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Zhao Y, Zhao L, Jin H, Xie Y, Chen L, Zhang W, Dong L, Zhang L, Huang Y, Wan K, Yang Q, Wang S. Plasma methylated GNB4 and Riplet as a novel dual-marker panel for the detection of hepatocellular carcinoma. Epigenetics 2024; 19:2299044. [PMID: 38154055 PMCID: PMC10761049 DOI: 10.1080/15592294.2023.2299044] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
Early detection of hepatocellular carcinoma (HCC) can greatly improve the survival rate of patients. We aimed to develop a novel marker panel based on cell-free DNA (cfDNA) methylation for the detection of HCC. The differentially methylated CpG sites (DMCs) specific for HCC blood diagnosis were selected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, then validated by the whole genome bisulphite sequencing (WGBS) of 12 paired HCC and paracancerous tissues. The clinical performance of the panel was evaluated using tissue samples [32 HCC, chronic liver disease (CLD), and healthy individuals] and plasma cohorts (173 HCC, 199 CLD, and 98 healthy individuals). The combination of G protein subunit beta 4 (GNB4) and Riplet had the optimal area under the curve (AUC) in seven candidates through TCGA, GEO, and WGBS analyses. In tissue validation, the GNB4 and Riplet showed an AUC of 100% with a sensitivity and specificity of 100% for detecting any-stage HCC. In plasma, it demonstrated a high sensitivity of 84.39% at 91.92% specificity, with an AUC of 92.51% for detecting any-stage HCC. The dual-marker panel had a higher sensitivity of 78.26% for stage I HCC than alpha-fetoprotein (AFP) of 47.83%, and a high sensitivity of 70.27% for detecting a single tumour (size ≤3 cm). In conclusion, we developed a novel dual-marker panel that demonstrates high accuracy in detecting HCC, surpassing the performance of AFP testing.
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Affiliation(s)
- Yanteng Zhao
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lei Zhao
- Plastic maxillofacial surgery, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi, China
| | - Huifang Jin
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Xie
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liyinghui Chen
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wei Zhang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Lanlan Dong
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Lianglu Zhang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Yue Huang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Kangkang Wan
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Qiankun Yang
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shaochi Wang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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2
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Wang B, Wang M, Lin Y, Zhao J, Gu H, Li X. Circulating tumor DNA methylation: a promising clinical tool for cancer diagnosis and management. Clin Chem Lab Med 2024; 62:2111-2127. [PMID: 38443752 DOI: 10.1515/cclm-2023-1327] [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: 11/23/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Cancer continues to pose significant challenges to the medical community. Early detection, accurate molecular profiling, and adequate assessment of treatment response are critical factors in improving the quality of life and survival of cancer patients. Accumulating evidence shows that circulating tumor DNA (ctDNA) shed by tumors into the peripheral blood preserves the genetic and epigenetic information of primary tumors. Notably, DNA methylation, an essential and stable epigenetic modification, exhibits both cancer- and tissue-specific patterns. As a result, ctDNA methylation has emerged as a promising molecular marker for noninvasive testing in cancer clinics. In this review, we summarize the existing techniques for ctDNA methylation detection, describe the current research status of ctDNA methylation, and present the potential applications of ctDNA-based assays in the clinic. The insights presented in this article could serve as a roadmap for future research and clinical applications of ctDNA methylation.
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Affiliation(s)
- Binliang Wang
- Department of Respiratory Medicine, Huangyan Hospital Affiliated to Wenzhou Medical University, Taizhou, P.R. China
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Ya Lin
- Zhejiang University of Chinese Medicine, Hangzhou, P.R. China
| | - Jinlan Zhao
- Scientific Research Department, Zhejiang Shengting Medical Company, Hangzhou, P.R. China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P.R. China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, P.R. China
| | - Xiangjuan Li
- Department of Gynaecology, Hangzhou Obstetrics and Gynecology Hospital, Hangzhou, P.R. China
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Liu J, Shen H, Yang Y, Yang M, Zhang Q, Chen K, Li X. Transformer-based representation learning and multiple-instance learning for cancer diagnosis exclusively from raw sequencing fragments of bisulfite-treated plasma cell-free DNA. Mol Oncol 2024. [PMID: 39380154 DOI: 10.1002/1878-0261.13745] [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: 12/15/2023] [Revised: 07/31/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024] Open
Abstract
Early cancer diagnosis from bisulfite-treated cell-free DNA (cfDNA) fragments requires tedious data analytical procedures. Here, we present a deep-learning-based approach for early cancer interception and diagnosis (DECIDIA) that can achieve accurate cancer diagnosis exclusively from bisulfite-treated cfDNA sequencing fragments. DECIDIA relies on transformer-based representation learning of DNA fragments and weakly supervised multiple-instance learning for classification. We systematically evaluate the performance of DECIDIA for cancer diagnosis and cancer type prediction on a curated dataset of 5389 samples that consist of colorectal cancer (CRC; n = 1574), hepatocellular cell carcinoma (HCC; n = 1181), lung cancer (n = 654), and non-cancer control (n = 1980). DECIDIA achieved an area under the receiver operating curve (AUROC) of 0.980 (95% CI, 0.976-0.984) in 10-fold cross-validation settings on the CRC dataset by differentiating cancer patients from cancer-free controls, outperforming benchmarked methods that are based on methylation intensities. Noticeably, DECIDIA achieved an AUROC of 0.910 (95% CI, 0.896-0.924) on the externally independent HCC testing set in distinguishing HCC patients from cancer-free controls, although there was no HCC data used in model development. In the settings of cancer-type classification, we observed that DECIDIA achieved a micro-average AUROC of 0.963 (95% CI, 0.960-0.966) and an overall accuracy of 82.8% (95% CI, 81.8-83.9). In addition, we distilled four sequence signatures from the raw sequencing reads that exhibited differential patterns in cancer versus control and among different cancer types. Our approach represents a new paradigm towards eliminating the tedious data analytical procedures for liquid biopsy that uses bisulfite-treated cfDNA methylome.
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Affiliation(s)
- Jilei Liu
- Tianjin Cancer Institute, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, China
| | - Hongru Shen
- Tianjin Cancer Institute, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, China
| | - Yichen Yang
- Tianjin Cancer Institute, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, China
| | - Meng Yang
- Tianjin Cancer Institute, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, China
| | - Qiang Zhang
- Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Prevention and Control of Major Diseases in the Population Ministry of Education, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, China
| | - Xiangchun Li
- Tianjin Cancer Institute, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, China
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Wang Z, He Z, Lin R, Feng Z, Li X, Sui X, Gu L, Xia T, Zhou D, Zhao B, Li Y, Li Z, Bai Y. Evaluation of a plasma cell-free DNA methylation test for colorectal cancer diagnosis: a multicenter clinical study. BMC Med 2024; 22:436. [PMID: 39379942 DOI: 10.1186/s12916-024-03662-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 09/26/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND A blood-based diagnostic test is a promising strategy for colorectal cancer (CRC). The MethyDT test (IColohunter), which detects methylation levels of NTMT1 and MAP3K14-AS1, exhibited potential in discriminating CRC, but its clinical performance needs to be validated in large-scale populations. METHODS A multicenter, double-blinded, cross-sectional study that enrolled 1194 participants was performed. Plasma samples were collected to detect methylation levels of NTMT1 and MAP3K14-AS1 using quantitative methylation-specific PCR with the MethyDT test, and the accuracy was further evaluated by Sanger sequencing. RESULTS The sensitivities of the MethyDT test for detecting CRC, early stages of CRC (I and II), advanced adenoma (AA), and high-grade intraepithelial neoplasia (HGIN) were 91.2% (95% confidence interval [CI], 88.4-94.0), 87.4% (95% CI, 82.5-92.2), 43.5% (95% CI, 35.7-51.4), and 72.7% (95% CI, 57.5-87.9), respectively. The specificities for participants with non-AA, interfering diseases (ID), and no evidence of disease (NED) were 85.0% (95% CI, 78.8-91.3), 93.7% (95% CI, 91.4-95.9) and 97.3% (95% CI, 90.5-99.7), respectively, and its overall specificity for all-controls was 92.4% (95% CI, 90.3-94.4). The consistency of the MethyDT test with pathology for CRC was high with a kappa value of 0.830 (95% CI, 0.795-0.865). Additionally, the MethyDT test was comparable to Sanger sequencing for detecting methylation with kappa values > 0.97. CONCLUSIONS The MethyDT test demonstrates excellent sensitivity and specificity for CRC and high consistency with Sanger sequencing for methylation, suggesting it may serve as a potential noninvasive diagnostic tool for the detection of CRC. TRIAL REGISTRATION This clinical trial has been registered in ClinicalTrials.gov (NCT05508503).
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Affiliation(s)
- Zhijie Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Zixuan He
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Rong Lin
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhijie Feng
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiuling Li
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Xiangyu Sui
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Lun Gu
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Tian Xia
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Dihan Zhou
- Wuhan Ammunition Life-Tech Co, Ltd, Wuhan, China
| | - Bali Zhao
- Wuhan Ammunition Life-Tech Co, Ltd, Wuhan, China
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China.
| | - Yu Bai
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China.
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Acharyya S, Kumar SH, Chouksey A, Soni N, Nazeer N, Mishra PK. The enigma of mitochondrial epigenetic alterations in air pollution-induced neurodegenerative diseases. Neurotoxicology 2024:S0161-813X(24)00120-7. [PMID: 39374796 DOI: 10.1016/j.neuro.2024.10.002] [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: 07/18/2024] [Revised: 09/13/2024] [Accepted: 10/02/2024] [Indexed: 10/09/2024]
Abstract
The incidence of neurodegenerative diseases is a growing concern worldwide, affecting individuals from diverse backgrounds. Although these pathologies are primarily associated with aging and genetic susceptibility, their severity varies among the affected population. Numerous studies have indicated air pollution as a significant contributor to the increasing prevalence of neurodegeneration. Cohort studies have provided compelling evidence of the association between prolonged exposure to different air toxicants and cognitive decline, behavioural deficits, memory impairment, and overall neuronal health deterioration. Furthermore, molecular research has revealed that air pollutants can disrupt the body's protective mechanisms, participate in neuroinflammatory pathways, and cause neuronal epigenetic modifications. The mitochondrial epigenome is particularly interesting to the scientific community due to its potential to significantly impact our understanding of neurodegenerative diseases' pathogenesis and their release in the peripheral circulation. While protein hallmarks have been extensively studied, the possibility of using circulating epigenetic signatures, such as methylated DNA fragments, miRNAs, and genome-associated factors, as diagnostic tools and therapeutic targets requires further groundwork. The utilization of circulating epigenetic signatures holds promise for developing novel prognostic strategies, creating paramount point-of-care devices for disease diagnosis, identifying therapeutic targets, and developing clinical data-based disease models utilizing multi-omics technologies and artificial intelligence, ultimately mitigating the threat and prevalence of neurodegeneration.
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Affiliation(s)
- Sayanti Acharyya
- Division of Environmental Biotechnology, Genetics & Molecular Biology (EBGMB), ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Sruthy Hari Kumar
- Division of Environmental Biotechnology, Genetics & Molecular Biology (EBGMB), ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Apoorva Chouksey
- Division of Environmental Biotechnology, Genetics & Molecular Biology (EBGMB), ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Nikita Soni
- Division of Environmental Biotechnology, Genetics & Molecular Biology (EBGMB), ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Nazim Nazeer
- Division of Environmental Biotechnology, Genetics & Molecular Biology (EBGMB), ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Pradyumna Kumar Mishra
- Division of Environmental Biotechnology, Genetics & Molecular Biology (EBGMB), ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India; Faculty of Medical Research, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Goldkorn A, Tangen C, Plets M, Bsteh D, Xu T, Pinski JK, Ingles S, Triche TJ, MacVicar GR, Vaena DA, Crispino AW, McConkey DJ, Lara PN, Hussain MHA, Quinn DI, Dorff TB, Lerner SP, Thompson I, Agarwal N. Circulating Tumor Cell Count and Overall Survival in Patients With Metastatic Hormone-Sensitive Prostate Cancer. JAMA Netw Open 2024; 7:e2437871. [PMID: 39374015 DOI: 10.1001/jamanetworkopen.2024.37871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/08/2024] Open
Abstract
Importance In metastatic hormone-sensitive prostate cancer (mHSPC), new first-line combination therapies have enhanced overall survival (OS), but clinical outcomes for individual patients vary greatly and are difficult to predict. Peripheral blood circulating tumor cell (CTC) count is the most extensively validated prognostic liquid biomarker in metastatic castration-resistant prostate cancer (mCRPC), and recent studies have suggested that it may also be informative in mHSPC. Objective To examine the prognostic value of CTC count in men with mHSPC. Design, Setting, and Participants In this prognostic study, peripheral blood was drawn at registration (baseline) and at progression to mCRPC in the S1216 study (March 1, 2013, to July 15, 2017), a phase 3, prospective, randomized clinical trial in men with mHSPC. The CTCs were enumerated using a US Food and Drug Administration-cleared isolation platform. Counts were categorized as 0, 1 to 4, or 5 or more CTCs per 7.5 mL based on the prognostic value of these cut points in prior studies. The data analysis was performed between October 28, 2022, and June 15, 2023. Exposure Metastatic hormone-sensitive prostate cancer. Main Outcomes and Measures Circulating tumor cell count was evaluated for an association with 3 prespecified trial end points: OS, progression-free survival, and 7-month prostate-specific antigen, after adjusting for other baseline covariates using proportional hazards and logistic regression models. Results Of 1313 S1216 participants (median [IQR] age, 68 [44-92] years), evaluable samples from 503 (median [IQR] age, 69 [46-90] years) with newly diagnosed mHSPC were collected at baseline, and 93 samples were collected at progression. Baseline counts were 5 or more CTCs per 7.5 mL in 60 samples (11.9%), 1 to 4 CTCs per 7.5 mL in 107 samples (21.3%), and 0 CTCs per 7.5 mL in 336 samples (66.8%). Median OS for men with 5 or more CTCs per 7.5 mL was 27.9 months (95% CI, 24.1-31.2 months) compared with 56.2 months (95% CI, 45.7-69.8 months) for men with 1 to 4 CTCs per 7.5 mL and not reached at 78.0 months follow-up for men with 0 CTCs per 7.5 mL. After adjusting for baseline clinical covariates, men with 5 or more CTCs per 7.5 mL at baseline had a significantly higher hazard of death (hazard ratio, 3.22; 95% CI, 2.22-4.68) and disease progression (hazard ratio, 2.46; 95% CI, 1.76-3.43) and a lower likelihood of prostate-specific antigen complete response (odds ratio, 0.26; 95% CI, 0.12-0.54) compared with men with 0 CTCs per 7.5 mL at baseline. Adding baseline CTC count to other known prognostic factors (covariates only: area under the curve, 0.73; 95% CI, 0.67-0.79) resulted in an increased prognostic value for 3-year survival (area under the curve, 0.79; 95% CI, 0.73-0.84). Conclusions and Relevance In this prognostic study, the findings validate CTC count as a prognostic biomarker that improved upon existing prognostic factors and estimated vastly divergent survival outcomes regardless of subsequent lines of therapy. As such, baseline CTC count in mHSPC may serve as a valuable noninvasive biomarker to identify men likely to have poor survival who may benefit from clinical trials of intensified or novel regimens.
