cancer-associated diagnostic signature were chemokines, cytokines, or secreted proteins, we set out to report the stromal staining pattern of the diagnostic signature as well as CD3+ (T-cell) cell and CD68+ (macrophage) cell staining in human bladder tumors as a snapshot of the tumor immune landscape. Immunohistochemical staining was performed on 213 tumor specimens and 74 benign controls. Images were digitally captured and quantitated using Aperio (Vista, CA). The expression patterns were correlated with tumor grade, tumor stage, and outcome measures. We noted a positive correlation of seven of the 10 proteins (excluding A1AT and IL8 which had a negative association and VEGFA had no association) in bladder cancer. The overexpression of MMP10 was associated with higher grade disease, while overexpression of MMP10, PAI1, SDC1 and ANG were associated with high stage bladder cancer and CA9 was associated with low stage bladder cancer. Increased tumor infiltration of CD68+ cells were associated with higher stage disease. Overall survival was significantly reduced in bladder cancer patients' whose tumors expressed eight or more of the 10 proteins that comprise the bladder cancer diagnostic panel. These findings confirm that the chemokines, cytokines, and secreted proteins in a urine-based diagnostic panel are atypically expressed, not only in the epithelial component of bladder tumors, but also in the stromal component of bladder tumors and portends a worse overall survival. Thus, when assessing immunohistochemical staining, it is important to report staining patterns within the stroma as well as the entire stroma itself.
Collapse
Affiliation(s)
- Hideki Furuya
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (H.F.); (K.H.); (Y.T.); (K.C.)
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Surgery, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA;
| | - Owen T.M. Chan
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (H.F.); (K.H.); (Y.T.); (K.C.)
| | - Kanani Hokutan
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (H.F.); (K.H.); (Y.T.); (K.C.)
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Yutaro Tsukikawa
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (H.F.); (K.H.); (Y.T.); (K.C.)
| | - Keanu Chee
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (H.F.); (K.H.); (Y.T.); (K.C.)
| | - Landon Kozai
- John A. Burn School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA;
| | - Keith S. Chan
- Department of Pathology, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA;
| | - Yunfeng Dai
- Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA;
| | - Regan S. Wong
- Department of Surgery, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA;
| | - Charles J. Rosser
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (H.F.); (K.H.); (Y.T.); (K.C.)
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Surgery, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA;
- Correspondence:
| |
Collapse
|
31
|
Wang W, Wang S, Chu X, Liu H, Xiang M. Predicting the Lung Squamous Cell Carcinoma Diagnosis and Prognosis Markers by Unique DNA Methylation and Gene Expression Profiles. J Comput Biol 2019; 27:1041-1054. [PMID: 31710242 DOI: 10.1089/cmb.2019.0138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The early diagnosis of lung squamous cell carcinoma (LUSC) is difficult, causing an unsatisfactory prognosis. Therefore, the 5-year survival rate of LUSC is poor. This study aimed at screening the potential diagnostic and prognostic markers for LUSC. The data of LUSC gene expression profiles and DNA methylation were obtained from The Cancer Genome Atlas (TCGA) database; the differentially expressed genes (DEGs) and the differentially methylated genes (DMGs) were screened out by an independent t-test and Benjamini/Hochberg methods. Further, the classifiers of the gene expression and DNA methylation markers in LUSC were constructed. After that, diagnostic and prognostic markers in LUSC were analyzed by the protein-protein interaction (PPI) network. The DEGs and the DMGs from TCGA database of LUSC were screened out. After strict filtration, we identified three potential DMGs (POU domain, class 4, transcription factor 2 [POU4F2], EN1, single-minded homolog 1 [SIM1]) for early diagnosis and seven potential DEGs (G-protein coupled receptor 78 [GPR78], PCDHA5, myosin binding protein H [MYBPH], RTL3, KIAA0408, HSD3B2, PCDHA12) for prognosis of LUSC. The tumor-normal tissue classification model and prognosis model were validated in two independent datasets. In addition, the PPI network was constructed, including three DMGs and the five DEGs (GPR78, MYBPH, KIAA0408, HSD3B2, PCDHA12) of the seven DEGs. The potential DMGs (POU4F2, EN1, SIM1) and DEGs (GPR78, MYBPH, KIAA0408, HSD3B2, PCDHA12) for the diagnosis and prognosis of LUSC identified in this article are expected to be further applied in clinical practice of the treatment of LUSC.
