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Yang X, Wu C, Liu W, Fu K, Tian Y, Wei X, Zhang W, Sun P, Luo H, Huang J. A clinical-information-free method for early diagnosis of lung cancer from the patients with pulmonary nodules based on backpropagation neural network model. Comput Struct Biotechnol J 2024; 24:404-411. [PMID: 38813092 PMCID: PMC11134880 DOI: 10.1016/j.csbj.2024.05.010] [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: 11/09/2023] [Revised: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
Lung cancer is the main cause of cancer-related deaths worldwide. Due to lack of obvious clinical symptoms in the early stage of the lung cancer, it is hard to distinguish between malignancy and pulmonary nodules. Understanding the immune responses in the early stage of malignant lung cancer patients may provide new insights for diagnosis. Here, using high-through-put sequencing, we obtained the TCRβ repertoires in the peripheral blood of 100 patients with Stage I lung cancer and 99 patients with benign pulmonary nodules. Our analysis revealed that the usage frequencies of TRBV, TRBJ genes, and V-J pairs and TCR diversities indicated by D50s, Shannon indexes, Simpson indexes, and the frequencies of the largest TCR clone in the malignant samples were significantly different from those in the benign samples. Furthermore, reduced TCR diversities were correlated with the size of pulmonary nodules. Moreover, we built a backpropagation neural network model with no clinical information to identify lung cancer cases from patients with pulmonary nodules using 15 characteristic TCR clones. Based on the model, we have created a web server named "Lung Cancer Prediction" (LCP), which can be accessed at http://i.uestc.edu.cn/LCP/index.html.
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Affiliation(s)
- Xin Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Changchun Wu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wenwen Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Kaiyu Fu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu 610041, China
| | - Yuke Tian
- 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 610041, China
| | - Xing Wei
- Department of Thoracic Surgery, 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 610041, China
| | - Wei Zhang
- 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 610041, China
| | - Ping Sun
- Department of Health Management Center & Institute of Health Management, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Huaichao Luo
- Department of Clinical Laboratory, 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 610041, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, China
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2
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Sirajee AS, Kabiraj D, De S. Cell-free nucleic acid fragmentomics: A non-invasive window into cellular epigenomes. Transl Oncol 2024; 49:102085. [PMID: 39178576 PMCID: PMC11388671 DOI: 10.1016/j.tranon.2024.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/01/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024] Open
Abstract
Clinical genomic profiling of cell-free nucleic acids (e.g. cell-free DNA or cfDNA) from blood and other body fluids has ushered in a new era in non-invasive diagnostics and treatment monitoring strategies for health conditions and diseases such as cancer. Genomic analysis of cfDNAs not only identifies disease-associated mutations, but emerging findings suggest that structural, topological, and fragmentation characteristics of cfDNAs reveal crucial information about the location of source tissues, their epigenomes, and other clinically relevant characteristics, leading to the burgeoning field of fragmentomics. The field has seen rapid developments in computational and genomics methodologies for conducting large-scale studies on health conditions and diseases - that have led to fundamental, mechanistic discoveries as well as translational applications. Several recent studies have shown the clinical utilities of the cfDNA fragmentomics technique which has the potential to be effective for early disease diagnosis, determining treatment outcomes, and risk-free continuous patient monitoring in a non-invasive manner. In this article, we outline recent developments in computational genomic methodologies and analysis strategies, as well as the emerging insights from cfNA fragmentomics. We conclude by highlighting the current challenges and opportunities.