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Affiliation(s)
- Amir Goldkorn
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Catherine Tangen
- SWOG Statistics and Data Management Center, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Melissa Plets
- SWOG Statistics and Data Management Center, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Daniel Bsteh
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Tong Xu
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Jacek K Pinski
- USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Sue Ingles
- Keck School of Medicine of USC, Los Angeles, California
| | | | | | - Daniel A Vaena
- Holden Comprehensive Cancer Center, University of Iowa Health Care, Iowa City
| | | | | | - Primo N Lara
- UC Davis Comprehensive Cancer Center, Sacramento, California
| | - Maha H A Hussain
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David I Quinn
- USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Tanya B Dorff
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Seth Paul Lerner
- Scott Department of Urology, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | | | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, Salt Lake City
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Xu S, Chen T, Yu J, Wan L, Zhang J, Chen J, Wei W, Li X. Insights into the regulatory role of epigenetics in moyamoya disease: Current advances and future prospectives. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102281. [PMID: 39188306 PMCID: PMC11345382 DOI: 10.1016/j.omtn.2024.102281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Moyamoya disease (MMD) is a progressive steno-occlusive cerebrovascular disorder that predominantly affecting East Asian populations. The intricate interplay of distinct and overlapping mechanisms, including genetic associations such as the RNF213-p.R4810K variant, contributes to the steno-occlusive lesions and moyamoya vessels. However, genetic mutations alone do not fully elucidate the occurrence of MMD, suggesting a potential role for epigenetic factors. Accruing evidence has unveiled the regulatory role of epigenetic markers, including DNA methylation, histone modifications, and non-coding RNAs (ncRNAs), in regulating pivotal cellular and molecular processes implicated in the pathogenesis of MMD by modulating endothelial cells and smooth muscle cells. The profile of these epigenetic markers in cerebral vasculatures and circulation has been determined to identify potential diagnostic biomarkers and therapeutic targets. Furthermore, in vitro studies have demonstrated the multifaceted effects of modulating specific epigenetic markers on MMD pathogenesis. These findings hold great potential for the discovery of novel therapeutic targets, translational studies, and clinical applications. In this review, we comprehensively summarize the current understanding of epigenetic mechanisms, including DNA methylation, histone modifications, and ncRNAs, in the context of MMD. Furthermore, we discuss the potential challenges and opportunities that lie ahead in this rapidly evolving field.
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Affiliation(s)
- Shuangxiang Xu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tongyu Chen
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jin Yu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Lei Wan
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jianjian Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jincao Chen
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wei Wei
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xiang Li
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430071, China
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- Sino-Italian Ascula Brain Science Joint Laboratory, Wuhan University, Wuhan 430071, China
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8
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Huang FF, Di XF, Bai MH. Analysis of urine cell-free DNA in bladder cancer diagnosis by emerging bioactive technologies and materials. Front Bioeng Biotechnol 2024; 12:1458362. [PMID: 39295845 PMCID: PMC11408225 DOI: 10.3389/fbioe.2024.1458362] [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: 07/02/2024] [Accepted: 08/23/2024] [Indexed: 09/21/2024] Open
Abstract
Urinary cell-free DNA (UcfDNA) is gaining recognition as an important biomarker for diagnosing bladder cancer. UcfDNA contains tumor derived DNA sequences, making it a viable candidate for non-invasive early detection, diagnosis, and surveillance of bladder cancer. The quantification and qualification of UcfDNA have demonstrated high sensitivity and specificity in the molecular characterization of bladder cancer. However, precise analysis of UcfDNA for clinical bladder cancer diagnosis remains challenging. This review summarizes the history of UcfDNA discovery, its biological properties, and the quantitative and qualitative evaluations of UcfDNA for its clinical significance and utility in bladder cancer patients, emphasizing the critical role of UcfDNA in bladder cancer diagnosis. Emerging bioactive technologies and materials currently offer promising tools for multiple UcfDNA analysis, aiming to achieve more precise and efficient capture of UcfDNA, thereby significantly enhancing diagnostic accuracy. This review also highlights breakthroughs in detection technologies and substrates with the potential to revolutionize bladder cancer diagnosis in clinic.
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Affiliation(s)
- Fei-Fei Huang
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Xiao-Fei Di
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Mo-Han Bai
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
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9
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Behrouzi R, Clipson A, Simpson KL, Blackhall F, Rothwell DG, Dive C, Mouliere F. Cell-free and extrachromosomal DNA profiling of small cell lung cancer. Trends Mol Med 2024:S1471-4914(24)00218-1. [PMID: 39232927 DOI: 10.1016/j.molmed.2024.08.004] [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: 05/30/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/06/2024]
Abstract
Small cell lung cancer (SCLC) is highly aggressive with poor prognosis. Despite a relative prevalence of circulating tumour DNA (ctDNA) in SCLC, liquid biopsies are not currently implemented, unlike non-SCLC where cell-free DNA (cfDNA) mutation profiling in the blood has utility for guiding targeted therapies and assessing minimal residual disease. cfDNA methylation profiling is highly sensitive for SCLC detection and holds promise for disease monitoring and molecular subtyping; cfDNA fragmentation profiling has also demonstrated clinical potential. Extrachromosomal DNA (ecDNA), that is often observed in SCLC, promotes tumour heterogeneity and chemotherapy resistance and can be detected in blood. We discuss how these cfDNA profiling modalities can be harnessed to expand the clinical applications of liquid biopsy in SCLC.
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Affiliation(s)
- Roya Behrouzi
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK; Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, UK; Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK; Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Alexandra Clipson
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
| | - Kathryn L Simpson
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK; Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Fiona Blackhall
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK; Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, UK
| | - Dominic G Rothwell
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
| | - Caroline Dive
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK; Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Florent Mouliere
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK.
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Xue R, Li X, Yang L, Yang M, Zhang B, Zhang X, Li L, Duan X, Yan R, He X, Cui F, Wang L, Wang X, Wu M, Zhang C, Zhao J. Evaluation and integration of cell-free DNA signatures for detection of lung cancer. Cancer Lett 2024; 604:217216. [PMID: 39233043 DOI: 10.1016/j.canlet.2024.217216] [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: 05/29/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Cell-free DNA (cfDNA) analysis has shown potential in detecting early-stage lung cancer based on non-genetic features. To distinguish patients with lung cancer from healthy individuals, peripheral blood were collected from 926 lung cancer patients and 611 healthy individuals followed by cfDNA extraction. Low-pass whole genome sequencing and targeted methylation sequencing were conducted and various features of cfDNA were evaluated. With our customized algorithm using the most optimal features, the ensemble stacked model was constructed, called ESim-seq (Early Screening tech with Integrated Model). In the independent validation cohort, the ESim-seq model achieved an area under the curve (AUC) of 0.948 (95 % CI: 0.915-0.981), with a sensitivity of 79.3 % (95 % CI: 71.5-87.0 %) across all stages at a specificity of 96.0 % (95 % CI: 90.6-100.0 %). Specifically, the sensitivity of the ESim-seq model was 76.5 % (95 % CI: 67.3-85.8 %) in stage I patients, 100 % (95 % CI: 100.0-100.0 %) in stage II patients, 100 % (95 % CI: 100.0-100.0 %) in stage III patients and 87.5 % (95 % CI: 64.6%-100.0 %) in stage IV patients in the independent validation cohort. Besides, we constructed LCSC model (Lung Cancer Subtype multiple Classification), which was able to accurately distinguish patients with small cell lung cancer from those with non-small cell lung cancer, achieving an AUC of 0.961 (95 % CI: 0.949-0.957). The present study has established a framework for assessing cfDNA features and demonstrated the benefits of integrating multiple features for early detection of lung cancer.
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Affiliation(s)
- Ruyue Xue
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaomin Li
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China; Cancer Center, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Lu Yang
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China; Cancer Center, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Meijia Yang
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bei Zhang
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Xu Zhang
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoran Duan
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Rui Yan
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xianying He
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fangfang Cui
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Linlin Wang
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoqiang Wang
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Mengsi Wu
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Chao Zhang
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Jie Zhao
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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11
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Cepeda J, Racca ME, Cardozo MA, Gaydou L, Muñoz-de-Toro M, Milesi MM, Varayoud J, Rossetti MF, Ramos JG. Plasma cell-free DNA as a monitoring tool for high-risk pregnancies associated with antiphospholipid syndrome. Thromb Res 2024; 241:109108. [PMID: 39096850 DOI: 10.1016/j.thromres.2024.109108] [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: 04/22/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
INTRODUCTION Despite thromboprophylaxis, women with antiphospholipid syndrome (APS) face high-risk pregnancies due to proinflammatory and prothrombotic states. This highlights the need for new monitoring and prognostic tools. Recent insights into the pathophysiological role of neutrophil activation and extracellular trap (NET) formation in this syndrome led to the exploration of plasma cell-free DNA (cfDNA), a derivative of NETosis, as a promising biomarker. MATERIALS AND METHODS cfDNA was isolated and quantified from plasma samples of healthy pregnant women (control group, HC) and women with APS (APS group). We assessed the physiological variability of cfDNA across the three trimesters in HC. Levels of cfDNA were compared between APS and HC by gestational trimester. ROC curve analysis was performed to evaluate the efficacy of cfDNA levels for classifying APS patients. Furthermore, cfDNA levels in pregnant women with APS with obstetric complications were compared to those from uncomplicated pregnancies. RESULTS Among HC, cfDNA significantly increased in the third trimester compared to the first and second. Elevated cfDNA levels in APS compared to HC were observed in the first and second trimesters. First-trimester cfDNA levels demonstrated the highest classification ability to discriminate between APS and HC patients (AUC: 0.906). Among APS, those with complicated pregnancies (fetal growth restriction, preeclampsia, placenta accreta) exhibited significantly elevated cfDNA levels in the second trimester. CONCLUSIONS Elevated levels of cfDNA in pregnant women with APS, particularly among those with obstetric complications, supports further investigation into the potential of cfDNA as a valuable tool in the obstetric management of women with APS.
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Affiliation(s)
- Julieta Cepeda
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - M Emilia Racca
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina; Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - M Alejandra Cardozo
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina; Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina; Laboratorios BLUT, Santa Fe, Argentina
| | - Luisa Gaydou
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina; Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Mónica Muñoz-de-Toro
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina; Cátedra de Patología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - M Mercedes Milesi
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina; Cátedra de Fisiología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Jorgelina Varayoud
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina; Cátedra de Fisiología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - M Florencia Rossetti
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Jorge G Ramos
- Instituto de Salud y Ambiente del Litoral (ISAL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina; Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina.