Collapse
Affiliation(s)
- Weiqing Wang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Shaohua Wang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Xiao Chu
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Hui Liu
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Ming Xiang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| |
Collapse
|
32
|
Shi S, Ye S, Wu X, Xu M, Zhuo R, Liao Q, Xi Y. A Two-DNA Methylation Signature to Improve Prognosis Prediction of Clear Cell Renal Cell Carcinoma. Yonsei Med J 2019; 60:1013-1020. [PMID: 31637882 PMCID: PMC6813151 DOI: 10.3349/ymj.2019.60.11.1013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Effective biomarkers and models are needed to improve the prognostic prospects of clear cell renal cell carcinoma (ccRCC). The purpose of this work was to identify DNA methylation biomarkers and to evaluate the utility of DNA methylation analysis for ccRCC prognosis. MATERIALS AND METHODS An overview of genome-wide methylation of ccRCC tissues derived from The Cancer Genome Atlas (TCGA) database was download for analysis. DNA methylation signatures were identified using Cox regression methods. The potential clinical significance of methylation biomarkers acting as a novel prognostic markers was analyzed using the Kaplan-Meier method and receiver operating characteristic (ROC) curves. RESULTS This study analyzed data for 215 patients with information on 23171 DNA methylation sites and identified a two-DNA methylation signature (cg18034859, cg24199834) with the help of a step-wise multivariable Cox regression model. The area under the curve of ROCs for the two-DNA methylation signature was 0.819. The study samples were stratified into low- and high-risk classifications based on an optimal threshold, and the two groups showed markedly different survival rates. Moreover, the two-DNA methylation marker was suitable for patients of varying ages, sex, stages (I and IV), and histologic grade (G2). CONCLUSION The two-DNA methylation signature was deemed to be a potential novel prognostic biomarker of use in increasing the accuracy of predicting overall survival of ccRCC patients.
Collapse
Affiliation(s)
- Shanping Shi
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Shazhou Ye
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Xiaoyue Wu
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Mingjun Xu
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Renjie Zhuo
- Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Qi Liao
- Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Yang Xi
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, Zhejiang, China.
| |
Collapse
|
33
|
Silenced ZNF154 Is Associated with Longer Survival in Resectable Pancreatic Cancer. Int J Mol Sci 2019; 20:ijms20215437. [PMID: 31683647 PMCID: PMC6862440 DOI: 10.3390/ijms20215437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/23/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer has become the third leading cause of cancer-related death in the Western world despite advances in therapy of other cancerous lesions. Late diagnosis due to a lack of symptoms during early disease allows metastatic spread of the tumor. Most patients are considered incurable because of metastasized disease. On a cellular level, pancreatic cancer proves to be rather resistant to chemotherapy. Hence, early detection and new therapeutic targets might improve outcomes. The detection of DNA promoter hypermethylation has been described as a method to identify putative genes of interest in cancer entities. These genes might serve as either biomarkers or might lead to a better understanding of the molecular mechanisms involved. We checked tumor specimens from 80 patients who had undergone pancreatic resection for promoter hypermethylation of the zinc finger protein ZNF154. Then, we further characterized the effects of ZNF154 on cell viability and gene expression by in vitro experiments. We found a significant association between ZNF154 hypermethylation and better survival in patients with resectable pancreatic cancer. Moreover, we suspect that the cell growth suppressor SLFN5 might be linked to a silenced ZNF154 in pancreatic cancer.
Collapse
|
34
|
Agreda Castañeda F, Raventós Busquets C, Morote Robles J. Urinary markers in the surveillance of non-muscle invasive bladder cancer. A literature review. Actas Urol Esp 2019; 43:404-413. [PMID: 31097210 DOI: 10.1016/j.acuro.2019.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/13/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND The surveillance of non-muscle-invasive bladder cancer (NMIBC) is usually performed by cystoscopy and cytology. Until today, no effective urinary biomarker has been used to reduce the morbidity and cost associated with these procedures. OBJECTIVE To describe the performance of urinary biomarkers in the surveillance of NMIBC. EVIDENCE ACQUISITION on August 1, 2018, a bibliographic search was carried out in Pubmed, Embase and Cochrane Library, limited to the last 10 years, with the terms: bladder cancer, recurrence, detection and urine marker.973 registers were obtained, and 27 publications were selected following the PRISMA recommendations. EVIDENCE SYNTHESIS The negative predictive values (NPV) of several assays could reduce the number of cystoscopies in NMIBC surveillance. Six transcription-factor trials had an NPV rate greater than 90%, and one of them can be performed at the control point. Six transcription-factors evaluations describe anticipated diagnosis between 68% and 83% of their "false positives". Two transcription factors and one protein assays proved reduction between 23% and 35% of surveillance cystoscopies. Nowadays, cell-based assays are restricted to reflex test after doubtful cytologies. CONCLUSION There are few studies analysing the improvement of the NMIBC surveillance protocols. Several transcription factor assays are more precise and allow anticipatory diagnosis. Currently, there are no comparative studies between alternative surveillance protocols and classic ones.
Collapse
|
35
|
Hu J, Zhou L, Song Z, Xiong M, Zhang Y, Yang Y, Chen K, Chen Z. The identification of new biomarkers for bladder cancer: A study based on TCGA and GEO datasets. J Cell Physiol 2019; 234:15607-15618. [PMID: 30779109 DOI: 10.1002/jcp.28208] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Bladder cancer (BC) is one of the most common neoplastic diseases worldwide. With the highest recurrence rate among all cancers, treatment of BC only improved a little in the last 30 years. Available biomarkers are not sensitive enough for the diagnosis of BC, whereas the standard diagnostic method, cystoscopy, is an invasive test and expensive. Hence, seeking new biomarkers of BC is urgent and challenging. With that order, we screened the overlapped differentially expressed genes (DEGs) of GSE13507 and TCGA BLCA datasets. Subsequent protein-protein interactions network analysis recognized the hub genes among these DEGs. Further functional analysis including Gene Ontology and KEGG pathway analysis and gene set enrichment analysis were processed to investigate the role of these genes and potential underlying mechanisms in BC. Kaplan-Meier analysis and Cox hazard ratio analysis were carried out to clarify the diagnostic and prognostic role of these genes. In conclusion, our present study demonstrated that ACTA2, CDC20, MYH11, TGFB3, TPM1, VIM, and DCN are all potential diagnostic biomarkers for BC. And may also be potential treatment targets for clinical implication in the future.