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Affiliation(s)
- Ahmad Salman Sirajee
- Department of Pathology and Laboratory Medicine, Rutgers Cancer Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Debajyoti Kabiraj
- Department of Pathology and Laboratory Medicine, Rutgers Cancer Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Subhajyoti De
- Department of Pathology and Laboratory Medicine, Rutgers Cancer Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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3
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Wang PH, Yang ST. Winners of the 2023 honor awards for excellence at the annual meeting of the Chinese Medical Association-Taipei: Part III. J Chin Med Assoc 2024; 87:815-816. [PMID: 38916213 DOI: 10.1097/jcma.0000000000001126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/26/2024] Open
Affiliation(s)
- Peng-Hui Wang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Female Cancer Foundation, Taipei, Taiwan, ROC
| | - Szu-Ting Yang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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4
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Jee J, Brannon AR, Singh R, Derkach A, Fong C, Lee A, Gray L, Pichotta K, Luthra A, Diosdado M, Haque M, Guo J, Hernandez J, Garg K, Wilhelm C, Arcila ME, Pavlakis N, Clarke S, Shah SP, Razavi P, Reis-Filho JS, Ladanyi M, Schultz N, Zwicker J, Berger MF, Li BT, Mantha S. DNA liquid biopsy-based prediction of cancer-associated venous thromboembolism. Nat Med 2024:10.1038/s41591-024-03195-0. [PMID: 39147831 DOI: 10.1038/s41591-024-03195-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024]
Abstract
Cancer-associated venous thromboembolism (VTE) is a major source of oncologic cost, morbidity and mortality. Identifying high-risk patients for prophylactic anticoagulation is challenging and adds to clinician burden. Circulating tumor DNA (ctDNA) sequencing assays ('liquid biopsies') are widely implemented, but their utility for VTE prognostication is unknown. Here we analyzed three plasma sequencing cohorts: a pan-cancer discovery cohort of 4,141 patients with non-small cell lung cancer (NSCLC) or breast, pancreatic and other cancers; a prospective validation cohort consisting of 1,426 patients with the same cancer types; and an international generalizability cohort of 463 patients with advanced NSCLC. ctDNA detection was associated with VTE independent of clinical and radiographic features. A machine learning model trained on liquid biopsy data outperformed previous risk scores (discovery, validation and generalizability c-indices 0.74, 0.73 and 0.67, respectively, versus 0.57, 0.61 and 0.54 for the Khorana score). In real-world data, anticoagulation was associated with lower VTE rates if ctDNA was detected (n = 2,522, adjusted hazard ratio (HR) = 0.50, 95% confidence interval (CI): 0.30-0.81); ctDNA- patients (n = 1,619) did not benefit from anticoagulation (adjusted HR = 0.89, 95% CI: 0.40-2.0). These results provide preliminary evidence that liquid biopsies may improve VTE risk stratification in addition to clinical parameters. Interventional, randomized prospective studies are needed to confirm the clinical utility of liquid biopsies for guiding anticoagulation in patients with cancer.
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Affiliation(s)
- Justin Jee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Rose Brannon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rohan Singh
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andriy Derkach
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Adrian Lee
- GenesisCare, University of Sydney, Sydney, New South Wales, Australia
| | - Lauren Gray
- GenesisCare, University of Sydney, Sydney, New South Wales, Australia
| | - Karl Pichotta
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anisha Luthra
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Mohammad Haque
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiannan Guo
- Resolution Bioscience, Exact Sciences, Kirkland, WA, USA
| | | | - Kavita Garg
- Resolution Bioscience, Exact Sciences, Kirkland, WA, USA
| | - Clare Wilhelm
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Nick Pavlakis
- GenesisCare, University of Sydney, Sydney, New South Wales, Australia
| | - Stephen Clarke
- GenesisCare, University of Sydney, Sydney, New South Wales, Australia
| | - Sohrab P Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jorge S Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - Jeffrey Zwicker
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Simon Mantha
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Long Z, Gao Y, Han Z, Yuan H, Yu Y, Pei B, Jia Y, Ye J, Shi Y, Zhang M, Zhao Y, Wu D, Wang F. Discovery and Validation of Methylation Signatures in Circulating Cell-Free DNA for the Detection of Colorectal Cancer. Biomolecules 2024; 14:996. [PMID: 39199384 PMCID: PMC11353097 DOI: 10.3390/biom14080996] [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: 05/18/2024] [Revised: 07/25/2024] [Accepted: 08/09/2024] [Indexed: 09/01/2024] Open
