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Kaur P, Nazeer N, Gurjar V, Tiwari R, Mishra PK. Nanophotonic waveguide-based sensing of circulating cell-free mitochondrial DNA: implications for personalized medicine. Drug Discov Today 2024; 29:104086. [PMID: 38960132 DOI: 10.1016/j.drudis.2024.104086] [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: 11/30/2023] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Circulating cell-free mitochondrial DNA (ccf-mtDNA) has emerged as a promising biomarker, with potential implications for disease diagnosis. Changes in mtDNA, such as deletions, mutations or variations in the number of copies, have been associated with mitochondrial disorders, heart diseases, cancer and age-related non-communicable diseases. Previous methods, such as polymerase chain reaction-based approaches, next-generation sequencing and imaging-based techniques, have shown improved accuracy in identifying rare mtDNA variants or mutations, but they have limitations. This article explains the basic principles and benefits of using planar optical waveguide-based detection devices, which represent an advanced approach in the field of sensing.
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Affiliation(s)
- Prasan Kaur
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Nazim Nazeer
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Vikas Gurjar
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Rajnarayan Tiwari
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Pradyumna Kumar Mishra
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India.
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de Queiroz LF, Silva MSDME, de Souza HSP, Rosas SLB, Carvalho MDGDC. hTERT gene methylation in circulating DNA, tumor, and surrounding tissue in breast cancer: a prospective study. SAO PAULO MED J 2024; 142:e2023140. [PMID: 38747873 PMCID: PMC11087006 DOI: 10.1590/1516-3180.2023.0140.r1.04032024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/08/2023] [Accepted: 03/04/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND The human telomerase reverse transcriptase (hTERT) enzyme, encoded by the hTERT gene, synthesizes protective telomeric sequences on chromosomes and plays a fundamental role in cancer formation. Methylation of the hTERT gene has an upregulatory effect, increasing hTERT enzyme synthesis and allowing continuous tumor cell division. OBJECTIVE In a group of patients with breast cancer, we aimed to analyze the methylation status of hTERT in the tumor, surrounding tissue, and circulating free deoxyribonucleic acid (cfDNA) of blood collected on the day of mastectomy and then approximately one year later. DESIGN AND SETTING A prospective study was conducted at a university hospital in Rio de Janeiro, Brazil. METHODS Samples were collected from 15 women with breast cancer on the day of mastectomy and approximately one year postoperatively. cfDNA was analyzed by sodium bisulfite conversion, followed by polymerase chain reaction, electrophoresis, and silver nitrate staining. RESULTS Methylation of hTERT was detected in the tumors and surrounding tissues of all 15 patients. Five patients displayed hTERT methylation in the cfDNA from the blood of the first collection. Of the ten patients who returned for the second collection, three showed methylation. Two patients with methylation in the first collection did not display methylation in the second collection. One patient with no methylation in the first collection displayed methylation in the second collection, and one patient had a diminished level of methylation in the second collection. CONCLUSION Only one-third of patients displayed methylation in their cfDNA, which may be related to the success of chemotherapy.
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Affiliation(s)
- Luiz Fernando de Queiroz
- MD, PhD. Molecular Biologist, Department of Pathology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
| | - Marcelo Soares da Mota e Silva
- MD, PhD. Molecular Biologist, Department of Pathology, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
| | - Heitor Siffert Pereira de Souza
- MD, PhD. Physician and Full Professor, Department of Internal Medicine, School of Medicine, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
| | - Siane Lopes Bittencourt Rosas
- MD, PhD. Molecular Biologist, Department of Internal Medicine, School of Medicine, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
| | - Maria da Glória da Costa Carvalho
- MD, PhD. Physician and Associate Professor, Department of Pathology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
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Gupta S, Singh B, Abhishek R, Gupta S, Sachan M. The emerging role of liquid biopsy in oral squamous cell carcinoma detection: advantages and challenges. Expert Rev Mol Diagn 2024; 24:311-331. [PMID: 38607339 DOI: 10.1080/14737159.2024.2340997] [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: 12/11/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
INTRODUCTION Oral Squamous Cell Carcinoma (OSCC), the sixth most widespread malignancy in the world, accounts for 90% of all cases of oral cancer. The primary risk factors are tobacco chewing, alcohol consumption, viral infection, and genetic modifications. OSCC has a high morbidity rate due to the lack of early diagnostic methods. Nowadays, liquid biopsy plays a vital role in the initial diagnosis of oral cancer. ctNAs extracted from saliva and serum/plasma offer meaningful insights into tumor genetics and dynamics. The interplay of these elements in saliva and serum/plasma showcases their significance in advancing noninvasive, effective OSCC detection and monitoring. AREAS COVERED This review mainly focused on the role of liquid biopsy as an emerging point in the diagnosis and prognosis of OSCC and the current advancements and challenges associated with liquid biopsy. EXPERT OPINION Liquid biopsy is regarded as a new, minimally invasive, real-time monitoring tool for cancer diagnosis and prognosis. Many biomolecules found in bodily fluids, including ctDNA, ctRNA, CTCs, and EVs, are significant biomarkers to identify cancer in its early stages. Despite these groundbreaking strides, challenges persist. Standardization of sample collection, isolation, processing, and detection methods is imperative for ensuring result reproducibility across diverse studies.