Collapse
Affiliation(s)
- Junyi Hu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lijie Zhou
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhengshuai Song
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ming Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Youpeng Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yu Yang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ke Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhaohui Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| |
Collapse
|
36
|
Mishra NK, Southekal S, Guda C. Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma. Front Genet 2019; 10:624. [PMID: 31379917 PMCID: PMC6659773 DOI: 10.3389/fgene.2019.00624] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 06/14/2019] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common and among the deadliest of pancreatic cancers. Its 5-year survival is only ∼8%. Pancreatic cancers are a heterogeneous group of diseases, of which PDAC is particularly aggressive. Like many other cancers, PDAC also starts as a pre-invasive precursor lesion (known as pancreatic intraepithelial neoplasia, PanIN), which offers an opportunity for both early detection and early treatment. Even advanced PDAC can benefit from prognostic biomarkers. However, reliable biomarkers for early diagnosis or those for prognosis of therapy remain an unfulfilled goal for PDAC. In this study, we selected 153 PDAC patients from the TCGA database and used their clinical, DNA methylation, gene expression, and micro-RNA (miRNA) and long non-coding RNA (lncRNA) expression data for multi-omics analysis. Differential methylations at about 12,000 CpG sites were observed in PDAC tumor genomes, with about 61% of them hypermethylated, predominantly in the promoter regions and in CpG-islands. We correlated promoter methylation and gene expression for mRNAs and identified 17 genes that were previously recognized as PDAC biomarkers. Similarly, several genes (B3GNT3, DMBT1, DEPDC1B) and lncRNAs (PVT1, and GATA6-AS) are strongly correlated with survival, which have not been reported in PDAC before. Other genes such as EFR3B, whose biological roles are not well known in mammals are also found to strongly associated with survival. We further identified 406 promoter methylation target loci associated with patients survival, including known esophageal squamous cell carcinoma biomarkers, cg03234186 (ZNF154), and cg02587316, cg18630667, and cg05020604 (ZNF382). Overall, this is one of the first studies that identified survival associated genes using multi-omics data from PDAC patients.
Collapse
Affiliation(s)
- Nitish Kumar Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Siddesh Southekal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| |
Collapse
|
37
|
Larsen LK, Lind GE, Guldberg P, Dahl C. DNA-Methylation-Based Detection of Urological Cancer in Urine: Overview of Biomarkers and Considerations on Biomarker Design, Source of DNA, and Detection Technologies. Int J Mol Sci 2019; 20:ijms20112657. [PMID: 31151158 PMCID: PMC6600406 DOI: 10.3390/ijms20112657] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
Changes in DNA methylation have been causally linked with cancer and provide promising biomarkers for detection in biological fluids such as blood, urine, and saliva. The field has been fueled by genome-wide characterization of DNA methylation across cancer types as well as new technologies for sensitive detection of aberrantly methylated DNA molecules. For urological cancers, urine is in many situations the preferred "liquid biopsy" source because it contains exfoliated tumor cells and cell-free tumor DNA and can be obtained easily, noninvasively, and repeatedly. Here, we review recent advances made in the development of DNA-methylation-based biomarkers for detection of bladder, prostate, renal, and upper urinary tract cancers, with an emphasis on the performance characteristics of biomarkers in urine. For most biomarkers evaluated in independent studies, there was great variability in sensitivity and specificity. We discuss issues that impact the outcome of DNA-methylation-based detection of urological cancer and account for the great variability in performance, including genomic location of biomarkers, source of DNA, and technical issues related to the detection of rare aberrantly methylated DNA molecules. Finally, we discuss issues that remain to be addressed to fully exploit the potential of DNA-methylation-based biomarkers in the clinic, including the need for prospective trials and careful selection of control groups.
Collapse
Affiliation(s)
| | - Guro Elisabeth Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, NO-0424 Oslo, Norway.