Abstract
This study was conducted with the primary objective of assessing the performance of cfDNA methylation in the detection of colorectal cancer (CRC). Five tumor tissue, 20 peripheral blood leucocyte, and 169 cfDNA samples were collected for whole-genome bisulfite sequencing (WGBS) analysis. Bioinformatic analysis was conducted to identify differentially methylated regions (DMRs) and their functional characteristics. Quantitative methylation-specific PCR (qMSP) was used to validate the methylation levels of DMRs in the tissues and leucocytes. cfDNA samples from CRC patients and healthy controls were used to evaluate the performance of the DMR analysis. WGBS analysis revealed a decrease in DNA methylation levels in the CpG context in CRC tumor tissues compared with adjacent normal tissues. A total of 132 DMRs in cfDNA were identified as potential markers for diagnosing CRC. In a cohort of 95 CRC patients and 74 healthy controls, a combination of the three DMRs (DAB1, PPP2R5C, and FAM19A5) yielded an AUC of 0.763, achieving 64.21% sensitivity and 78.38% specificity in discriminating CRC patients from healthy controls. This study provides insights into DNA methylation patterns in CRC and identifies a set of DMRs in cfDNA with potential diagnostic value for CRC. These DMRs hold promise as biomarkers for CRC detection, offering promise for non-invasive CRC diagnosis. Further research is warranted to validate these findings in larger cohorts.
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Affiliation(s)
- Zhiping Long
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Yu Gao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Zhen Han
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Heli Yuan
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Yue Yu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Bing Pei
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Yanjie Jia
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Jingyu Ye
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Ying Shi
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Min Zhang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Di Wu
- Department of Colorectal Surgery, Tumor Hospital of Harbin Medical University, Harbin Medical University, Harbin 150081, China
| | - Fan Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
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6
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Stetson D, Labrousse P, Russell H, Shera D, Abbosh C, Dougherty B, Barrett JC, Hodgson D, Hadfield J. Next-Generation Molecular Residual Disease Assays: Do We Have the Tools to Evaluate Them Properly? J Clin Oncol 2024; 42:2736-2740. [PMID: 38754043 DOI: 10.1200/jco.23.02301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/27/2024] [Accepted: 03/05/2024] [Indexed: 05/18/2024] Open
Affiliation(s)
- Dan Stetson
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Paul Labrousse
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Hugh Russell
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - David Shera
- Oncology Biometrics, AstraZeneca, Gaithersburg, MD
| | - Chris Abbosh
- Cancer Biomarker Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Brian Dougherty
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Darren Hodgson
- Cancer Biomarker Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - James Hadfield
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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7
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Goggins M. The role of biomarkers in the early detection of pancreatic cancer. Fam Cancer 2024; 23:309-322. [PMID: 38662265 PMCID: PMC11309746 DOI: 10.1007/s10689-024-00381-4] [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: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024]
Abstract
Pancreatic surveillance can detect early-stage pancreatic cancer and achieve long-term survival, but currently involves annual endoscopic ultrasound and MRI/MRCP, and is recommended only for individuals who meet familial/genetic risk criteria. To improve upon current approaches to pancreatic cancer early detection and to expand access, more accurate, inexpensive, and safe biomarkers are needed, but finding them has remained elusive. Newer approaches to early detection, such as using gene tests to personalize biomarker interpretation, and the increasing application of artificial intelligence approaches to integrate complex biomarker data, offer promise that clinically useful biomarkers for early pancreatic cancer detection are on the horizon.
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Affiliation(s)
- Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, 1550 Orleans Street, Baltimore, MD, 21231, USA.