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12
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Zhen L, Tang X, Xu Z, Huang Y, Qian X, Lin H, Li C, Cui R, Fang H, Yang H, Qiu J, Fang Z, Peng X, Jin Y, Nie J, Guo S, Wang Y, Zhong M, Gu H, Xu H. Early Diagnosis of Colorectal Cancer Based on Bisulfite-free Site-specific Methylation Identification PCR Strategy: High-Sensitivity, Accuracy, and Primary Medical Accessibility. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401137. [PMID: 38868913 PMCID: PMC11434020 DOI: 10.1002/advs.202401137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/26/2024] [Indexed: 06/14/2024]
Abstract
Due to its decade-long progression, colorectal cancer (CRC) is most suitable for population screening to achieve a significant reduction in its incidence and mortality. DNA methylation has emerged as a potential marker for the early detection of CRC. However, the current mainstream methylation detection method represented by bisulfite conversion has issues such as tedious operation, DNA damage, and unsatisfactory sensitivity. Herein, a new high-performance CRC screening tool based on the promising specific terminal-mediated polymerase chain reaction (STEM-PCR) strategy is developed. CRC-related methylation-specific candidate CpG sites are first prescreened through The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases using self-developed bioinformatics. Next, 9 homebrew colorectal cancer DNA methylated STEM‒PCR assays (ColoC-mSTEM) with high sensitivity (0.1%) and high specificity are established to identify candidate sites. The clinical diagnostic performance of these selected methylation sites is confirmed and validated by a case-control study. The optimized diagnostic model has an overall sensitivity of 94.8% and a specificity of 95.0% for detecting early-stage CRC. Taken together, ColoC-mSTEM, based on a single methylation-specific site, is a promising diagnostic approach for the early detection of CRC which is perfectly suitable for the screening needs of CRC in primary healthcare institutions.
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Affiliation(s)
- Linqing Zhen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Hefei Cancer Early Screening Innovation Technology Institute, Anhui Province, China
| | - Xinlu Tang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zhengguo Xu
- Medical community of Linhai First People's Hospital, Zhejiang, 317000, P. R. China
| | - Yizhou Huang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Hefei Cancer Early Screening Innovation Technology Institute, Anhui Province, China
| | - Xiaohua Qian
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Hefei Cancer Early Screening Innovation Technology Institute, Anhui Province, China
| | - Haiping Lin
- Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Chao Li
- Medical community of Linhai First People's Hospital, Zhejiang, 317000, P. R. China
| | - Rong Cui
- Jiading Hospital of Traditional Chinese medicine, Shanghai, 201800, P. R. China
| | - Hongsheng Fang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, P. R. China
| | - Hao Yang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Hefei Cancer Early Screening Innovation Technology Institute, Anhui Province, China
| | - Jiani Qiu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Hefei Cancer Early Screening Innovation Technology Institute, Anhui Province, China
| | - Zhaoqi Fang
- Shanghai Healzone Biotechnology Co., LTD, Shanghai, 200000, P. R. China
| | - Xiaohuan Peng
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Hefei Cancer Early Screening Innovation Technology Institute, Anhui Province, China
| | - Yifeng Jin
- Jiading Hospital of Traditional Chinese medicine, Shanghai, 201800, P. R. China
| | - Jianing Nie
- Shanghai Healzone Biotechnology Co., LTD, Shanghai, 200000, P. R. China
| | - Shiwei Guo
- Medical community of Linhai First People's Hospital, Zhejiang, 317000, P. R. China
| | - Yuguang Wang
- Medical community of Linhai First People's Hospital, Zhejiang, 317000, P. R. China
| | - Ming Zhong
- Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Hongchen Gu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Hefei Cancer Early Screening Innovation Technology Institute, Anhui Province, China
| | - Hong Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Hefei Cancer Early Screening Innovation Technology Institute, Anhui Province, China
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13
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Zhang Y. LncRNA-encoded peptides in cancer. J Hematol Oncol 2024; 17:66. [PMID: 39135098 PMCID: PMC11320871 DOI: 10.1186/s13045-024-01591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Long non-coding RNAs (lncRNAs), once considered transcriptional noise, have emerged as critical regulators of gene expression and key players in cancer biology. Recent breakthroughs have revealed that certain lncRNAs can encode small open reading frame (sORF)-derived peptides, which are now understood to contribute to the pathogenesis of various cancers. This review synthesizes current knowledge on the detection, functional roles, and clinical implications of lncRNA-encoded peptides in cancer. We discuss technological advancements in the detection and validation of sORFs, including ribosome profiling and mass spectrometry, which have facilitated the discovery of these peptides. The functional roles of lncRNA-encoded peptides in cancer processes such as gene transcription, translation regulation, signal transduction, and metabolic reprogramming are explored in various types of cancer. The clinical potential of these peptides is highlighted, with a focus on their utility as diagnostic biomarkers, prognostic indicators, and therapeutic targets. The challenges and future directions in translating these findings into clinical practice are also discussed, including the need for large-scale validation, development of sensitive detection methods, and optimization of peptide stability and delivery.
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Affiliation(s)
- Yaguang Zhang
- Laboratory of Gastrointestinal Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
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14
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Yang Z, Zeng J, Chen Y, Wang M, Luo H, Huang AL, Deng H, Hu Y. Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy. Virol Sin 2024; 39:655-666. [PMID: 38852920 PMCID: PMC11401475 DOI: 10.1016/j.virs.2024.06.003] [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: 01/24/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024] Open
Abstract
The landscape of hepatitis B virus (HBV) integration in the plasma cell-free DNA (cfDNA) of HBV-infected patients with different stages of liver diseases [chronic hepatitis B (CHB), liver cirrhosis (LC), and hepatocellular carcinoma (HCC)] remains unclear. In this study, we developed an improved strategy for detecting HBV DNA integration in plasma cfDNA, based on DNA probe capture and next-generation sequencing. Using this optimized strategy, we successfully detected HBV integration events in chimeric artificial DNA samples and HBV-infected HepG2-NTCP cells at day one post infection, with high sensitivity and accuracy. The characteristics of HBV integration events in the HBV-infected HepG2-NTCP cells and plasma cfDNA from HBV-infected individuals (CHB, LC, and HCC) were further investigated. A total of 112 and 333 integration breakpoints were detected in the HepG2-NTCP cells and 22 out of 25 (88%) clinical HBV-infected samples, respectively. In vivo analysis showed that the normalized number of support unique sequences (nnsus) in HCC was significantly higher than in CHB or LC patients (P values < 0.05). All integration breakpoints are randomly distributed on human chromosomes and are enriched in the HBV genome around nt 1800. The majority of integration breakpoints (61.86%) are located in the gene-coding region. Both non-homologous end-joining (NHEJ) and microhomology-mediated end-joining (MMEJ) interactions occurred during HBV integration across the three different stages of liver diseases. Our study provides evidence that HBV DNA integration can be detected in the plasma cfDNA of HBV-infected patients, including those with CHB, LC, or HCC, using this optimized strategy.
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Affiliation(s)
- Zerui Yang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Jingyan Zeng
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yueyue Chen
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Mengchun Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Hongchun Luo
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, China.
| | - Haijun Deng
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, China.
| | - Yuan Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, China.
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15
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De Wilde J, Van Paemel R, De Koker A, Roelandt S, Van de Velde S, Callewaert N, Van Dorpe J, Creytens D, De Wilde B, De Preter K. A Fast, Affordable, and Minimally Invasive Diagnostic Test for Cancer of Unknown Primary Using DNA Methylation Profiling. J Transl Med 2024; 104:102091. [PMID: 38830578 DOI: 10.1016/j.labinv.2024.102091] [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: 10/10/2023] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/05/2024] Open
Abstract
Currently, we cannot provide a conclusive diagnosis for 3% to 5% of people who are confronted with cancer. These patients have cancer of unknown primary (CUP), ie, a metastasized cancer for which the tissue of origin cannot be determined. Studies have shown that the DNA methylation profile is a unique "fingerprint" that can be used to classify tumors. Here we used cell-free reduced representation bisulfite sequencing (cfRRBS), a technique that allows us to identify the methylation profile starting from minimal amounts of highly fragmented DNA, for CUP diagnosis on formalin-fixed paraffin-embedded (FFPE) tissue and liquid biopsies. We collected 80 primary tumor FFPE samples covering 16 tumor entities together with 15 healthy plasma samples to use as a custom cfRRBS reference data set. Entity-specific methylation regions are defined for each entity to build a classifier based on nonnegative least squares deconvolution. This classification framework was tested on 30 FFPE, 19 plasma, and 40 pleural and peritoneal effusion samples of both known metastatic tumors and clinical CUPs for which pathological investigation finally resulted in a cancer diagnosis. Using this framework, 27 of 30 FFPE (all CUPs) and 16 of 19 plasma samples (10/13 CUPs) obtained an accurate diagnosis, with a minimal DNA input of 400 pg. Diagnosis of the 40 pleural and peritoneal effusion samples is possible in 9 of 27 samples with negative/inconclusive cytology (6/13 CUPs), showing that cell-free DNA (cfDNA) methylation profiling could complement routine cytologic analysis. However, a low "cfDNA - high-molecular weight DNA ratio" has a considerable impact on the prediction accuracy. Moreover, the accuracy improves significantly if the predicted tumor percentage is >7%. This proof-of-concept study shows the feasibility of using DNA methylation profiling on FFPE and liquid biopsy samples such as blood, ascites, and pleural effusions in a fast and affordable way. Our novel RRBS-based technique requires minimal DNA input, can be performed in <1 week, and is highly adaptable to specific diagnostic problems as we only use 5 FFPE references per tumor entity. We believe that cfRRBS methylation profiling could be a valuable addition to the pathologist's toolbox in the diagnosis of CUPs.
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Affiliation(s)
- Jilke De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ruben Van Paemel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Andries De Koker
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Sofie Van de Velde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Nico Callewaert
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
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16
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Penny L, Main SC, De Michino SD, Bratman SV. Chromatin- and nucleosome-associated features in liquid biopsy: implications for cancer biomarker discovery. Biochem Cell Biol 2024; 102:291-298. [PMID: 38478957 DOI: 10.1139/bcb-2024-0004] [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] [Indexed: 06/12/2024] Open
Abstract
Cell-free DNA (cfDNA) from the bloodstream has been studied for cancer biomarker discovery, and chromatin-derived epigenetic features have come into the spotlight for their potential to expand clinical applications. Methylation, fragmentation, and nucleosome positioning patterns of cfDNA have previously been shown to reveal epigenomic and inferred transcriptomic information. More recently, histone modifications have emerged as a tool to further identify tumor-specific chromatin variants in plasma. A number of sequencing methods have been developed to analyze these epigenetic markers, offering new insights into tumor biology. Features within cfDNA allow for cancer detection, subtype and tissue of origin classification, and inference of gene expression. These methods provide a window into the complexity of cancer and the dynamic nature of its progression. In this review, we highlight the array of epigenetic features in cfDNA that can be extracted from chromatin- and nucleosome-associated organization and outline potential use cases in cancer management.
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Affiliation(s)
- Lucas Penny
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Sasha C Main
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Steven D De Michino
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON M5T 1P5, Canada
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17
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Li K, Zhu Q, Yang J, Zheng Y, Du S, Song M, Peng Q, Yang R, Liu Y, Qi L. Imaging and Liquid Biopsy for Distinguishing True Progression From Pseudoprogression in Gliomas, Current Advances and Challenges. Acad Radiol 2024; 31:3366-3383. [PMID: 38614827 DOI: 10.1016/j.acra.2024.03.019] [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: 12/10/2023] [Revised: 01/14/2024] [Accepted: 03/18/2024] [Indexed: 04/15/2024]
Abstract
RATIONALE AND OBJECTIVES Gliomas are aggressive brain tumors with a poor prognosis. Assessing treatment response is challenging because magnetic resonance imaging (MRI) may not distinguish true progression (TP) from pseudoprogression (PsP). This review aims to discuss imaging techniques and liquid biopsies used to distinguish TP from PsP. MATERIALS AND METHODS This review synthesizes existing literature to examine advances in imaging techniques, such as magnetic resonance diffusion imaging (MRDI), perfusion-weighted imaging (PWI) MRI, and liquid biopsies, for identifying TP or PsP through tumor markers and tissue characteristics. RESULTS Advanced imaging techniques, including MRDI and PWI MRI, have proven effective in delineating tumor tissue properties, offering valuable insights into glioma behavior. Similarly, liquid biopsy has emerged as a potent tool for identifying tumor-derived markers in biofluids, offering a non-invasive glimpse into tumor evolution. Despite their promise, these methodologies grapple with significant challenges. Their sensitivity remains inconsistent, complicating the accurate differentiation between TP and PSP. Furthermore, the absence of standardized protocols across platforms impedes the reliability of comparisons, while inherent biological variability adds complexity to data interpretation. CONCLUSION Their potential applications have been highlighted, but gaps remain before routine clinical use. Further research is needed to develop and validate these promising methods for distinguishing TP from PsP in gliomas.
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Affiliation(s)
- Kaishu Li
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China; Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China.; Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qihui Zhu
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Junyi Yang
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Yin Zheng
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Siyuan Du
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Meihui Song
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Qian Peng
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Runwei Yang
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China
| | - Yawei Liu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China
| | - Ling Qi
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China.
