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Malalasekera AP, Neththikumara N, Somasundaram P, Pathirana S, Ediriweera C, Ediriweera D, Goonewardena SAS, Perera ND, Abeygunasekara A, Jayasekara RW, Wettasinghe K, Lokuhetty MDS, Dissanayake VHW. Clinical Exome Gene Panel Analysis of a Cohort of Urothelial Bladder Cancer Patients from Sri Lanka. Asian Pac J Cancer Prev 2023; 24:1533-1542. [PMID: 37247272 PMCID: PMC10495915 DOI: 10.31557/apjcp.2023.24.5.1533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Bladder cancer has a high rate of recurrence and high mortality rates in those who progress to muscle invasive disease. Biomarkers and molecular sub classification of tumours beyond standard histopathology has been proposed to address therapeutic dilemmas. The Cancer Genome Atlas project and other studies have contributed to the enhanced knowledge base of the mutational landscape of urothelial bladder cancer. Once again, these are mostly from Caucasian and Chinese patients, with data from the rest of Asia and Sri Lanka being sparse. The objective of this study was to assess the genomic variations of a cohort of urothelial bladder cancer patients in Sri Lanka. METHODS The molecular genetic study was conducted on formalin fixed paraffin embedded tumour samples of 24 patients, prospectively enrolled from 2013 to 2017. The samples were sequenced and variant distribution performed based on a 70-gene panel. RESULTS Total number of filtered mutations in the 24 patients was 10453. Median mutations per patient were 450 (range 22-987). The predominant mutational change was C>T and G>A. The top 5 mutated genes in our cohort were SYNE1, SYNE2, KMT2C, LRP2, and ANK2. The genes were clustered into 3 groups dependent on the number of mutations per patient per gene. The genes of cluster 1 and 2 mapped to Chromatin modifying enzymes and Generic Transcription Pathway. The chromatin remodelling pathway accounted for the largest proportion (22%) of mutations. CONCLUSIONS Clinical exome sequencing utilising a gene panel yielded a high mutation rate in our patients. The predominant mutational change was C>T and G>A. Three clusters of genes were identified. SYNE1 was the gene with the most mutations. The mutations comprised predominantly of genes of the chromatin remodelling pathway.
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Affiliation(s)
- Ajith P Malalasekera
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
| | - Nilaksha Neththikumara
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
| | - Praveenan Somasundaram
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
| | - Sajeewani Pathirana
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
| | | | - Dileepa Ediriweera
- Health Data Science Unit, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.
| | | | - Neville D Perera
- Department of Urology, National Hospital of Sri Lanka, Colombo, Sri Lanka.
| | | | - Rohan W Jayasekara
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
| | - Kalum Wettasinghe
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
| | - M Dilani S Lokuhetty
- Department of Pathology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
| | - Vajira H W Dissanayake
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
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Liu F, Wang Y, Gu H, Wang X. Technologies and applications of single-cell DNA methylation sequencing. Theranostics 2023; 13:2439-2454. [PMID: 37215576 PMCID: PMC10196823 DOI: 10.7150/thno.82582] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/09/2023] [Indexed: 05/24/2023] Open
Abstract
DNA methylation is the most stable epigenetic modification. In mammals, it usually occurs at the cytosine of CpG dinucleotides. DNA methylation is essential for many physiological and pathological processes. Aberrant DNA methylation has been observed in human diseases, particularly cancer. Notably, conventional DNA methylation profiling technologies require a large amount of DNA, often from a heterogeneous cell population, and provide an average methylation level of many cells. It is often not realistic to collect sufficient numbers of cells, such as rare cells and circulating tumor cells in peripheral blood, for bulk sequencing assays. It is therefore essential to develop sequencing technologies that can accurately profile DNA methylation using small numbers of cells or even single cells. Excitingly, many single-cell DNA methylation sequencing and single-cell omics sequencing technologies have been developed, and applications of these methods have greatly expanded our understanding of the molecular mechanism of DNA methylation. Here, we summaries single-cell DNA methylation and multi-omics sequencing methods, delineate their applications in biomedical sciences, discuss technical challenges, and present our perspective on future research directions.