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Affiliation(s)
- Sudha Gupta
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
| | - Brijesh Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
| | - Rajul Abhishek
- Department of Surgical Oncology, Motilal Nehru Medical College, Prayagraj, 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, Prayagraj, India
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Wang R, Yang Y, Lu T, Cui Y, Li B, Liu X. Circulating cell-free DNA-based methylation pattern in plasma for early diagnosis of esophagus cancer. PeerJ 2024; 12:e16802. [PMID: 38313016 PMCID: PMC10838104 DOI: 10.7717/peerj.16802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024] Open
Abstract
With the increased awareness of early tumor detection, the importance of detecting and diagnosing esophageal cancer in its early stages has been underscored. Studies have consistently demonstrated the crucial role of methylation levels in circulating cell-free DNA (cfDNA) in identifying and diagnosing early-stage cancer. cfDNA methylation pertains to the methylation state within the genomic scope of cfDNA and is strongly associated with cancer development and progression. Several research teams have delved into the potential application of cfDNA methylation in identifying early-stage esophageal cancer and have achieved promising outcomes. Recent research supports the high sensitivity and specificity of cfDNA methylation in early esophageal cancer diagnosis, providing a more accurate and efficient approach for early detection and improved clinical management. Accordingly, this review aims to present an overview of methylation-based cfDNA research with a focus on the latest developments in the early detection of esophageal cancer. Additionally, this review summarizes advanced analytical technologies for cfDNA methylation that have significantly benefited from recent advancements in separation and detection techniques, such as methylated DNA immunoprecipitation sequencing (MeDIP-seq). Recent findings suggest that biomarkers based on cfDNA methylation may soon find successful applications in the early detection of esophageal cancer. However, large-scale prospective clinical trials are required to identify the potential of these biomarkers.
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Affiliation(s)
- Rui Wang
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Yue Yang
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Tianyu Lu
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Youbin Cui
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Bo Li
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Xin Liu
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
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Zhou Z, Ou-yang C, Chen Q, Ren Z, Guo X, Lei M, Liu C, Yang X. Trafficking and effect of released DNA on cGAS-STING signaling pathway and cardiovascular disease. Front Immunol 2023; 14:1287130. [PMID: 38152400 PMCID: PMC10751357 DOI: 10.3389/fimmu.2023.1287130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/01/2023] [Indexed: 12/29/2023] Open
Abstract
Evidence from clinical research and animal studies indicates that inflammation is an important factor in the occurrence and development of cardiovascular disease (CVD). Emerging evidence shows that nucleic acids serve as crucial pathogen-associated molecular patterns (PAMPs) or non-infectious damage-associated molecular patterns (DAMPs), are released and then recognized by pattern recognition receptors (PRRs), which activates immunological signaling pathways for host defense. Mechanistically, the released nucleic acids activate cyclic GMP-AMP synthase (cGAS) and its downstream receptor stimulator of interferon genes (STING) to promote type I interferons (IFNs) production, which play an important regulatory function during the initiation of an innate immune response to various diseases, including CVD. This pathway represents an essential defense regulatory mechanism in an organism's innate immune system. In this review, we outline the overall profile of cGAS-STING signaling, summarize the latest findings on nucleic acid release and trafficking, and discuss their potential role in CVD. This review also sheds light on potential directions for future investigations on CVD.