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Li Y, Fan Z, Meng Y, Yang J, Li P, Liu S, Pang C, Du L, Wang Y, Zhan H. ZFHX3 methylation in peripheral blood monocytes as a potential biomarker for pancreatic cancer detection. Pancreatology 2024; 24:771-778. [PMID: 38853072 DOI: 10.1016/j.pan.2024.05.529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/26/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is the digestive malignancy with poor prognosis, and there is still a lack of effective diagnostic biomarkers. OBJECTIVE We aimed to explore the diagnostic efficiency of DNA methylation in peripheral blood monocytes (PBMCs) in PDAC. METHODS 850K BeadChips were used to detect genome-wide methylation of PBMCs. For the selected sites, MethylTarget assays was used for further verification. The support vector machine was used to establish the combined panel. RESULTS A total of 167 PDAC patients and 113 healthy controls were included in this study and were divided into three sets. In the discovery set, we found 4625 differentially methylated positions (DMPs) between cancer group and healthy controls. ZFHX3 (0.16 ± 0.04 vs. 0.18 ± 0.04, P = 0.001), cg01904886 (0.84 ± 0.05 vs. 0.81 ± 0.04, P = 0.02) and NUMBL (0.96 ± 0.005 vs. 0.957 ± 0.005, P = 0.04) were found to be significantly different in training set. The locus with more significant differences, namely ZFHX3, was used for further validation and to establish a combined diagnostic panel with CA19-9. In the validation set, the ROC curve indicated that the AUC value of ZFHX3 was 0.75. The AUC value of the combined model (AUC = 0.92) was higher than that of CA19-9 alone (AUC = 0.88). In patients with normal CA19-9 levels, the ZFHX3 methylation biomarker still maintained good diagnostic efficacy (AUC = 0.71). CONCLUSION Our study preliminarily suggests that ZFHX3 methylation combined with CA19-9 can improve the detection rate of PDAC. Especially in patients with normal CA19-9, ZFHX3 methylation can maintain stable diagnostic efficacy. The diagnostic value of ZFHX3 methylation still needs to be prospectively validated.
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Affiliation(s)
- Yongzheng Li
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China; Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Zhiyao Fan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Yufan Meng
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Jian Yang
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Peilong Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Shujie Liu
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Chaoyu Pang
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yunshan Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Hanxiang Zhan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China.
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19
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Huang M, Deng S, Li M, Yang Z, Guo J, Deng Y, Chen D, Yan B. Clinical diagnostic value of methylated SEPT9 combined with NLR, PLR and LMR in colorectal cancer. BMC Gastroenterol 2024; 24:240. [PMID: 39075402 PMCID: PMC11287835 DOI: 10.1186/s12876-024-03332-6] [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: 12/22/2023] [Accepted: 07/22/2024] [Indexed: 07/31/2024] Open
Abstract
PURPOSE This study aimed to investigate clinical diagnostic values of mSEPT9 combined with NLR, PLR and LMR in CRC. METHODS 329 subjects composed of 120 CRC patients, 105 polyps patients and 104 healthy participants were prospectively recruited. Clinicopathologic features were collected and analyzed. Plasma samples were collected for mSEPT9, NLR, PLR and LMR test. The sensitivity, specificity and AUC of each biomarker separately or in combination were estimated by the ROC curve. RESULTS The levels of NLR, PLR and the PDR of mSEPT9 in CRC patients were significantly higher than those in non-CRC subjects, while LMR was the opposite. The PDR of mSEPT9 in CRC patients was significantly correlated with age, tumor size, tumor stage and M stage. ROC curve analysis demonstrated moderate diagnostic values of mSEPT9, NLR, PLR and LMR in CRC patients with AUC of 0.78 (Se = 0.68, and Sp = 0.89), 0.78 (Se = 0.68, and Sp = 0.83), 0.80 (Se = 0.68, and Sp = 0.81), and 0.77 (Se = 0.72, and Sp = 0.73), respectively. Moreover, combination of these four biomarkers dramatically enhanced the diagnostic accuracy of CRC (AUC = 0.92, Se = 0.90, and Sp = 0.87), especially for CRC patients with large tumors (AUC = 0.95) or distal metastasis (AUC = 0.95). CONCLUSION mSEPT9, NLR, PLR and LMR showed the potential to be reliable biomarkers for the diagnosis of CRC. And the combined application of these biomarkers further improved the diagnostic accuracy of CRC significantly.
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Affiliation(s)
- Meiyuan Huang
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, Hunan, 412007, China
| | - Shuang Deng
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, Hunan, 412007, China
| | - Ming Li
- Trauma Center, ZhuZhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, Hunan, 412007, China
| | - Zhenyu Yang
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, Hunan, 412007, China
| | - Jiaxing Guo
- Department of Hematology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, Hunan, 412007, China
| | - Yi Deng
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, Hunan, 412007, China
| | - Dongliang Chen
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, Hunan, 412007, China.
| | - Bokang Yan
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, Hunan, 412007, China.
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20
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Pallocca M, Betti M, Baldinelli S, Palombo R, Bucci G, Mazzarella L, Tonon G, Ciliberto G. Clinical bioinformatics desiderata for molecular tumor boards. Brief Bioinform 2024; 25:bbae447. [PMID: 39297878 PMCID: PMC11411775 DOI: 10.1093/bib/bbae447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/28/2024] [Accepted: 08/30/2024] [Indexed: 09/26/2024] Open
Abstract
Clinical Bioinformatics is a knowledge framework required to interpret data of medical interest via computational methods. This area became of dramatic importance in precision oncology, fueled by cancer genomic profiling: most definitions of Molecular Tumor Boards require the presence of bioinformaticians. However, all available literature remained rather vague on what are the specific needs in terms of digital tools and expertise to tackle and interpret genomics data to assign novel targeted or biomarker-driven targeted therapies to cancer patients. To fill this gap, in this article, we present a catalog of software families and human skills required for the tumor board bioinformatician, with specific examples of real-world applications associated with each element presented.
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Affiliation(s)
- Matteo Pallocca
- Institute of Experimental Endocrinology and Oncology, National Research Council, Via Sergio Pansini, 5, 80131 Naples, Italy
| | - Martina Betti
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
| | - Sara Baldinelli
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
| | - Ramona Palombo
- Institute of Experimental Endocrinology and Oncology, National Research Council, Via Sergio Pansini, 5, 80131 Naples, Italy
| | - Gabriele Bucci
- Center for OMICS Sciences, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milan, Italy
| | - Luca Mazzarella
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, IRCCS IEO - European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
- Department of Experimental Oncology, IRCCS IEO - European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, and Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milan, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
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21
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Markandran K, Clemente KNM, Tan E, Attal K, Chee QZ, Cheung C, Chen CK. The Future of Kawasaki Disease Diagnosis: Liquid Biopsy May Hold the Key. Int J Mol Sci 2024; 25:8062. [PMID: 39125631 PMCID: PMC11311979 DOI: 10.3390/ijms25158062] [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: 06/11/2024] [Revised: 07/13/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
Kawasaki disease (KD) is a febrile illness characterised by systemic inflammation of small- and medium-sized blood vessels, which commonly occurs in young children. Although self-limiting, there is a risk of developing coronary artery lesions as the disease progresses, with delay in diagnosis and treatment. Unfortunately, the diagnosis of KD continues to remain a clinical dilemma. Thus, this article not only summarises the key research gaps associated with KD, but also evaluates the possibility of using circulating endothelial injury biomarkers, such as circulating endothelial cells, endothelial microparticles and vascular endothelial cell-free DNA, as diagnostic and prognostic tools for KD: a "liquid biopsy" approach. The challenges of translating liquid biopsies to use in KD and the opportunities for improvement in its diagnosis and management that such translation may provide are discussed. The use of endothelial damage markers, which are easily obtained via blood collection, as diagnostic tools is promising, and we hope this will be translated to clinical applications in the near future.
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Affiliation(s)
- Kasturi Markandran
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (K.M.)
| | - Kristine Nicole Mendoza Clemente
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (K.M.)
| | - Elena Tan
- School of Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Karan Attal
- School of Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Qiao Zhi Chee
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive, Nanyang Technological University, Singapore 636921, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (K.M.)
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
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22
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Bian Y, Gao Y, Lu C, Tian B, Xin L, Lin H, Zhang Y, Zhang X, Zhou S, Wan K, Zhou J, Li Z, Chen H, Wang L. Genome-wide methylation profiling identified methylated KCNA3 and OTOP2 as promising diagnostic markers for esophageal squamous cell carcinoma. Chin Med J (Engl) 2024; 137:1724-1735. [PMID: 37650127 PMCID: PMC11268817 DOI: 10.1097/cm9.0000000000002832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Early detection of esophageal squamous cell carcinoma (ESCC) can considerably improve the prognosis of patients. Aberrant cell-free DNA (cfDNA) methylation signatures are a promising tool for detecting ESCC. However, available markers based on cell-free DNA methylation are still inadequate. This study aimed to identify ESCC-specific cfDNA methylation markers and evaluate the diagnostic performance in the early detection of ESCC. METHODS We performed whole-genome bisulfite sequencing (WGBS) for 24 ESCC tissues and their normal adjacent tissues. Based on the WGBS data, we identified 21,469,837 eligible CpG sites (CpGs). By integrating several methylation datasets, we identified several promising ESCC-specific cell-free DNA methylation markers. Finally, we developed a dual-marker panel based on methylated KCNA3 and OTOP2 , and then, we evaluated its performance in our training and validation cohorts. RESULTS The ESCC diagnostic model constructed based on KCNA3 and OTOP2 had an AUC of 0.91 [95% CI: 0.85-0.95], and an optimal sensitivity and specificity of 84.91% and 94.32%, respectively, in the training cohort. In the independent validation cohort, the AUC was 0.88 [95% CI: 0.83-0.92], along with an optimal sensitivity of 81.5% and specificity of 92.9%. The model sensitivity for stage I-II ESCC was 78.4%, which was slightly lower than the sensitivity of the model (85.7%) for stage III-IV ESCC. CONCLUSION The dual-target panel based on cfDNA showed excellent performance for detecting ESCC and might be an alternative strategy for screening ESCC.
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Affiliation(s)
- Yan Bian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Ye Gao
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Chaojing Lu
- Department of Thoracic Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Bo Tian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Lei Xin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Han Lin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yanhui Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xun Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Siwei Zhou
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Kangkang Wan
- Wuhan Ammunition Life-tech Co., Ltd., Wuhan, Hubei 430000, China
| | - Jun Zhou
- Wuhan Ammunition Life-tech Co., Ltd., Wuhan, Hubei 430000, China
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Hezhong Chen
- Department of Thoracic Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Luowei Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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Chinnappan R, Makhzoum T, Arai M, Hajja A, Abul Rub F, Alodhaibi I, Alfuwais M, Elahi MA, Alshehri EA, Ramachandran L, Mani NK, Abrahim S, Mir MS, Al-Kattan K, Mir TA, Yaqinuddin A. Recent Advances in Biosensor Technology for Early-Stage Detection of Hepatocellular Carcinoma-Specific Biomarkers: An Overview. Diagnostics (Basel) 2024; 14:1519. [PMID: 39061656 PMCID: PMC11276200 DOI: 10.3390/diagnostics14141519] [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: 06/06/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Hepatocellular carcinoma is currently the most common malignancy of the liver. It typically occurs due to a series of oncogenic mutations that lead to aberrant cell replication. Most commonly, hepatocellular carcinoma (HCC) occurs as a result of pre-occurring liver diseases, such as hepatitis and cirrhosis. Given its aggressive nature and poor prognosis, the early screening and diagnosis of HCC are crucial. However, due to its plethora of underlying risk factors and pathophysiologies, patient presentation often varies in the early stages, with many patients presenting with few, if any, specific symptoms in the early stages. Conventionally, screening and diagnosis are performed through radiological examination, with diagnosis confirmed by biopsy. Imaging modalities tend to be limited by their requirement of large, expensive equipment; time-consuming operation; and a lack of accurate diagnosis, whereas a biopsy's invasive nature makes it unappealing for repetitive use. Recently, biosensors have gained attention for their potential to detect numerous conditions rapidly, cheaply, accurately, and without complex equipment and training. Through their sensing platforms, they aim to detect various biomarkers, such as nucleic acids, proteins, and even whole cells extracted by a liquid biopsy. Numerous biosensors have been developed that may detect HCC in its early stages. We discuss the recent updates in biosensing technology, highlighting its competitive potential compared to conventional methodology and its prospects as a tool for screening and diagnosis.
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Affiliation(s)
- Raja Chinnappan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Tariq Makhzoum
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Momo Arai
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Amro Hajja
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Farah Abul Rub
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Ibrahim Alodhaibi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Mohammed Alfuwais
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Muhammad Affan Elahi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Eman Abdullah Alshehri
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Lohit Ramachandran
- Microfluidics, Sensors & Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; (L.R.); (N.K.M.)
| | - Naresh Kumar Mani
- Microfluidics, Sensors & Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; (L.R.); (N.K.M.)
| | - Shugufta Abrahim
- Graduate School of Science and Engineering for Education, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan;
| | - Mohammad Shabab Mir
- School of Pharmacy, Desh Bhagat University, Mandi Gobindgarh 147301, Punjab, India;
| | - Khaled Al-Kattan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
- Lung Health Centre Department, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Tanveer Ahmad Mir
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
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24
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Zhu Q, Xie J, Mei W, Zeng C. Methylated circulating tumor DNA in hepatocellular carcinoma: A comprehensive analysis of biomarker potential and clinical implications. Cancer Treat Rev 2024; 128:102763. [PMID: 38763055 DOI: 10.1016/j.ctrv.2024.102763] [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: 02/12/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
The intricate epigenetic landscape of hepatocellular carcinoma (HCC) is profoundly influenced by alterations in DNA methylation patterns. Understanding these alterations is crucial for unraveling the molecular mechanisms underlying HCC pathogenesis. Methylated circulating tumor DNA (ctDNA) presents itself as an encouraging avenue for biomarker discovery and holds substantial clinical implications in HCC management. This review comprehensively outlines the studies concerning DNA methylation in HCC and underscores the significance of methylated ctDNA within this context. Moreover, a variety of cfDNA methylation-based methodologies, such as 5hmC profiling, bisulfite-based, restriction enzyme-dependent, and enrichment-based methods, provide in-depth insights into the molecular pathology of HCC. Additionally, the integration of methylated ctDNA analysis into clinical practice represents a significant advancement in personalized HCC management. By facilitating cancer screening, prognosis assessment, and treatment response prediction, the utilization of methylated ctDNA signifies a pivotal stride toward enhancing patient care and outcomes in HCC.