| | - Per Guldberg
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
| | - Christina Dahl
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
| |
Collapse
|
38
|
Köhler CU, Bonberg N, Ahrens M, Behrens T, Hovanec J, Eisenacher M, Noldus J, Deix T, Braun K, Gohlke H, Walter M, Tannapfel A, Tam Y, Sommerer F, Marcus K, Jöckel KH, Erbel R, Cantor CR, Käfferlein HU, Brüning T. Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters. Int J Cancer 2019; 145:2861-2872. [PMID: 31008534 DOI: 10.1002/ijc.32356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Urothelial cancer (UCa) is the most predominant cancer of the urinary tract and noninvasive diagnosis using hypermethylation signatures in urinary cells is promising. Here, we assess gender differences in a newly identified set of methylation biomarkers. UCa-associated hypermethylated sites were identified in urine of a male screening cohort (n = 24) applying Infinium-450K-methylation arrays and verified in two separate mixed-gender study groups (n = 617 in total) using mass spectrometry as an independent technique. Additionally, tissue samples (n = 56) of mixed-gender UCa and urological controls (UCt) were analyzed. The hypermethylation signature of UCa in urine was specific and sensitive across all stages and grades of UCa and independent on hematuria. Individual CpG sensitivities reached up to 81.3% at 95% specificity. Albeit similar methylation differences in tissue of both genders, differences were less pronounced in urine from women, most likely due to the frequent presence of squamous epithelial cells and leukocytes. Increased repression of methylation levels was observed at leukocyte counts ≥500/μl urine which was apparent in 30% of female and 7% of male UCa cases, further confirming the significance of the relative amounts of cancerous and noncancerous cells in urine. Our study shows that gender difference is a most relevant issue when evaluating the performance of urinary biomarkers in cancer diagnostics. In case of UCa, the clinical benefits of methylation signatures to male patients may outweigh those in females due to the general composition of women's urine. Accordingly, these markers offer a diagnostic option specifically in males to decrease the number of invasive cystoscopies.
Collapse
Affiliation(s)
- Christina U Köhler
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Nadine Bonberg
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Maike Ahrens
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Thomas Behrens
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Jan Hovanec
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | | | - Joachim Noldus
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Thomas Deix
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Katharina Braun
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | | | - Michael Walter
- c.ATG Core Facility for NGS and Microarrays, University of Tübingen, Tübingen, Germany
| | - Andrea Tannapfel
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Yu Tam
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Florian Sommerer
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Katrin Marcus
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Charles R Cantor
- Department of Biomedical Engineering, School of Medicine, Boston University, Boston, MA
| | - Heiko U Käfferlein
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| |
Collapse
|
39
|
Wasenang W, Chaiyarit P, Proungvitaya S, Limpaiboon T. Serum cell-free DNA methylation of OPCML and HOXD9 as a biomarker that may aid in differential diagnosis between cholangiocarcinoma and other biliary diseases. Clin Epigenetics 2019; 11:39. [PMID: 30832707 PMCID: PMC6399934 DOI: 10.1186/s13148-019-0634-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is a fatal cancer of the bile duct epithelial cell lining. The misdiagnosis of CCA and other biliary diseases may occur due to the similarity of clinical manifestations and blood tests resulting in inappropriate or delayed treatment. Thus, an accurate and less-invasive method for differentiating CCA from other biliary diseases is inevitable. METHODS We quantified methylation of OPCML, HOXA9, and HOXD9 in serum cell-free DNA (cfDNA) of CCA patients and other biliary diseases using methylation-sensitive high-resolution melting (MS-HRM). Their potency as differential biomarkers between CCA and other biliary diseases was also evaluated by using receiver operating characteristic (ROC) curves. RESULTS The significant difference of methylation levels of OPCML and HOXD9 was observed in serum cfDNA of CCA compared to other biliary diseases. Assessment of serum cfDNA methylation of OPCML and HOXD9 as differential biomarkers of CCA and other biliary diseases showed the area under curve (AUC) of 0.850 (0.759-0.941) for OPCML which sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy were 80.00%, 90.00%, 88.88%, 81.81%, and 85.00%, respectively. The AUC of HOXD9 was 0.789 (0.686-0.892) with sensitivity, specificity, PPV, NPV, and accuracy of 67.50%, 90.00%, 87.09%, 73.46%, and 78.75%, respectively. The combined marker between OPCML and HOXD9 showed sensitivity, specificity, PPV, and NPV of 62.50%, 100%, 100%, and 72.72%, respectively, which may be helpful to prevent a misdiagnosis between CCA and other biliary diseases. CONCLUSIONS Our findings suggest the application of serum cfDNA methylation of OPCML and HOXD9 for differential diagnosis of CCA and other biliary diseases due to its less invasiveness and clinically practical method which may benefit the patients by preventing the misdiagnosis of CCA and avoiding unnecessary surgical intervention.
Collapse
Affiliation(s)
- Wiphawan Wasenang
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Biomedical Sciences, Graduate School, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Ponlatham Chaiyarit
- Research Group of Chronic Inflammatory Oral Diseases and Systemic Diseases Associated with Oral Health, Department of Oral Diagnosis, Faculty of Dentistry, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Siriporn Proungvitaya
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Temduang Limpaiboon
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| |
Collapse
|
40
|
Rink M, Schwarzenbach H, Vetterlein MW, Riethdorf S, Soave A. The current role of circulating biomarkers in non-muscle invasive bladder cancer. Transl Androl Urol 2019; 8:61-75. [PMID: 30976570 PMCID: PMC6414344 DOI: 10.21037/tau.2018.11.05] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Non-muscle invasive bladder cancer (NMIBC) is characterized by its high rate of disease recurrence and relevant disease progression rates. Up to today clinical models are insufficiently predicting outcomes for reliable patient counseling and treatment decision-making. This particularly is a serious problem in patients with high-risk NMIBC who are at high risk for failure of local treatment and thus candidates for early radical cystectomy or even systemic (neoadjuvant) chemotherapy. Next to its clinical variability, bladder cancer is genetically a highly heterogeneous disease. There is an essential need of biomarkers for improving clinical staging, real-time monitoring of disease with or without active treatment, as well as improved outcome prognostication. Liquid biopsies of circulating biomarkers in the blood and urine are promising non-invasive diagnostics that hold the potential facilitating these needs. In this review we report the latest data and evidence on cell-free circulating tumor desoxyribonucleic acid (ctDNA) and circulating tumor cells (CTC) in NMIBC. We summarize their current status in clinical diagnostics, discuss limitations and address future needs.