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Affiliation(s)
- Fang Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230026, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou, 310000, China
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230026, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Xiaoxue Wang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, 110001, China
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Li S, Xin K, Pan S, Wang Y, Zheng J, Li Z, Liu X, Liu B, Xu Z, Chen X. Blood-based liquid biopsy: insights into early detection, prediction, and treatment monitoring of bladder cancer. Cell Mol Biol Lett 2023; 28:28. [PMID: 37016296 PMCID: PMC10074703 DOI: 10.1186/s11658-023-00442-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Bladder cancer (BC) is a clinical challenge worldwide with late clinical presentation, poor prognosis, and low survival rates. Traditional cystoscopy and tissue biopsy are routine methods for the diagnosis, prognosis, and monitoring of BC. However, due to the heterogeneity and limitations of tumors, such as aggressiveness, high cost, and limited applicability of longitudinal surveillance, the identification of tumor markers has attracted significant attention in BC. Over the past decade, liquid biopsies (e.g., blood) have proven to be highly efficient methods for the discovery of BC biomarkers. This noninvasive sampling method is used to analyze unique tumor components released into the peripheral circulation and allows serial sampling and longitudinal monitoring of tumor progression. Several liquid biopsy biomarkers are being extensively studied and have shown promising results in clinical applications of BC, including early detection, detection of microscopic residual disease, prediction of recurrence, and response to therapy. Therefore, in this review, we aim to provide an update on various novel blood-based liquid biopsy markers and review the advantages and current limitations of liquid biopsy in BC therapy. The role of blood-based circulating tumor cells, circulating tumor DNA, cell-free RNA, exosomes, metabolomics, and proteomics in diagnosis, prognosis, and treatment monitoring, and their applicability to the personalized management of BC, are highlighted.
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Affiliation(s)
- Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Kerong Xin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Shen Pan
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yang Wang
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, Liaoning, People's Republic of China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Xuefeng Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Bitian Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
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Couto-Cunha A, Jerónimo C, Henrique R. Circulating Tumor Cells as Biomarkers for Renal Cell Carcinoma: Ready for Prime Time? Cancers (Basel) 2022; 15:cancers15010287. [PMID: 36612281 PMCID: PMC9818240 DOI: 10.3390/cancers15010287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
Renal cell carcinoma (RCC) is among the 15 most common cancers worldwide, with rising incidence. In most cases, this is a silent disease until it reaches advance stages, demanding new effective biomarkers in all domains, from detection to post-therapy monitoring. Circulating tumor cells (CTC) have the potential to provide minimally invasive information to guide assessment of the disease's aggressiveness and therapeutic strategy, representing a special pool of neoplastic cells which bear metastatic potential. In some tumor models, CTCs' enumeration has been associated with prognosis, but there is a largely unexplored potential for clinical applicability encompassing screening, diagnosis, early detection of metastases, prognosis, response to therapy and monitoring. Nonetheless, lack of standardization and high cost hinder the translation into clinical practice. Thus, new methods for collection and analysis (genomic, proteomic, transcriptomic, epigenomic and metabolomic) are needed to ascertain the role of CTC as a RCC biomarker. Herein, we provide a critical overview of the most recently published data on the role and clinical potential of CTCs in RCC, addressing their biology and the molecular characterization of this remarkable set of tumor cells. Furthermore, we highlight the existing and emerging techniques for CTC enrichment and detection, exploring clinical applications in RCC. Notwithstanding the notable progress in recent years, the use of CTCs in a routine clinical scenario of RCC patients requires further research and technological development, enabling multimodal analysis to take advantage of the wealth of information they provide.
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Affiliation(s)
- Anabela Couto-Cunha
- Integrated Master in Medicine, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Department of Pathology & Cancer Biology & Epigenetics Group—Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Centre Raquel Seruca (P.CCC Raquel Seruca), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Rui Henrique
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Department of Pathology & Cancer Biology & Epigenetics Group—Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Centre Raquel Seruca (P.CCC Raquel Seruca), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Correspondence: or
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Amantini C, Maggi F, Rossi de Vermandois JA, Gubbiotti M, Giannantoni A, Mearini E, Nabissi M, Tomassoni D, Santoni G, Morelli MB. The Prognostic Value of the Circulating Tumor Cell-Based Four mRNA Scoring System: A New Non-Invasive Setting for the Management of Bladder Cancer. Cancers (Basel) 2022; 14:3118. [PMID: 35804889 PMCID: PMC9264990 DOI: 10.3390/cancers14133118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/10/2022] Open
Abstract
Bladder cancer (BC) is one of the most expensive lifetime cancers to treat because of the high recurrence rate, repeated surgeries, and long-term cystoscopy monitoring and treatment. The lack of an accurate classification system predicting the risk of recurrence or progression leads to the search for new biomarkers and strategies. Our pilot study aimed to identify a prognostic gene signature in circulating tumor cells (CTCs) isolated by ScreenCell devices from muscle invasive and non-muscle invasive BC patients. Through the PubMed database and Cancer Genome Atlas dataset, a panel of 15 genes modulated in BC with respect to normal tissues was selected. Their expression was evaluated in CTCs and thanks to the univariate and multivariate Cox regression analysis, EGFR, TRPM4, TWIST1, and ZEB1 were recognized as prognostic biomarkers. Thereafter, by using the risk score model, we demonstrated that this 4-gene signature significantly grouped patients into high- and low-risk in terms of recurrence free survival (HR = 2.704, 95% CI = 1.010−7.313, Log-rank p < 0.050). Overall, we identified a new prognostic signature that directly impacted the prediction of recurrence, improving the choice of the best treatment for BC patients.