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Affiliation(s)
- Qian Zhu
- Department of Gastroenterology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Jiaqi Xie
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Wuxuan Mei
- Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen 518110, China.
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Schmithals C, Kakoschky B, Denk D, von Harten M, Klug JH, Hintermann E, Dropmann A, Hamza E, Jacomin AC, Marquardt JU, Zeuzem S, Schirmacher P, Herrmann E, Christen U, Vogl TJ, Waidmann O, Dooley S, Finkelmeier F, Piiper A. Tumour-specific activation of a tumour-blood transport improves the diagnostic accuracy of blood tumour markers in mice. EBioMedicine 2024; 105:105178. [PMID: 38889481 PMCID: PMC11237870 DOI: 10.1016/j.ebiom.2024.105178] [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: 09/14/2023] [Revised: 04/12/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND The accuracy of blood-based early tumour recognition is compromised by signal production at non-tumoral sites, low amount of signal produced by small tumours, and variable tumour production. Here we examined whether tumour-specific enhancement of vascular permeability by the particular tumour homing peptide, iRGD, which carries dual function of binding to integrin receptors overexpressed in the tumour vasculature and is known to promote extravasation via neuropilin-1 receptor upon site-specific cleavage, might be useful to improve blood-based tumour detection by inducing a yet unrecognised vice versa tumour-to-blood transport. METHODS To detect an iRGD-induced tumour-to-blood transport, we examined the effect of intravenously injected iRGD on blood levels of α-fetoprotein (AFP) and autotaxin in several mouse models of hepatocellular carcinoma (HCC) or in mice with chronic liver injury without HCC, and on prostate-specific antigen (PSA) levels in mice with prostate cancer. FINDINGS Intravenously injected iRGD rapidly and robustly elevated the blood levels of AFP in several mouse models of HCC, but not in mice with chronic liver injury. The effect was primarily seen in mice with small tumours and normal basal blood AFP levels, was attenuated by an anti-neuropilin-1 antibody, and depended on the concentration gradient between tumour and blood. iRGD treatment was also able to increase blood levels of autotaxin in HCC mice, and of PSA in mice with prostate cancer. INTERPRETATION We conclude that iRGD induces a tumour-to-blood transport in a tumour-specific fashion that has potential of improving diagnosis of early stage cancer. FUNDING Deutsche Krebshilfe, DKTK, LOEWE-Frankfurt Cancer Institute.
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Affiliation(s)
- Christian Schmithals
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany
| | - Bianca Kakoschky
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany
| | - Dominic Denk
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Maike von Harten
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany
| | - Jan Henrik Klug
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany
| | - Edith Hintermann
- Pharmazentrum Frankfurt / ZAFES, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Anne Dropmann
- Molecular Hepatology-Alcohol Associated Diseases, Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Germany
| | - Eman Hamza
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Suez University, Faculty of Science, Zoology Department, Suez, Egypt
| | - Anne Claire Jacomin
- Frankfurt Cancer Institute, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany; Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Jens U Marquardt
- Department of Medicine I, University Medical Centre Schleswig-Holstein - Campus Lübeck, Lübeck, Germany
| | - Stefan Zeuzem
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/M., a Partnership Between DKFZ and University Hospital Frankfurt/M., Germany
| | | | - Eva Herrmann
- Goethe University Frankfurt, University Hospital, Institute of Biostatistics and Mathematical Modelling, Germany
| | - Urs Christen
- Pharmazentrum Frankfurt / ZAFES, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Thomas J Vogl
- Goethe University Frankfurt, University Hospital, Institute for Diagnostic and Interventional Radiology, Germany
| | - Oliver Waidmann
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Centrum für Hämatologie und Onkologie Bethanien, Frankfurt/Main, Germany
| | - Steven Dooley
- Molecular Hepatology-Alcohol Associated Diseases, Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Germany
| | - Fabian Finkelmeier
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Albrecht Piiper
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/M., a Partnership Between DKFZ and University Hospital Frankfurt/M., Germany.
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Cheng JC, Swarup N, Morselli M, Huang WL, Aziz M, Caggiano C, Kordi M, Patel A, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong DW. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Res 2024; 52:e50. [PMID: 38797520 PMCID: PMC11194076 DOI: 10.1093/nar/gkae276] [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: 10/08/2023] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Whole-genome bisulfite sequencing (BS-Seq) measures cytosine methylation changes at single-base resolution and can be used to profile cell-free DNA (cfDNA). In plasma, ultrashort single-stranded cfDNA (uscfDNA, ∼50 nt) has been identified together with 167 bp double-stranded mononucleosomal cell-free DNA (mncfDNA). However, the methylation profile of uscfDNA has not been described. Conventional BS-Seq workflows may not be helpful because bisulfite conversion degrades larger DNA into smaller fragments, leading to erroneous categorization as uscfDNA. We describe the '5mCAdpBS-Seq' workflow in which pre-methylated 5mC (5-methylcytosine) single-stranded adapters are ligated to heat-denatured cfDNA before bisulfite conversion. This method retains only DNA fragments that are unaltered by bisulfite treatment, resulting in less biased uscfDNA methylation analysis. Using 5mCAdpBS-Seq, uscfDNA had lower levels of DNA methylation (∼15%) compared to mncfDNA and was enriched in promoters and CpG islands. Hypomethylated uscfDNA fragments were enriched in upstream transcription start sites (TSSs), and the intensity of enrichment was correlated with expressed genes of hemopoietic cells. Using tissue-of-origin deconvolution, we inferred that uscfDNA is derived primarily from eosinophils, neutrophils, and monocytes. As proof-of-principle, we show that characteristics of the methylation profile of uscfDNA can distinguish non-small cell lung carcinoma from non-cancer samples. The 5mCAdpBS-Seq workflow is recommended for any cfDNA methylation-based investigations.
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Affiliation(s)
- Jordan C Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Wei-Lun Huang
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christa Caggiano
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - David Chia
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Zaitlen
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Steve Dubinett
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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27
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Li Y, Wu J, Feng Y, Wang D, Tao H, Wen J, Jiang F, Qian P, Liu Y. Kinetics of plasma cell-free DNA as a prospective biomarker to predict the prognosis and radiotherapy effect of esophageal cancer. Cancer Radiother 2024; 28:242-250. [PMID: 38876937 DOI: 10.1016/j.canrad.2023.11.002] [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: 07/02/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 06/16/2024]
Abstract
PURPOSE The lack of reliable biomarkers for the prognosis and radiotherapy efficacy in esophageal cancer (EC) necessitates further research. The aim of our study was to investigate the predictive utility of plasma cell-free DNA (cfDNA) kinetics in patients with EC. MATERIALS AND METHODS We retrospectively analyzed the clinical data and cfDNA levels (pre-radiotherapy [pre-RT] and post-radiotherapy [post-RT]) and the cfDNA kinetics (cfDNA ratio: post-RT cfDNA/pre-RT cfDNA) of 88 patients. We employed Kaplan-Meier curves to examine the relationship between cfDNA and overall survival (OS) as well as progression-free survival (PFS). Univariate and multivariate Cox regression analyses were executed to ascertain the independent risk factors in EC. RESULTS The pre-RT cfDNA levels were positively correlated with clinical stage (P=0.001). The pre-RT cfDNA levels (cutoff value=16.915ng/mL), but not the post-RT cfDNA levels, were linked to a diminished OS (P<0.001) and PFS (P=0.0137). CfDNA kinetics (cutoff value=0.883) were positively associated with OS (P=0.0326) and PFS (P=0.0020). Notably, we identified independent risk factors for OS in EC treated with RT, including cfDNA ratio (high/low) (HR=0.447 [0.221-0.914] P=0.025), ECOG (0/1/2) (HR=0.501 [0.285-0.880] p=0.016), and histological type (esophagal squamous cell carcinoma [ESCC]/non-ESCC) (HR=3.973 [1.074-14.692] P=0.039). CONCLUSION Plasma cfDNA kinetics is associated with prognosis and radiotherapy effect in EC undergoing RT, suggesting potential clinical application of a cheap and simple blood-based test.
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Affiliation(s)
- Y Li
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - J Wu
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - Y Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - D Wang
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - H Tao
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - J Wen
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - F Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - P Qian
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China.
| | - Y Liu
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China.
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28
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Ren S, Yu C, Huang Q. Diagnostic value of combined detection of plasma cfDNA concentration and integrity in NSCLC. Lung Cancer Manag 2024; 13:LMT64. [PMID: 38812772 PMCID: PMC11131340 DOI: 10.2217/lmt-2023-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 05/31/2024] Open
Abstract
Aim: To evaluate the value of combined detection of plasma cfDNA concentration and integrity in the early diagnosis of NSCLC. Methods: Real-time fluorescence quantitative PCR was used to determine the concentration and integrity of plasma cfDNA in 71 NSCLC patients and 53 healthy people. Results: Combined detection of plasma cfDNA concentration and integrity had higher diagnostic power in differentiating NSCLC patients with stage I/II from healthy people than detection of plasma cfDNA concentration alone or integrity alone. The AUC, sensitivity and specificity of the combined detection of plasma cfDNA concentration and integrity were 0.781, 0.62 and 0.85. Conclusion: Combined detection of plasma cfDNA concentration and integrity could improve the diagnostic value in NSCLC detection.
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Affiliation(s)
- Sai Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
- Department of Laboratory Medicine, People's Hospital of Chongqing Liang Jiang New Area, Chongqing, 401121, PR China
| | - Chunli Yu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
- Department of Laboratory Medicine, Chengdu Xinhua Hospital, Chengdu, 610055, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
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29
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Li SJ, Gao X, Wang ZH, Li J, Zeng LT, Dang YM, Ma YQ, Zhang LQ, Wang QY, Zhang YM, Liu HL, Qi RM, Cai JP. Cell-free DNA methylation patterns in aging and their association with inflamm-aging. Epigenomics 2024; 16:715-731. [PMID: 38869474 PMCID: PMC11318736 DOI: 10.1080/17501911.2024.2340958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/05/2024] [Indexed: 06/14/2024] Open
Abstract
Aim: Liquid biopsies analyzing cell-free DNA (cfDNA) methylation in plasma offer a noninvasive diagnostic for diseases, with the potential of aging biomarkers underexplored. Methods: Utilizing enzymatic methyl-seq (EM-seq), this study assessed cfDNA methylation patterns in aging with blood from 35 healthy individuals. Results: It found aging signatures, including higher cfDNA levels and variations in fragment sizes, plus approximately 2000 age-related differentially methylated CpG sites. A biological age predictive model based on 48 CpG sites showed a strong correlation with chronological age, verified by two datasets. Age-specific epigenetic shifts linked to inflammation were revealed through differentially methylated regions profiling and Olink proteomics. Conclusion: These findings suggest cfDNA methylation as a potential aging biomarker and might exacerbate immunoinflammatory reactivity in older individuals.
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Affiliation(s)
- Si-Jia Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
| | - Xin Gao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
| | - Zi-Hui Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
| | - Jin Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Lv-Tao Zeng
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Ya-Min Dang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
| | - Ya-Qing Ma
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Li-Qun Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Qing-Yu Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Ying-Min Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Hong-Lei Liu
- School of Biomedical Engineering, Capital Medical University, 100730, PR China
| | - Ruo-Mei Qi
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
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30
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Beigi YZ, Lanjanian H, Fayazi R, Salimi M, Hoseyni BHM, Noroozizadeh MH, Masoudi-Nejad A. Heterogeneity and molecular landscape of melanoma: implications for targeted therapy. MOLECULAR BIOMEDICINE 2024; 5:17. [PMID: 38724687 PMCID: PMC11082128 DOI: 10.1186/s43556-024-00182-2] [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: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Uveal cancer (UM) offers a complex molecular landscape characterized by substantial heterogeneity, both on the genetic and epigenetic levels. This heterogeneity plays a critical position in shaping the behavior and response to therapy for this uncommon ocular malignancy. Targeted treatments with gene-specific therapeutic molecules may prove useful in overcoming radiation resistance, however, the diverse molecular makeups of UM call for a patient-specific approach in therapy procedures. We need to understand the intricate molecular landscape of UM to develop targeted treatments customized to each patient's specific genetic mutations. One of the promising approaches is using liquid biopsies, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), for detecting and monitoring the disease at the early stages. These non-invasive methods can help us identify the most effective treatment strategies for each patient. Single-cellular is a brand-new analysis platform that gives treasured insights into diagnosis, prognosis, and remedy. The incorporation of this data with known clinical and genomics information will give a better understanding of the complicated molecular mechanisms that UM diseases exploit. In this review, we focused on the heterogeneity and molecular panorama of UM, and to achieve this goal, the authors conducted an exhaustive literature evaluation spanning 1998 to 2023, using keywords like "uveal melanoma, "heterogeneity". "Targeted therapies"," "CTCs," and "single-cellular analysis".