Collapse
Affiliation(s)
- Michael Rink
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Heidi Schwarzenbach
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte W Vetterlein
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sabine Riethdorf
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Armin Soave
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
41
|
Wu Y, Jiang G, Zhang N, Liu S, Lin X, Perschon C, Zheng SL, Ding Q, Wang X, Na R, Sun J, Xu J. HOXA9, PCDH17, POU4F2, and ONECUT2 as a Urinary Biomarker Combination for the Detection of Bladder Cancer in Chinese Patients with Hematuria. Eur Urol Focus 2018; 6:284-291. [PMID: 30309818 DOI: 10.1016/j.euf.2018.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/12/2018] [Accepted: 09/28/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND DNA methylation biomarkers for bladder cancer (BCa) have not been evaluated extensively in the Chinese population. OBJECTIVE To develop and validate a urinary biomarker combination of methylation assays in a group of Chinese patients with hematuria. DESIGN, SETTING, AND PARTICIPANTS A total of 192 urine samples were collected and evaluated from patients with microscopic or gross hematuria, including 97 BCa patients and 95 controls with benign diseases. A two-stage study was conducted: the first stage being assay construction and the second stage being assay validation. Eighty-one urine samples were analyzed for the hypermethylation of eight selected genes in stage 1 and then a four-gene panel was constructed. An additional 111 urine samples were analyzed using the four-gene panel (including HOXA9, PCDH17, POU4F2, and ONECUT2) for independent validation. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The positive predictive value (PPV) and negative predictive value (NPV) were calculated for the combination methylation assay. Uni- and multivariate binary logistic regression analyses (backward elimination, conditional) were performed to calculate the association between BCa and each predictor variable. RESULTS AND LIMITATIONS The combination assay of HOXA9, PCDH17, POU4F2, and ONECUT2 was selected based on the results of multivariate logistic regression analysis in stage 1. Using a strategy of three-level risk stratification, the assay yielded a consistent PPV of 100%. With an estimated BCa prevalence of 10% in a general hematuria population, the assay would result in an overall NPV of 98%. This combined methylation biomarker would yield an overall area under the receiver operating characteristic curve of 0.871 (with a sensitivity of 90.5% and a specificity of 73.2%) if using the prediction model from multivariate regression analysis. In addition, over half of BCa cases would be predicted accurately and ∼60% of unnecessary cystoscopies could be spared. This study had several limitations. First, the sample size was relatively small. Second, it was performed in a case-control population rather than in a natural hematuria cohort. CONCLUSIONS A combination methylation assay of HOXA9, PCDH17, POU4F2, and ONECUT2 resulted in high PPV and NPV in Chinese patients with hematuria. With accurate risk prediction, the urinary biomarker combination could spare a sizeable proportion of low-risk patients from extensive and invasive examination. PATIENT SUMMARY In the present study, we looked at the predictive performance of a urinary biomarker combination of HOXA9, PCDH17, POU4F2, and ONECUT2. We found that this urinary biomarker combination may help discriminate bladder cancer from other benign diseases in patients with hematuria, resulting in a reduction of unnecessary invasive examination in patients at low risk.
Collapse
Affiliation(s)
- Yishuo Wu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Guangliang Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, PR China
| | - Ning Zhang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Shenghua Liu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Xiaoling Lin
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Qiang Ding
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Xiang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Rong Na
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China.
| | - Jishan Sun
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA.
| | - Jianfeng Xu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA.
| |
Collapse
|
42
|
Wang C, Pu W, Zhao D, Zhou Y, Lu T, Chen S, He Z, Feng X, Wang Y, Li C, Li S, Jin L, Guo S, Wang J, Wang M. Identification of Hyper-Methylated Tumor Suppressor Genes-Based Diagnostic Panel for Esophageal Squamous Cell Carcinoma (ESCC) in a Chinese Han Population. Front Genet 2018; 9:356. [PMID: 30233644 PMCID: PMC6133993 DOI: 10.3389/fgene.2018.00356] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/20/2018] [Indexed: 12/22/2022] Open
Abstract
DNA methylation-based biomarkers were suggested to be promising for early cancer diagnosis. However, DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC), especially in Chinese Han populations have not been identified and evaluated quantitatively. Candidate tumor suppressor genes (N = 65) were selected through literature searching and four public high-throughput DNA methylation microarray datasets including 136 samples totally were collected for initial confirmation. Targeted bisulfite sequencing was applied in an independent cohort of 94 pairs of ESCC and normal tissues from a Chinese Han population for eventual validation. We applied nine different classification algorithms for the prediction to evaluate to the prediction performance. ADHFE1, EOMES, SALL1 and TFPI2 were identified and validated in the ESCC samples from a Chinese Han population. All four candidate regions were validated to be significantly hyper-methylated in ESCC samples through Wilcoxon rank-sum test (ADHFE1, P = 1.7 × 10-3; EOMES, P = 2.9 × 10-9; SALL1, P = 3.9 × 10-7; TFPI2, p = 3.4 × 10-6). Logistic regression based prediction model shown a moderately ESCC classification performance (Sensitivity = 66%, Specificity = 87%, AUC = 0.81). Moreover, advanced classification method had better performances (random forest and naive Bayes). Interestingly, the diagnostic performance could be improved in non-alcohol use subgroup (AUC = 0.84). In conclusion, our data demonstrate the methylation panel of ADHFE1, EOMES, SALL1 and TFPI2 could be an effective methylation-based diagnostic assay for ESCC.