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Affiliation(s)
- Consuelo Amantini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (F.M.); (D.T.)
| | - Federica Maggi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (F.M.); (D.T.)
| | | | | | - Antonella Giannantoni
- Department of Medical and Surgical Sciences, University of Siena, 53100 Siena, Italy;
- Neurosciences, Functional and Surgical Urology Unit, Santa Maria alle Scotte Hospital, 53100 Siena, Italy
| | - Ettore Mearini
- Urologic and Andrologic Clinics, University of Perugia, 05100 Perugia, Italy; (J.A.R.d.V.); (E.M.)
| | - Massimo Nabissi
- School of Pharmacy, University of Camerino, 62032 Camerino, Italy; (M.N.); (G.S.)
| | - Daniele Tomassoni
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (F.M.); (D.T.)
| | - Giorgio Santoni
- School of Pharmacy, University of Camerino, 62032 Camerino, Italy; (M.N.); (G.S.)
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Song JW, Suh J, Lee SW, Yoo JK, Lee U, Han JH, Kwak C, Kang M, Kim YR, Jeong CW, Choi JW. Isolation and Genomic Analysis of Single Circulating Tumor Cell Using Human Telomerase Reverse Transcriptase and Desmoglein-2. SMALL METHODS 2022; 6:e2100938. [PMID: 35038250 DOI: 10.1002/smtd.202100938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/06/2021] [Indexed: 06/14/2023]
Abstract
As epithelial cells in the circulation are considered to originate from the tumor, the epithelial cell adhesion molecule has been commonly used as a standard marker for circulating tumor cells (CTCs) isolation. However, it seems to disappear after the epithelial-mesenchymal transition that most cancer cells undergo for intravasation. Thus, more advanced techniques for CTC detection are needed to better understand the clinical significance of CTCs. A cancer cell-specifically-infecting or replicating virus that codes a fluorescent monitor gene can be a solution to efficiently detect CTCs. Thus, the authors designed an adenovirus to bind to desmoglein-2, which is highly expressed in most cancer cells. A cancer-specific human telomerase reverse transcriptase promoter is inserted to control a viral E1 region. The adenovirus is utilized to compare the number of CTCs from renal cell carcinoma and prostate cancer patients before and after surgery. The isolated two or three CTCs are eligible for whole genome sequencing. The genomic analysis proves the difference of variants between primary tumors and CTCs. Taken together, it is a fast and exact serial method for CTC isolation and the enriched genome sequencing may be used to determine the prognosis and as a point-of-care system for patients with cancer.
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Affiliation(s)
- Jae Won Song
- Department of Pharmacy and Department of Regulatory Science, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jungyo Suh
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Seok Won Lee
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jung Ki Yoo
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
- Research Center of Curigin Ltd., Seoul, 04778, Republic of Korea
| | - Uijeong Lee
- Artificial Intelligence Laboratory of Oncocross Ltd., Seoul, 04168, Republic of Korea
| | - Jang Hee Han
- Department of Urology, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Cheol Kwak
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Minyong Kang
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Department of Health Sciences and Technology SAIHST Sungkyunkwan University
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Yi Rang Kim
- Artificial Intelligence Laboratory of Oncocross Ltd., Seoul, 04168, Republic of Korea
| | - Chang Wook Jeong
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jin Woo Choi
- Department of Pharmacy and Department of Regulatory Science, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
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