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Affiliation(s)
- Yasaman Zohrab Beigi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hossein Lanjanian
- Software Engineering Department, Engineering Faculty, Istanbul Topkapi University, Istanbul, Turkey
| | - Reyhane Fayazi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Behnaz Haji Molla Hoseyni
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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31
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Conca V, Ciracì P, Boccaccio C, Minelli A, Antoniotti C, Cremolini C. Waiting for the "liquid revolution" in the adjuvant treatment of colon cancer patients: a review of ongoing trials. Cancer Treat Rev 2024; 126:102735. [PMID: 38613871 DOI: 10.1016/j.ctrv.2024.102735] [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: 12/01/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/15/2024]
Abstract
Since colon cancer has a high rate of shedding of tumour fragments into the blood, several research efforts are now focused on the investigation of the minimal residual disease through the detection of ctDNA to tailor the adjuvant therapy of colon cancer patients and optimize its cost/effectiveness balance. The negative prognostic impact of detectable ctDNA in patients' blood after radical surgery for colon cancer is well established. Several clinical trials adopting heterogeneous designs and techniques are now ongoing to translate promises into daily practice by answering five general questions: i) is a ctDNA-guided decision making efficacious in the post-operative management of colon cancer patients? ii) are de-escalation strategies possible in ctDNA-negative cases? iii) are escalation strategies useful to improve the prognosis of ctDNA-positive patients? iv) when MRD is identified at the end of the adjuvant chemotherapy, is another post-adjuvant systemic therapy efficacious? v) can we exploit ctDNA technologies in the follow up of colon cancer patients? This review focuses on currently ongoing trials and how their results may affect the ctDNA "liquid revolution" of early colon cancer.
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Affiliation(s)
- V Conca
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - P Ciracì
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Boccaccio
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A Minelli
- Division of Medical Oncology, Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - C Antoniotti
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.
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32
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Lin M, Hu L, Shen S, Liu J, Liu Y, Xu Y, Chen H, Sugimoto K, Li J, Kamitsukasa I, Hiwasa T, Wang H, Xu A. Atherosclerosis-related biomarker PABPC1 predicts pan-cancer events. Stroke Vasc Neurol 2024; 9:108-125. [PMID: 37311641 PMCID: PMC11103157 DOI: 10.1136/svn-2022-002246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Atherosclerosis (AS) and tumours are the leading causes of death worldwide and share common risk factors, detection methods and molecular markers. Therefore, searching for serum markers shared by AS and tumours is beneficial to the early diagnosis of patients. METHODS The sera of 23 patients with AS-related transient ischaemic attack were screened by serological identification of antigens through recombinant cDNA expression cloning (SEREX), and cDNA clones were identified. Pathway function enrichment analysis was performed on cDNA clones to identify their biological pathways and determine whether they were related to AS or tumours. Subsequently, gene-gene and protein-protein interactions were performed and AS-associated markers would be discovered. The expression of AS biomarkers in human normal organs and pan-cancer tumour tissues were explored. Then, immune infiltration level and tumour mutation burden of various immune cells were evaluated. Survival curves analysis could show the expression of AS markers in pan-cancer. RESULTS AS-related sera were screened by SEREX, and 83 cDNA clones with high homology were obtained. Through functional enrichment analysis, it was found that their functions were closely related to AS and tumour functions. After multiple biological information interaction screening and the external cohort validating, poly(A) binding protein cytoplasmic 1 (PABPC1) was found to be a potential AS biomarker. To assess whether PABPC1 was related to pan-cancer, its expression in different tumour pathological stages and ages was screened. Since AS-associated proteins were closely related to cancer immune infiltration, we investigated and found that PABPC1 had the same role in pan-cancer. Finally, analysis of Kaplan-Meier survival curves revealed that high PABPC1 expression in pan-cancer was associated with high risk of death. CONCLUSIONS Through the findings of SEREX and bioinformatics pan-cancer analysis, we concluded that PABPC1 might serve as a potential biomarker for the prediction and diagnosis of AS and pan-cancer.
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Affiliation(s)
- Miao Lin
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Liubing Hu
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
- The Biomedical Translational Research Institute,Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Si Shen
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Radiology, Medical Imaging Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jiyue Liu
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yanyan Liu
- The Biomedical Translational Research Institute,Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Yixian Xu
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Honglin Chen
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Radiology, Medical Imaging Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Kazuo Sugimoto
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Neurology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jianshuang Li
- The Biomedical Translational Research Institute,Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Ikuo Kamitsukasa
- Department of Neurology, Chiba Rosai Hospital, Chiba, Japan
- Department of Neurology, Chibaken Saiseikai Narashino Hospital, Chiba, Japan
| | - Takaki Hiwasa
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hao Wang
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Anding Xu
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
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Abstract
With the rapid development of science and technology, cell-free DNA (cfDNA) is rapidly becoming an important biomarker for tumor diagnosis, monitoring and prognosis, and this cfDNA-based liquid biopsy technology has great potential to become an important part of precision medicine. cfDNA is the total amount of free DNA in the systemic circulation, including DNA fragments derived from tumor cells and all other somatic cells. Tumor cells release fragments of DNA into the bloodstream, and this source of cfDNA is called circulating tumor DNA (ctDNA). cfDNA detection has become a major focus in the field of tumor research in recent years, which provides a new opportunity for non-invasive diagnosis and prognosis of cancer. In this paper, we discuss the limitations of the study on the origin and dynamics analysis of ctDNA, and how to solve these problems in the future. Although the future faces major challenges, it also contains great potential.
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Liu SC. Circulating tumor DNA in liquid biopsy: Current diagnostic limitation. World J Gastroenterol 2024; 30:2175-2178. [PMID: 38681986 PMCID: PMC11045476 DOI: 10.3748/wjg.v30.i15.2175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
With the rapid development of science and technology, cell-free DNA (cfDNA) is rapidly becoming an important biomarker for tumor diagnosis, monitoring and prognosis, and this cfDNA-based liquid biopsy technology has great potential to become an important part of precision medicine. cfDNA is the total amount of free DNA in the systemic circulation, including DNA fragments derived from tumor cells and all other somatic cells. Tumor cells release fragments of DNA into the bloodstream, and this source of cfDNA is called circulating tumor DNA (ctDNA). cfDNA detection has become a major focus in the field of tumor research in recent years, which provides a new opportunity for non-invasive diagnosis and prognosis of cancer. In this paper, we discuss the limitations of the study on the origin and dynamics analysis of ctDNA, and how to solve these problems in the future. Although the future faces major challenges, it also contains great potential.
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Affiliation(s)
- Shi-Cai Liu
- School of Medical Information, Wannan Medical College, Wuhu 241002, Anhui Province, China
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Xu J, Zhao Y, Chen Z, Wei L. Clinical Application of Different Liquid Biopsy Components in Hepatocellular Carcinoma. J Pers Med 2024; 14:420. [PMID: 38673047 PMCID: PMC11051574 DOI: 10.3390/jpm14040420] [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: 02/23/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer, usually occurring in the background of chronic liver disease. HCC lethality rate is in the third highest place in the world. Patients with HCC have concealed early symptoms and possess a high-level of heterogeneity. Once diagnosed, most of the tumors are in advanced stages and have a poor prognosis. The sensitivity and specificity of existing detection modalities and protocols are suboptimal. HCC calls for more sophisticated and individualized therapeutic regimens. Liquid biopsy is non-invasive, repeatable, unaffected by location, and can be monitored dynamically. It has emerged as a useable aid in achieving precision malignant tumor treatment. Circulating tumor cells (CTCs), circulating nucleic acids, exosomes and tumor-educated platelets are the commonest components of a liquid biopsy. It possesses the theoretical ability to conquer the high heterogeneity and the difficulty of early detection for HCC patients. In this review, we summarize the common enrichment techniques and the clinical applications in HCC for different liquid biopsy components. Tumor recurrence after HCC-related liver transplantation is more insidious and difficult to treat. The clinical use of liquid biopsy in HCC-related liver transplantation is also summarized in this review.
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Affiliation(s)
| | | | | | - Lai Wei
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan 430030, China; (J.X.); (Y.Z.); (Z.C.)
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Dai L, Johnson-Buck A, Laird PW, Tewari M, Walter NG. Ultrasensitive amplification-free quantification of a methyl CpG-rich cancer biomarker by single-molecule kinetic fingerprinting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.587997. [PMID: 38645159 PMCID: PMC11030368 DOI: 10.1101/2024.04.06.587997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker in liquid biopsies of cell-free DNA. Currently, quantification of DNA methylation relies heavily on bisulfite conversion followed by PCR amplification and NGS or microarray analysis. PCR is subject to potential bias in differential amplification of bisulfite-converted methylated versus unmethylated sequences. Here, we combine bisulfite conversion with single-molecule kinetic fingerprinting to develop an amplification-free assay for DNA methylation at the branched-chain amino acid transaminase 1 (BCAT1) promoter. Our assay selectively responds to methylated sequences with a limit of detection below 1 fM and a specificity of 99.9999%. Evaluating complex genomic DNA matrices, we reliably distinguish 2-5% DNA methylation at the BCAT1 promoter in whole blood DNA from completely unmethylated whole-genome amplified DNA. Taken together, these results demonstrate the feasibility and sensitivity of our amplification-free, single-molecule quantification approach to improve the early detection of methylated cancer DNA biomarkers.
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Affiliation(s)
- Liuhan Dai
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Muneesh Tewari
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
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Yang X, Li Q, Zeng T. Peripheral CD4 + T cells correlate with response and survival in patients with advanced non-small cell lung cancer receiving chemo-immunotherapy. Front Immunol 2024; 15:1364507. [PMID: 38650951 PMCID: PMC11033411 DOI: 10.3389/fimmu.2024.1364507] [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] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Background The aim of the present study was to explore the potential of peripheral immune cells in predicting the response and prognosis of patients with advanced non-small cell lung cancer (NSCLC) receiving anti-PD-1 immunotherapy and platinum-based chemotherapy. Participants and Methods We utilized flow cytometry to examine the levels and dynamics of blood immune cells in 79 advanced NSCLC patients treated with the chemoimmunotherapy between December 2019 and January 2022. The pre- and post-treatment blood samples were collected within 3 days prior to the initiation of the first and third cycle of combination treatment, respectively. Progression-free survival (PFS) and overall survival (OS) analyses were conducted using Kaplan-Meier method and Cox regression models. Results The pre-treatment CD4+/Total T cells ratio was significantly higher in responders than non-responders (P < 0.05). The levels of pre-treatment total lymphocytes (P = 0.012), total B lymphocytes (P = 0.025), and NK cells (P = 0.022), and post-treatment NK cells (P = 0.011) and NKT cells (P = 0.035) were significantly associated with OS. Post-treatment CD8+/Total T cells ratio was positively correlated with OS (P = 0.038). In multivariate analysis, post-treatment NK cells and post-treatment CD4+CD8+/Total T cells ratio were negatively associated with OS (hazard ratio [HR] = 10.30, P = 0.038) and PFS (HR = 1.95, P = 0.022), respectively. Notably, significantly positive correlations were observed between CD4+/Total T cells ratio and prognosis both before and after treatment (P < 0.05). Conclusion To summarize, our finding reveals that high CD4+/total T cells ratio was associated with favorable response and prognosis, highlighting its potential as a predictive biomarker to guide the selection of likely responders to platinum and anti-PD-1 combination therapy.
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Affiliation(s)
- Xin Yang
- Department of Cardio-Thoracic Surgery, Deyang People’s Hospital, Deyang, Sichuan, China
| | - Qiao Li
- Department of Pathology, Deyang People’s Hospital, Deyang, Sichuan, China
| | - Tianyang Zeng
- Department of Thoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Zhou J, Chen Q, Ren R, Yang J, Liu B, Horton JR, Chang C, Li C, Maksoud L, Yang Y, Rotili D, Zhang X, Blumenthal RM, Chen T, Gao Y, Valente S, Mai A, Cheng X. Quinoline-based compounds can inhibit diverse enzymes that act on DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587980. [PMID: 38617249 PMCID: PMC11014617 DOI: 10.1101/2024.04.03.587980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
DNA methylation, as exemplified by cytosine-C5 methylation in mammals and adenine-N6 methylation in bacteria, is a crucial epigenetic mechanism driving numerous vital biological processes. Developing non-nucleoside inhibitors to cause DNA hypomethylation is a high priority, in order to treat a variety of significant medical conditions without the toxicities associated with existing cytidine-based hypomethylating agents. In this study, we have characterized fifteen quinoline-based analogs. Notably, compounds with additions like a methylamine ( 9 ) or methylpiperazine ( 11 ) demonstrate similar low micromolar inhibitory potency against both human DNMT1 (which generates C5-methylcytosine) and Clostridioides difficile CamA (which generates N6-methyladenine). Structurally, compounds 9 and 11 specifically intercalate into CamA-bound DNA via the minor groove, adjacent to the target adenine, leading to a substantial conformational shift that moves the catalytic domain away from the DNA. This study adds to the limited examples of DNA methyltransferases being inhibited by non-nucleotide compounds through DNA intercalation, following the discovery of dicyanopyridine-based inhibitors for DNMT1. Furthermore, our study shows that some of these quinoline-based analogs inhibit other enzymes that act on DNA, such as polymerases and base excision repair glycosylases. Finally, in cancer cells compound 11 elicits DNA damage response via p53 activation. Abstract Figure Highlights Six of fifteen quinoline-based derivatives demonstrated comparable low micromolar inhibitory effects on human cytosine methyltransferase DNMT1, and the bacterial adenine methyltransferases Clostridioides difficile CamA and Caulobacter crescentus CcrM. Compounds 9 and 11 were found to intercalate into a DNA substrate bound by CamA. These quinoline-based derivatives also showed inhibitory activity against various base excision repair DNA glycosylases, and DNA and RNA polymerases. Compound 11 provokes DNA damage response via p53 activation in cancer cells.