Collapse
Affiliation(s)
- Chenji Wang
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, China
| | - Weilin Pu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Dunmei Zhao
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, China
| | - Yinghui Zhou
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, China
| | - Ting Lu
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, China
| | - Sidi Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhenglei He
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, China
| | - Xulong Feng
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, China
| | - Ying Wang
- Genesky Biotechnologies Inc., Shanghai, China
| | - Caihua Li
- Genesky Biotechnologies Inc., Shanghai, China
| | - Shilin Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Shicheng Guo
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Minghua Wang
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, China
| |
Collapse
|
43
|
Lissa D, Ishigame T, Noro R, Tucker MJ, Bliskovsky V, Shema S, Beck JA, Bowman ED, Harris CC, Robles AI. HOXA9 methylation and blood vessel invasion in FFPE tissues for prognostic stratification of stage I lung adenocarcinoma patients. Lung Cancer 2018; 122:151-159. [PMID: 30032824 PMCID: PMC6662588 DOI: 10.1016/j.lungcan.2018.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/15/2018] [Accepted: 05/21/2018] [Indexed: 01/11/2023]
Abstract
OBJECTIVES Surgery with curative intent is the standard treatment for stage I lung adenocarcinoma. However, disease recurrence occurs in a third of patients. Prognostic biomarkers are needed to improve postoperative management. Here, we evaluate the utility of Homeobox A9 (HOXA9) promoter methylation, alone or in combination with Blood Vessel Invasion (BVI) assessment, for prognostic stratification of stage I lung adenocarcinoma patients. MATERIALS AND METHODS We developed a Droplet Digital PCR (ddPCR) assay to measure HOXA9 promoter methylation in formalin-fixed paraffin-embedded (FFPE) biospecimens generated during routine pathology. The prognostic value of HOXA9 promoter methylation and BVI, alone and in combination, was evaluated by Kaplan-Meier survival and Cox regression analyses in a cohort of 177 stage I lung adenocarcinoma patients from the NCI-MD study. RESULTS The ddPCR assay showed linearity, sensitivity and specificity for measuring HOXA9 promoter methylation down to 0.1% methylated DNA input. The HOXA9 promoter was methylated de novo in FFPE tumors (P < 0.0001). High methylation was independently associated with worse cancer-specific survival (Hazard Ratio [HR], 3.37; P = 0.0002) and identified high-risk stage IA and IB patients. Addition of this molecular marker improved a risk model comprised of clinical and pathologic parameters (age, gender, race, stage, and smoking history; nested likelihood ratio test; P = 0.0004) and increased the C-index from 0.60 (95% CI 0.51-0.69) to 0.68 (0.60-0.76). High methylation tumors displayed high frequency of TP53 mutations and other molecular characteristics associated with aggressiveness. BVI was independently associated with poor outcome (HR, 2.62; P = 0.054). A score that combined BVI with HOXA9 promoter methylation further stratified high-risk patients (trend P = 0.0001 comparing 0, 1 or 2 positive markers). CONCLUSIONS ddPCR can be used to quantify HOXA9 promoter methylation in FFPE samples. Alone or combined with BVI in a prognostic classifier, HOXA9 promoter methylation could potentially inform the clinical management of patients with early-stage lung adenocarcinoma.
Collapse
Affiliation(s)
- Delphine Lissa
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Teruhide Ishigame
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Rintaro Noro
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Marguerite J Tucker
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Valery Bliskovsky
- CCR Genomics Core, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Steven Shema
- CCR Genomics Core, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jessica A Beck
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
44
|
Bosschieter J, Lutz C, Segerink LI, Vis AN, Zwarthoff EC, A van Moorselaar RJ, van Rhijn BWG, Heymans MW, Jansma EP, Steenbergen RDM, Nieuwenhuijzen JA. The diagnostic accuracy of methylation markers in urine for the detection of bladder cancer: a systematic review. Epigenomics 2018; 10:673-687. [DOI: 10.2217/epi-2017-0156] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aim: Several urinary hypermethylation-markers (hmDNA) have been described for bladder cancer (BC) detection, but none have been able to replace cystoscopy yet. We systematically reviewed and evaluated current literature on urinary hmDNA markers for BC diagnostics. Patients & methods: A systematic search of PubMed, EMBASE.com and The Cochrane Library up to February 2017 using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines, was conducted. Results: A total of 30/42 studies included compared gene panels, with varying sensitivities (52–100%) and specificities (0–100%). Considerable heterogeneity across studies was observed and most was case–control studies. Conclusion: Reported diagnostic accuracy of urinary hmDNA for BC detection is highly variable and there is a lack of validation studies. Recent studies indicate that complementary markers are needed to allow for clinical implementation.