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Affiliation(s)
- Zimo Zhou
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
- State Key Laboratory of Trauma, Burns and Combined Injury, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Changhan Ou-yang
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Qingjie Chen
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Zhanhong Ren
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Xiying Guo
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Min Lei
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Chao Liu
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Xiaosong Yang
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China
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Shuai Y, Ma Z, Ju J, Wei T, Gao S, Kang Y, Yang Z, Wang X, Yue J, Yuan P. Liquid-based biomarkers in breast cancer: looking beyond the blood. J Transl Med 2023; 21:809. [PMID: 37957623 PMCID: PMC10644618 DOI: 10.1186/s12967-023-04660-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
In recent decades, using circulating tumor cell (CTC), circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), exosomes and etc. as liquid biomarkers has received enormous attention in various tumors, including breast cancer (BC). To date, efforts in the area of liquid biopsy predominantly focus on the analysis of blood-based markers. It is worth noting that the identifications of markers from non-blood sources provide unique advantages beyond the blood and these alternative sources may be of great significance in offering supplementary information in certain settings. Here, we outline the latest advances in the analysis of non-blood biomarkers, predominantly including urine, saliva, cerebrospinal fluid, pleural fluid, stool and etc. The unique advantages of such testings, their current limitations and the appropriate use of non-blood assays and blood assays in different settings are further discussed. Finally, we propose to highlight the challenges of these alternative assays from basic to clinical implementation and explore the areas where more investigations are warranted to elucidate its potential utility.
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Affiliation(s)
- You Shuai
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhonghua Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Endoscopy, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jie Ju
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tong Wei
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Songlin Gao
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yikun Kang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zixuan Yang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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An Investigation of the Prognostic Role of Genes Related to Lipid Metabolism in Head and Neck Squamous Cell Carcinoma. Int J Genomics 2023; 2023:9708282. [PMID: 36818393 PMCID: PMC9937776 DOI: 10.1155/2023/9708282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/06/2023] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) has become a prevalent malignancy, and its incidence and mortality rate are increasing worldwide. Accumulating evidence has indicated that lipid metabolism-related genes (LMRGs) are involved in the occurrence and development of HNSCC. This study investigated the latent association of lipid metabolism with HNSCC and established a prognostic signature based on LMRGs. A prognostic risk model composed of eight differentially expressed LMRGs (PHYH, CYP4F8, INMT, ELOVL6, PLPP3, BCHE, TPTE, and STAR) was constructed through The Cancer Genome Atlas database. Then, ELOVL6 expression was validated in oral squamous cell carcinoma (OSCC), which is a common type of HNSCC, by immunohistochemical analysis. ELOVL6 expression in the OSCC II/III group was significantly higher than that in the other three groups (normal, dysplasia, and OSCC I), and OSCC patients with high ELOVL6 expression had poorer survival than those with low ELOVL6 expression. In summary, the LMRG-based prognostic feature had prognostic predictive capacity. ELOVL6 may be a potential prognostic factor for HNSCC patients.
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Mäkitie AA, Agaimy A, Almangush A. Insight into Classification and Risk Stratification of Head and Neck Squamous Cell Carcinoma in Era of Emerging Biomarkers with Focus on Histopathologic Parameters. Cancers (Basel) 2022; 14:5514. [PMID: 36428607 PMCID: PMC9688658 DOI: 10.3390/cancers14225514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/12/2022] Open
Abstract
Tumor-node-metastasis (TNM) staging system is the cornerstone for treatment planning of head and neck squamous cell carcinoma (HNSCC). Many prognostic biomarkers have been introduced as modifiers to further improve the TNM classification of HNSCC. Here, we provide an overview on the use of the recent prognostic biomarkers, with a focus on histopathologic parameters, in improving the risk stratification of HNSCC and their application in the next generation of HNSCC staging systems.
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Affiliation(s)
- Antti A. Mäkitie
- Department of Otorhinolaryngology—Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska Hospital, 17176 Stockholm, Sweden
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Comprehensive Cancer Center (CCC) Erlangen-EMN, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Alhadi Almangush
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Department of Pathology, University of Helsinki, 00014 Helsinki, Finland
- Department of Oral and Maxillofacial Diseases, University of Helsinki, 00014 Helsinki, Finland
- Department of Pathology, University of Turku, 20521 Turku, Finland
- Faculty of Dentistry, Misurata University, Misurata 2478, Libya
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