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Pilala KM, Kotronopoulos G, Levis P, Giagkos GC, Stravodimos K, Vassilacopoulou D, Scorilas A, Avgeris M. MIR145 Core Promoter Methylation in Pretreatment Cell-Free DNA: A Liquid Biopsy Tool for Muscle-Invasive Bladder Cancer Treatment Outcome. JCO Precis Oncol 2024; 8:e2300414. [PMID: 38579191 DOI: 10.1200/po.23.00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/06/2024] [Accepted: 02/13/2024] [Indexed: 04/07/2024] Open
Abstract
PURPOSE The lack of personalized management of bladder cancer (BlCa) results in patients' lifelong post-treatment monitoring with invasive interventions, underlying the urgent need for tailored and minimally invasive health care services. On the basis of our previous findings on miR-143/145 cluster methylation in bladder tumors, we evaluated its clinical significance in pretreatment cell-free DNA (cfDNA) of patients with BlCa. MATERIALS AND METHODS Methylation analysis was performed in our screening cohort (120 patients with BlCa; 20 age-matched healthy donors) by bisulfite-based pyrosequencing. Tumor recurrence/progression for patients with non-muscle-invasive bladder cancer, and progression and mortality for patients with muscle-invasive bladder cancer (MIBC) were used as clinical end point events in survival analysis. Bootstrap analysis was applied for internal validation of Cox regression models and decision curve analysis for assessment of clinical benefit on disease prognosis. RESULTS Decreased methylation of MIR145 core promoter in pretreatment cfDNA was associated with short-term disease progression (multivariate Cox: hazard ratio [HR], 2.027 [95% CI, 1.157 to 3.551]; P = .010) and poor overall survival (multivariate Cox: HR, 2.098 [95% CI, 1.154 to 3.817]; P = .009) of patients with MIBC after radical cystectomy (RC). Multivariate models incorporating MIR145 promoter methylation in cfDNA with tumor stage clearly ameliorated patients' risk stratification, highlighting superior clinical benefit in MIBC prognostication. CONCLUSION Reduced pretreatment cfDNA methylation of MIR145 core promoter was markedly correlated with increased risk for short-term progression and worse survival of patients with MIBC after RC and adjuvant therapy, supporting modern personalized and minimally invasive prognosis. Methylation profiling of MIR145 core promoter in pretreatment cfDNA could serve as a minimally invasive and independent predictor of MIBC treatment outcome and emerge as a promising marker for blood-based test in BlCa.
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Affiliation(s)
- Katerina-Marina Pilala
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Kotronopoulos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Levis
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios-Christos Giagkos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Stravodimos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dido Vassilacopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece
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40
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Li D, Qian X, Wang Y, Yin Y, Sun H, Zhao H, Wu J, Qiu L. Molecular characterization and functional roles of circulating cell-free extrachromosomal circular DNA. Clin Chim Acta 2024; 556:117822. [PMID: 38325714 DOI: 10.1016/j.cca.2024.117822] [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: 12/24/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Circular DNA segments isolated from chromosomes are known as extrachromosomal circular DNA (eccDNA). Its distinct structure and characteristics, along with the variations observed in different disease states, makes it a promising biomarker. Recent studies have revealed the presence of eccDNAs in body fluids, indicating their involvement in various biological functions. This finding opens up avenues for utilizing eccDNAs as convenient and real-time biomarkers for disease diagnosis, treatment monitoring, and prognosis assessment through noninvasive analysis of body fluids. In this comprehensive review, we focused on elucidating the size profiles, potential mechanisms of formation and clearance, detection methods, and potential clinical applications of eccDNAs. We aimed to provide a valuable reference resource for future research in this field.
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Affiliation(s)
- Dandan Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Xia Qian
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Yingjie Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Yicong Yin
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Huishan Sun
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
| | - Jie Wu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
| | - Ling Qiu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
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Cheng JC, Swarup N, Wong DTW, Chia D. A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection. Front Oncol 2024; 14:1332004. [PMID: 38511142 PMCID: PMC10951391 DOI: 10.3389/fonc.2024.1332004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/07/2024] [Indexed: 03/22/2024] Open
Abstract
In clinical oncology, cell-free DNA (cfDNA) has shown immense potential in its ability to noninvasively detect cancer at various stages and monitor the progression of therapy. Despite the rapid improvements in cfDNA liquid biopsy approaches, achieving the required sensitivity to detect rare tumor-derived cfDNA still remains a challenge. For next-generation sequencing, the perceived presentation of cfDNA is strongly linked to the extraction and library preparation protocols. Conventional double-stranded DNA library preparation (dsDNA-LP) focuses on assessing ~167bp double-stranded mononucleosomal (mncfDNA) and its other oligonucleosomal cell-free DNA counterparts in plasma. However, dsDNA-LP methods fail to include short, single-stranded, or nicked DNA in the final library preparation, biasing the representation of the actual cfDNA populations in plasma. The emergence of single-stranded library preparation (ssDNA-LP) strategies over the past decade has now allowed these other populations of cfDNA to be studied from plasma. With the use of ssDNA-LP, single-stranded, nicked, and ultrashort cfDNA can be comprehensively assessed for its molecular characteristics and clinical potential. In this review, we overview the current literature on applications of ssDNA-LP on plasma cfDNA from a potential cancer liquid biopsy perspective. To this end, we discuss the molecular principles of single-stranded DNA adapter ligation, how library preparation contributes to the understanding of native cfDNA characteristics, and the potential for ssDNA-LP to improve the sensitivity of circulating tumor DNA detection. Additionally, we review the current literature on the newly reported species of plasma ultrashort single-stranded cell-free DNA plasma, which appear biologically distinct from mncfDNA. We conclude with a discussion of future perspectives of ssDNA-LP for liquid biopsy endeavors.
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Affiliation(s)
- Jordan C. Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
- Stanford Cancer Institute, Stanford University, Stanford, CA, United States
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - David T. W. Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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Verma S, Young S, Kennedy TAC, Carvalhana I, Black M, Baer K, Churchman E, Warner A, Allan AL, Izaguirre-Carbonell J, Dhani H, Louie AV, Palma DA, Breadner DA. Detection of Circulating Tumor DNA After Stereotactic Ablative Radiotherapy in Patients With Unbiopsied Lung Tumors (SABR-DETECT). Clin Lung Cancer 2024; 25:e87-e91. [PMID: 38101984 DOI: 10.1016/j.cllc.2023.11.013] [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: 08/08/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
For patients with stage I/IIA non-small-cell lung cancer (NSCLC), surgical resection is the standard treatment. However, some of these patients are not candidates for surgery or refuse a surgical option. Definitive stereotactic ablative radiotherapy (SABR) is a standard approach in these patients. Approximately 15% of patients undergoing SABR for localized NSCLC will experience a recurrence within 2 years. Furthermore, many of these patients are deemed appropriate for SABR without a tissue diagnosis, based on the likelihood of malignancy which can be calculated by validated models. A liquid biopsy, detecting ctDNA, would be useful in early detection of recurrences, and documenting a cancer diagnosis in patients without a biopsy. This is a multi-institutional study enrolling patients with suspected stage I/IIA NSCLC and a pretreatment likelihood of malignancy of ≥60% using the validated models for patients without a tissue diagnosis, in cohort 1 (n = 45). The second cohort will consist of biopsied patients (n = 30-60). SABR will be delivered as per risk-adapted protocol. Plasma will be collected for ctDNA analysis prior to the first fraction of SABR, 24 to 72 hours after first fraction, and at 3, 6, 9, 12, 18, and 24-months. The patients will be followed up with imaging at 3, 6, 9, 12, 18, and 24-months. The primary objective is to assess whether a cancer detection liquid biopsy platform can predict recurrence of NSCLC. The secondary objectives are to assess the impact of SABR on detection rates of ctDNA in patients undergoing SABR and to correlate ctDNA positivity and pretreatment probability of malignancy (NCT05921474).
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Affiliation(s)
- Saurav Verma
- Division of Medical Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Sympascho Young
- Division of Radiation Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Thomas A C Kennedy
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ilda Carvalhana
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Morgan Black
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Kathie Baer
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Emma Churchman
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Andrew Warner
- Division of Radiation Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Alison L Allan
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada; Department of Anatomy & Cell Biology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | | | | | - Alexander V Louie
- Division of Radiation Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - David A Palma
- Division of Radiation Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Daniel A Breadner
- Division of Medical Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada.
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43
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Giannini LAA, Boers RG, van der Ende EL, Poos JM, Jiskoot LC, Boers JB, van IJcken WFJ, Dopper EG, Pijnenburg YAL, Seelaar H, Meeter LH, van Rooij JGJ, Scheper W, Gribnau J, van Swieten JC. Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia. Ann Clin Transl Neurol 2024; 11:744-756. [PMID: 38481040 DOI: 10.1002/acn3.51997] [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: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Methylation of plasma cell-free DNA (cfDNA) has potential as a marker of brain damage in neurodegenerative diseases such as frontotemporal dementia (FTD). Here, we study methylation of cfDNA in presymptomatic and symptomatic carriers of genetic FTD pathogenic variants, next to healthy controls. METHODS cfDNA was isolated from cross-sectional plasma of 10 presymptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), 10 symptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), and 9 healthy controls. Genome-wide methylation of cfDNA was determined using a high-resolution sequencing technique (MeD-seq). Cumulative scores based on the identified differentially methylated regions (DMRs) were estimated for presymptomatic carriers (vs. controls and symptomatic carriers), and reevaluated in a validation cohort (8 presymptomatic: 3 C9orf72, 3 GRN, and 2 MAPT; 26 symptomatic: 7 C9orf72, 6 GRN, 12 MAPT, and 1 TARDBP; 13 noncarriers from genetic FTD families). RESULTS Presymptomatic carriers showed a distinctive methylation profile compared to healthy controls and symptomatic carriers. Cumulative DMR scores in presymptomatic carriers enabled to significantly differentiate presymptomatic carriers from healthy controls (p < 0.001) and symptomatic carriers (p < 0.001). In the validation cohort, these scores differentiated presymptomatic carriers from symptomatic carriers (p ≤ 0.007) only. Transcription-start-site methylation in presymptomatic carriers, generally associated with gene downregulation, was enriched for genes involved in ubiquitin-dependent processes, while gene body methylation, generally associated with gene upregulation, was enriched for genes involved in neuronal cell processes. INTERPRETATION A distinctive methylation profile of cfDNA characterizes the presymptomatic stage of genetic FTD, and could reflect neuronal death in this stage.
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Affiliation(s)
- Lucia A A Giannini
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emma L van der Ende
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jackie M Poos
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lize C Jiskoot
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elise G Dopper
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Harro Seelaar
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieke H Meeter
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wiep Scheper
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Human Genetics, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - John C van Swieten
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
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44
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Grossi I, Assoni C, Lorini L, Smussi D, Gurizzan C, Grisanti S, Paderno A, Mattavelli D, Piazza C, Pelisenco IA, De Petro G, Salvi A, Bossi P. Evaluation of DNA methylation levels of SEPT9 and SHOX2 in plasma of patients with head and neck squamous cell carcinoma using droplet digital PCR. Oncol Rep 2024; 51:52. [PMID: 38299234 PMCID: PMC10865173 DOI: 10.3892/or.2024.8711] [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: 07/14/2023] [Accepted: 12/12/2023] [Indexed: 02/02/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the seventh most commonly diagnosed cancer globally. HNSCC develops from the mucosa of the oral cavity, pharynx and larynx. Methylation levels of septin 9 (SEPT9) and short stature homeobox 2 (SHOX2) genes in circulating cell‑free DNA (ccfDNA) are considered epigenetic biomarkers and have shown predictive value in preliminary reports in HNSCC. Liquid biopsy is a non‑invasive procedure that collects tumor‑derived molecules, including ccfDNA. In the present study, a droplet digital PCR (ddPCR)‑based assay was developed to detect DNA methylation levels of circulating SEPT9 and SHOX2 in the plasma of patients with HNSCC. The assay was first set up using commercial methylated and unmethylated DNA. The dynamic changes in the methylation levels of SEPT9 and SHOX2 were then quantified in 20 patients with HNSCC during follow‑up. The results highlighted: i) The ability of the ddPCR‑based assay to detect very low copies of methylated molecules; ii) the significant decrease in SEPT9 and SHOX2 methylation levels in the plasma of patients with HNSCC at the first time points of follow‑up with respect to T0; iii) a different trend of longitudinally DNA methylation variations in small groups of stratified patients. The absolute and precise quantification of SEPT9 and SHOX2 methylation levels in HNSCC may be useful for studies with translational potential.