Collapse
Affiliation(s)
- Judith Bosschieter
- Department of Urology, VU University Medical Center, Amsterdam, The Netherlands
| | - Catrin Lutz
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Loes I Segerink
- BIOS Lab on a Chip group, MESA+ & MIRA institutes, University of Twente, Enschede, The Netherlands
| | - André N Vis
- Department of Urology, VU University Medical Center, Amsterdam, The Netherlands
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Bas WG van Rhijn
- Department of Urology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martijn W Heymans
- Department of Epidemiology & Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Elizabeth P Jansma
- Medical Library, VU University Medical Center, Amsterdam, The Netherlands
| | | | | |
Collapse
|
45
|
García-Giménez JL, Seco-Cervera M, Tollefsbol TO, Romá-Mateo C, Peiró-Chova L, Lapunzina P, Pallardó FV. Epigenetic biomarkers: Current strategies and future challenges for their use in the clinical laboratory. Crit Rev Clin Lab Sci 2017; 54:529-550. [PMID: 29226748 DOI: 10.1080/10408363.2017.1410520] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetic modifications and regulators represent potential molecular elements which control relevant physiological and pathological features, thereby contributing to the natural history of human disease. These epigenetic modulators can be employed as disease biomarkers, since they show several advantages and provide information about gene function, thus explaining differences among patient endophenotypes. In addition, epigenetic biomarkers can incorporate information regarding the effects of the environment and lifestyle on health and disease, and monitor the effect of applied therapies. Technologies used to analyze these epigenetic biomarkers are constantly improving, becoming much easier to use. Laboratory professionals can easily acquire experience and techniques are becoming more affordable. A high number of epigenetic biomarker candidates are being continuously proposed, making now the moment to adopt epigenetics in the clinical laboratory and convert epigenetic marks into reliable biomarkers. In this review, we describe some current promising epigenetic biomarkers and technologies being applied in clinical practice. Furthermore, we will discuss some laboratory strategies and kits to accelerate the adoption of epigenetic biomarkers into clinical routine. The likelihood is that over time, better markers will be identified and will likely be incorporated into future multi-target assays that might help to optimize its application in a clinical laboratory. This will improve cost-effectiveness, and consequently encourage the development of theragnosis and the application of precision medicine.
Collapse
Affiliation(s)
- José Luis García-Giménez
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain.,e EpiDisease S.L. Spin-Off of CIBERER (ISCIII) , Valencia , Spain
| | - Marta Seco-Cervera
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain
| | - Trygve O Tollefsbol
- f Department of Biology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Carlos Romá-Mateo
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain
| | - Lorena Peiró-Chova
- b INCLIVA Biomedical Research Institute , Valencia , Spain.,g INCLIVA Biobank , Valencia , Spain
| | - Pablo Lapunzina
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,h Institute of Medical and Molecular Genetics (INGEMM) , IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid , Madrid , Spain
| | - Federico V Pallardó
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain
| |
Collapse
|
46
|
Shindo T, Shimizu T, Nojima M, Niinuma T, Maruyama R, Kitajima H, Kai M, Itoh N, Suzuki H, Masumori N. Evaluation of Urinary DNA Methylation as a Marker for Recurrent Bladder Cancer: A 2-Center Prospective Study. Urology 2017; 113:71-78. [PMID: 29196070 DOI: 10.1016/j.urology.2017.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 11/08/2017] [Accepted: 11/14/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVE To clarify the clinical utility of urinary DNA methylation for detection of intravesical recurrence of non-muscle invasive BCa (NMIBC), we performed a 2-center prospective study. PATIENTS AND METHODS A series of 207 self-voided urine samples were prospectively collected from 132 patients with NMIBC who had undergone transurethral resection of BCa. Methylation of miRNA genes (miR-9-3, miR-124-2, miR-124-3, and miR-137) was analyzed using bisulfite pyrosequencing. The primary end point was detection of intravesical recurrence; the secondary end point was prediction of late recurrence. The number of methylated genes (M-score) or quantitative level of methylation were compared with outcomes. RESULTS Twenty-six urine specimens were collected on the same day intravesical recurrence was detected, and 14 were collected from patients whose recurrences were found during the subsequent follow-up period (0-632 days, mean, 342.2 days). For detection of current recurrence, M-scores achieved 61.5% sensitivity and 74.0% specificity, and the area under the ROC curve was 0.71. Regarding prediction of late recurrence, patients with a high M-score (≥3) showed worse recurrence-free survival (P <.01). Multivariate analysis revealed that high M-scores were independently associated with current (P = .028) and late recurrence (P = .026). Elevated levels of urinary DNA methylation were also strongly associated with recurrence and radical cystectomy. CONCLUSION Our data suggest that urinary methylation of miRNA genes may be a useful marker for detecting and predicting BCa recurrence.
Collapse
Affiliation(s)
- Tetsuya Shindo
- Department of Urology, Sapporo Medical University School of Medicine, Sapporo, Japan; Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takashi Shimizu
- Department of Urology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masanori Nojima
- Center for Translational Research, The Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| | - Takeshi Niinuma
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Reo Maruyama
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Kitajima
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masahiro Kai
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Naoki Itoh
- Department of Urology, NTT East Corporation Sapporo Hospital, Sapporo, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan.
| | - Naoya Masumori
- Department of Urology, Sapporo Medical University School of Medicine, Sapporo, Japan
| |
Collapse
|
47
|
Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
Collapse
Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| |
Collapse
|
48
|
Ma YY, Zhang Y, Mou XZ, Liu ZC, Ru GQ, Li E. High level of homeobox A9 and PBX homeobox 3 expression in gastric cancer correlates with poor prognosis. Oncol Lett 2017; 14:5883-5889. [PMID: 29113222 PMCID: PMC5661400 DOI: 10.3892/ol.2017.6937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/28/2017] [Indexed: 01/12/2023] Open
Abstract
The homeobox protein homeobox (HOXA9) is a transcriptional factor that regulates patterning during embryogenesis and controls cell differentiation. HOXA9 dysfunction has been implicated in certain cancers. However, the role of HOXA9 in gastric cancer is poorly understood. The present study investigated HOXA9 and its cofactor PBX homeobox 3 (PBX3) expression in patients with gastric cancer. Paired tissue samples from 24 patients and paraffin embedded tissues of gastric cancer patients (104 males and 24 females) were included. HOXA9 and PBX3 expression levels were determined by reverse transcription quantitative polymerase chain reaction in fresh tissues, and by immunohistochemical staining in paraffin embedded tissues. The association between HOXA9/PBX3 expression and clinicopathological features was established. The results demonstrated that HOXA9 and PBX3 mRNA levels were significantly upregulated (P=0.032 for HOXA9 and P=0.031 for PBX3) in gastric cancer tissue. Immunohistochemical staining revealed that HOXA9 expression was associated with differentiation, lymph node metastasis and tumor-node-metastasis (TNM) stage, and PBX3 expression was associated with lymph node metastasis and TNM stage. Correlation analysis revealed a high coincidental expression of HOXA9 and PBX3 levels in gastric cancer (r=0.391; P<0.001). Survival analysis showed that high expression of HOXA9 or PBX3 was associated with poor survival of gastric cancer, and multivariate analysis using Cox's regression model showed that PBX3 expression was an independent prognostic factor in gastric cancer. There was elevated expression of HOXA9 and PBX3 in gastric cancer patients, and high-level expression of those proteins was associated with poor prognosis of gastric cancer. The present study underlines the significance of HOXA9/PBX3 in the development of gastric cancer.
Collapse
Affiliation(s)
- Ying-Yu Ma
- Medical School and Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Yuancheng Zhang
- Medical School and Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Xiao-Zhou Mou
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Zheng-Chuang Liu
- Key Laboratory of Gastroenterology of Zhejiang, Hangzhou, Zhejiang 310014, P.R. China
| | - Guo-Qing Ru
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Erguang Li
- Medical School and Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| |
Collapse
|
49
|
Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya, North East India reveals novel genes. Genomics 2017; 110:112-123. [PMID: 28890207 DOI: 10.1016/j.ygeno.2017.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/22/2022]
Abstract
Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.
Collapse
|
50
|
Peng M, Chen C, Hulbert A, Brock MV, Yu F. Non-blood circulating tumor DNA detection in cancer. Oncotarget 2017; 8:69162-69173. [PMID: 28978187 PMCID: PMC5620327 DOI: 10.18632/oncotarget.19942] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023] Open
Abstract
Tumor DNA contains specific somatic alterations that are crucial for the diagnosis and treatment of cancer. Due to the spatial and temporal intra-tumor heterogeneity, multi-sampling is needed to adequately characterize the somatic alterations. Tissue biopsy, however, is limited by the restricted access to sample and the challenges to recapitulate the tumor clonal diversity. Non-blood circulating tumor DNA are tumor DNA fragments presents in non-blood body fluids, such as urine, saliva, sputum, stool, pleural fluid, and cerebrospinal fluid (CSF). Recent studies have demonstrated the presence of tumor DNA in these non-blood body fluids and their application to the diagnosis, screening, and monitoring of cancers. Non-blood circulating tumor DNA has an enormous potential for large-scale screening of local neoplasms because of its non-invasive nature, close proximity to the tumors, easiness and it is an economically viable option. It permits longitudinal assessments and allows sequential monitoring of response and progression. Enrichment of tumor DNA of local cancers in non-blood body fluids may help to archive a higher sensitivity than in plasma ctDNA. The direct contact of cancerous cells and body fluid may facilitate the detection of tumor DNA. Furthermore, normal DNA always dilutes the plasma ctDNA, which may be aggravated by inflammation and injury when very high amounts of normal DNA are released into the circulation. Altogether, our review indicate that non-blood circulating tumor DNA presents an option where the disease can be tracked in a simple and less-invasive manner, allowing for serial sampling informing of the tumor heterogeneity and response to treatment.
Collapse
Affiliation(s)
- Muyun Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| | - Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| | - Alicia Hulbert
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Malcolm V Brock
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| |
Collapse
|