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Affiliation(s)
- Ilaria Grossi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Claudia Assoni
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Luigi Lorini
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Davide Smussi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Cristina Gurizzan
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Salvatore Grisanti
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Alberto Paderno
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Davide Mattavelli
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Cesare Piazza
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Iulia Andreea Pelisenco
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Giuseppina De Petro
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Alessandro Salvi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Paolo Bossi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
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45
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Yang Q, Zhu X, Liu Y, He Z, Xu H, Zheng H, Huang Z, Wang D, Lin X, Guo P, Chen H. Reduced representative methylome profiling of cell-free DNA for breast cancer detection. Clin Epigenetics 2024; 16:33. [PMID: 38414041 PMCID: PMC10898043 DOI: 10.1186/s13148-024-01641-x] [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: 11/30/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Whole-genome methylation sequencing of cfDNA is not cost-effective for tumor detection. Here, we introduce reduced representative methylome profiling (RRMP), which employs restriction enzyme for depletion of AT-rich sequence to achieve enrichment and deep sequencing of CG-rich sequences. METHODS We first verified the ability of RRMP to enrich CG-rich sequences using tumor cell genomic DNA and analyzed differential methylation regions between tumor cells and normal whole blood cells. We then analyzed cfDNA from 29 breast cancer patients and 27 non-breast cancer individuals to detect breast cancer by building machine learning models. RESULTS RRMP captured 81.9% CpG islands and 75.2% gene promoters when sequenced to 10 billion base pairs, with an enrichment efficiency being comparable to RRBS. RRMP allowed us to assess DNA methylation changes between tumor cells and whole blood cells. Applying our approach to cfDNA from 29 breast cancer patients and 27 non-breast cancer individuals, we developed machine learning models that could discriminate between breast cancer and non-breast cancer controls (AUC = 0.85), suggesting possibilities for truly non-invasive cancer detection. CONCLUSIONS We developed a new method to achieve reduced representative methylome profiling of cell-free DNA for tumor detection.
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Affiliation(s)
- Qingmo Yang
- The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xingqiang Zhu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Yulu Liu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Zhi He
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Huan Xu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Hailing Zheng
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Zhiming Huang
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Dan Wang
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Xiaofang Lin
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Ping Guo
- Xiamen Huazao Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China.
| | - Hongliang Chen
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China.
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
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46
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Jiang YH, Liu YS, Wei YC, Jhang JF, Kuo HC, Huang HH, Chan MWY, Lin GL, Cheng WC, Lin SC, Wang HJ. Hypermethylation Loci of ZNF671, IRF8, and OTX1 as Potential Urine-Based Predictive Biomarkers for Bladder Cancer. Diagnostics (Basel) 2024; 14:468. [PMID: 38472940 DOI: 10.3390/diagnostics14050468] [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: 01/05/2024] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Bladder cancer (BCa) is a significant health issue and poses a healthcare burden on patients, highlighting the importance of an effective detection method. Here, we developed a urine DNA methylation diagnostic panel for distinguishing between BCa and non-BCa. In the discovery stage, an analysis of the TCGA database was conducted to identify BCa-specific DNA hypermethylation markers. In the validation phase, DNA methylation levels of urine samples were measured with real-time quantitative methylation-specific PCR (qMSP). Comparative analysis of the methylation levels between BCa and non-BCa, along with the receiver operating characteristic (ROC) analyses with machine learning algorithms (logistic regression and decision tree methods) were conducted to develop practical diagnostic panels. The performance evaluation of the panel shows that the individual biomarkers of ZNF671, OTX1, and IRF8 achieved AUCs of 0.86, 0.82, and 0.81, respectively, while the combined yielded an AUC of 0.91. The diagnostic panel using the decision tree algorithm attained an accuracy, sensitivity, and specificity of 82.6%, 75.0%, and 90.9%, respectively. Our results show that the urine-based DNA methylation diagnostic panel provides a sensitive and specific method for detecting and stratifying BCa, showing promise as a standard test that could enhance the diagnosis and prognosis of BCa in clinical settings.
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Affiliation(s)
- Yuan-Hong Jiang
- Department of Urology, Hualien Tzu Chi Hospital, Tzu Chi University, Hualien 970374, Taiwan
| | - Yu-Shu Liu
- Guzip Biomarkers Corporation, Hsinchu City 302041, Taiwan
- Phalanx Biotech, Hsinchu City 302041, Taiwan
| | - Yu-Chung Wei
- Graduate Institute of Statistics and Information Science, National Changhua University of Education, Changhua City 500207, Taiwan
| | - Jia-Fong Jhang
- Department of Urology, Hualien Tzu Chi Hospital, Tzu Chi University, Hualien 970374, Taiwan
| | - Hann-Chorng Kuo
- Department of Urology, Hualien Tzu Chi Hospital, Tzu Chi University, Hualien 970374, Taiwan
- Guzip Biomarkers Corporation, Hsinchu City 302041, Taiwan
| | - Hsin-Hui Huang
- Guzip Biomarkers Corporation, Hsinchu City 302041, Taiwan
- Phalanx Biotech, Hsinchu City 302041, Taiwan
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chiayi 621301, Taiwan
| | - Guan-Ling Lin
- Department of Biomedical Sciences, National Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chiayi 621301, Taiwan
| | - Wen-Chi Cheng
- Institute of Medical Sciences, Tzu Chi University, Hualien 970374, Taiwan
| | - Shu-Chuan Lin
- Guzip Biomarkers Corporation, Hsinchu City 302041, Taiwan
- Phalanx Biotech, Hsinchu City 302041, Taiwan
| | - Hung-Jung Wang
- Institute of Medical Sciences, Tzu Chi University, Hualien 970374, Taiwan
- Doctoral Degree Program in Translational Medicine, Tzu Chi University and Academia Sinica, Hualien 97004, Taiwan
- Department of Biomedical Sciences and Engineering, Tzu Chi University, Hualien 970374, Taiwan
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47
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Bae SY, Kamalanathan KJ, Galeano-Garces C, Konety BR, Antonarakis ES, Parthasarathy J, Hong J, Drake JM. Dissemination of Circulating Tumor Cells in Breast and Prostate Cancer: Implications for Early Detection. Endocrinology 2024; 165:bqae022. [PMID: 38366552 PMCID: PMC10904107 DOI: 10.1210/endocr/bqae022] [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: 12/23/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
Burgeoning evidence suggests that circulating tumor cells (CTCs) may disseminate into blood vessels at an early stage, seeding metastases in various cancers such as breast and prostate cancer. Simultaneously, the early-stage CTCs that settle in metastatic sites [termed disseminated tumor cells (DTCs)] can enter dormancy, marking a potential source of late recurrence and therapy resistance. Thus, the presence of these early CTCs poses risks to patients but also holds potential benefits for early detection and treatment and opportunities for possibly curative interventions. This review delves into the role of early DTCs in driving latent metastasis within breast and prostate cancer, emphasizing the importance of early CTC detection in these diseases. We further explore the correlation between early CTC detection and poor prognoses, which contribute significantly to increased cancer mortality. Consequently, the detection of CTCs at an early stage emerges as a critical imperative for enhancing clinical diagnostics and allowing for early interventions.
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Affiliation(s)
| | | | | | - Badrinath R Konety
- Astrin Biosciences, St. Paul, MN 55114, USA
- Allina Health Cancer Institute, Minneapolis, MN 55407, USA
- Department of Urology, University of Minnesota, Minneapolis, MN 55454, USA
| | - Emmanuel S Antonarakis
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Jiarong Hong
- Astrin Biosciences, St. Paul, MN 55114, USA
- Department of Mechanical Engineering and St. Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN 55414, USA
| | - Justin M Drake
- Astrin Biosciences, St. Paul, MN 55114, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
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48
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Huang Z, Fu Y, Yang H, Zhou Y, Shi M, Li Q, Liu W, Liang J, Zhu L, Qin S, Hong H, Liu Y. Liquid biopsy in T-cell lymphoma: biomarker detection techniques and clinical application. Mol Cancer 2024; 23:36. [PMID: 38365716 PMCID: PMC10874034 DOI: 10.1186/s12943-024-01947-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
T-cell lymphoma is a highly invasive tumor with significant heterogeneity. Invasive tissue biopsy is the gold standard for acquiring molecular data and categorizing lymphoma patients into genetic subtypes. However, surgical intervention is unfeasible for patients who are critically ill, have unresectable tumors, or demonstrate low compliance, making tissue biopsies inaccessible to these patients. A critical need for a minimally invasive approach in T-cell lymphoma is evident, particularly in the areas of early diagnosis, prognostic monitoring, treatment response, and drug resistance. Therefore, the clinical application of liquid biopsy techniques has gained significant attention in T-cell lymphoma. Moreover, liquid biopsy requires fewer samples, exhibits good reproducibility, and enables real-time monitoring at molecular levels, thereby facilitating personalized health care. In this review, we provide a comprehensive overview of the current liquid biopsy biomarkers used for T-cell lymphoma, focusing on circulating cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), Epstein-Barr virus (EBV) DNA, antibodies, and cytokines. Additionally, we discuss their clinical application, detection methodologies, ongoing clinical trials, and the challenges faced in the field of liquid biopsy.
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Affiliation(s)
- Zongyao Huang
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Fu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Hong Yang
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yehan Zhou
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Min Shi
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qingyun Li
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Junheng Liang
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Liuqing Zhu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Sheng Qin
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Huangming Hong
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Liu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
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49
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Galant N, Nicoś M, Kuźnar-Kamińska B, Krawczyk P. Variant Allele Frequency Analysis of Circulating Tumor DNA as a Promising Tool in Assessing the Effectiveness of Treatment in Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2024; 16:782. [PMID: 38398173 PMCID: PMC10887123 DOI: 10.3390/cancers16040782] [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: 01/22/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Despite the different possible paths of treatment, lung cancer remains one of the leading causes of death in oncological patients. New tools guiding the therapeutic process are under scientific investigation, and one of the promising indicators of the effectiveness of therapy in patients with NSCLC is variant allele frequency (VAF) analysis. VAF is a metric characterized as the measurement of the specific variant allele proportion within a genomic locus, and it can be determined using methods based on NGS or PCR. It can be assessed using not only tissue samples but also ctDNA (circulating tumor DNA) isolated from liquid biopsy. The non-invasive characteristic of liquid biopsy enables a more frequent collection of material and increases the potential of VAF analysis in monitoring therapy. Several studies have been performed on patients with NSCLC to evaluate the possibility of VAF usage. The research carried out so far demonstrates that the evaluation of VAF dynamics may be useful in monitoring tumor progression, remission, and recurrence during or after treatment. Moreover, the use of VAF analysis appears to be beneficial in making treatment decisions. However, several issues require better understanding and standardization before VAF testing can be implemented in clinical practice. In this review, we discuss the difficulties in the application of ctDNA VAF analysis in clinical routine, discussing the diagnostic and methodological challenges in VAF measurement in liquid biopsy. We highlight the possible applications of VAF-based measurements that are under consideration in clinical trials in the monitoring of personalized treatments for patients with NSCLC.
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Affiliation(s)
- Natalia Galant
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Marcin Nicoś
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Barbara Kuźnar-Kamińska
- Department of Pulmonology, Allergology and Respiratory Oncology, Poznan University of Medical Sciences, 61-710 Poznan, Poland;
| | - Paweł Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
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50
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Li Y, Cai M, Zhang W, Liu Y, Yuan X, Han N, Li J, Jin S, Ding C. Cas12a-based direct visualization of nanoparticle-stabilized fluorescence signal for multiplex detection of DNA methylation biomarkers. Biosens Bioelectron 2024; 244:115810. [PMID: 37924654 DOI: 10.1016/j.bios.2023.115810] [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: 09/11/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
The CRISPR-Cas12a RNA-guided complexes hold immense promise for nucleic acid detection. However, limitations arise from their specificity in detecting off-targets and the stability of the signal molecules. Here, we have developed a platform that integrates multiplex amplification and nanomolecular-reporting signals, allowing us to detect various clinically relevant nucleic acid targets with enhanced stability, sensitivity, and visual interpretation. Through the electrostatic co-assembly of the Oligo reporter with oppositely charged nanoparticles, we observed a significant enhancement in its stability in low-pollution environments, reaching up to a threefold increase compared to the original version. Additionally, the fluorescence efficiency was expanded by three orders of magnitude, broadening the detection range considerably. Utilizing a multiplex strategy, this assay can accomplish simultaneous detection of multiple targets and single-point indication detection of nine specific targets. This significant advancement heightened the sensitivity of disease screening and improved the accuracy of diagnosing disease-related changes. We tested this assay in a colorectal cancer model, demonstrating that it can identify DNA methylation features at the aM-level within 40-60 min. Validation using clinical samples yielded consistent results with qPCR and bisulfite sequencing, affirming the assay's reliability and potential for clinical applications.
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Affiliation(s)
- Yu Li
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Miaomiao Cai
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Wenwen Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Ying Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xiaoqing Yuan
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Na Han
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jing Li
- Yinchuan Hospital of Traditional Chinese Medicine, Ningxia, 750001, China
| | - Shengnan Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Chunming Ding
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
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