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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8
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Hua X, Zhou H, Wu HC, Furnari J, Kotidis CP, Rabadan R, Genkinger JM, Bruce JN, Canoll P, Santella RM, Zhang Z. Tumor detection by analysis of both symmetric- and hemi-methylation of plasma cell-free DNA. Nat Commun 2024; 15:6113. [PMID: 39030196 PMCID: PMC11271492 DOI: 10.1038/s41467-024-50471-1] [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: 10/31/2022] [Accepted: 07/08/2024] [Indexed: 07/21/2024] Open
Abstract
Aberrant DNA methylation patterns have been used for cancer detection. However, DNA hemi-methylation, present at about 10% CpG dinucleotides, has been less well studied. Here we show that a majority of differentially hemi-methylated regions (DHMRs) in liver tumor DNA or plasma cells free (cf) DNA do not overlap with differentially methylated regions (DMRs) of the same samples, indicating that DHMRs could serve as independent biomarkers. Furthermore, we analyzed the cfDNA methylomes of 215 samples from individuals with liver or brain cancer and individuals without cancer (controls), and trained machine learning models using DMRs, DHMRs or both. The models incorporated with both DMRs and DHMRs show a superior performance compared to models trained with DMRs or DHMRs, with AUROC being 0.978, 0.990, and 0.983 in distinguishing control, liver and brain cancer, respectively, in a validation cohort. This study supports the potential of utilizing both DMRs and DHMRs for multi-cancer detection.
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Affiliation(s)
- Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Hui-Chen Wu
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Julia Furnari
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Corina P Kotidis
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Raul Rabadan
- Program for Mathematical Genomics and Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jeanine M Genkinger
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Jeffrey N Bruce
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter Canoll
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Regina M Santella
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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9
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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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10
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Bisanzi S, Puliti D, Picozzi G, Romei C, Pistelli F, Deliperi A, Carreras G, Masala G, Gorini G, Zappa M, Sani C, Carrozzi L, Paci E, Kaaks R, Carozzi FM, Mascalchi M. Baseline Cell-Free DNA Can Predict Malignancy of Nodules Observed in the ITALUNG Screening Trial. Cancers (Basel) 2024; 16:2276. [PMID: 38927981 PMCID: PMC11201711 DOI: 10.3390/cancers16122276] [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: 05/15/2024] [Revised: 06/08/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The role of total plasma cell-free DNA (cfDNA) in lung cancer (LC) screening with low-dose computed tomography (LDCT) is uncertain. We hypothesized that cfDNA could support differentiation between malignant and benign nodules observed in LDCT. The baseline cfDNA was measured in 137 subjects of the ITALUNG trial, including 29 subjects with screen-detected LC (17 prevalent and 12 incident) and 108 subjects with benign nodules. The predictive capability of baseline cfDNA to differentiate malignant and benign nodules was compared to that of Lung-RADS classification and Brock score at initial LDCT (iLDCT). Subjects with prevalent LC showed both well-discriminating radiological characteristics of the malignant nodule (16 of 17 were classified as Lung-RADS 4) and markedly increased cfDNA (mean 18.8 ng/mL). The mean diameters and Brock scores of malignant nodules at iLDCT in subjects who were diagnosed with incident LC were not different from those of benign nodules. However, 75% (9/12) of subjects with incident LC showed a baseline cfDNA ≥ 3.15 ng/mL, compared to 34% (37/108) of subjects with benign nodules (p = 0.006). Moreover, baseline cfDNA was correlated (p = 0.001) with tumor growth, measured with volume doubling time. In conclusion, increased baseline cfDNA may help to differentiate subjects with malignant and benign nodules at LDCT.
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Affiliation(s)
- Simonetta Bisanzi
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Donella Puliti
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Giulia Picozzi
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Chiara Romei
- Division of Radiology, Cisanello Hospital, Azienda Ospedaliera Pisana, 56124 Pisa, Italy; (C.R.); (A.D.)
| | - Francesco Pistelli
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, 56126 Pisa, Italy, (L.C.)
- Pulmonary Unit, Cardiothoracic and Vascular Department, Pisa University Hospital, 56124 Pisa, Italy
| | - Annalisa Deliperi
- Division of Radiology, Cisanello Hospital, Azienda Ospedaliera Pisana, 56124 Pisa, Italy; (C.R.); (A.D.)
| | - Giulia Carreras
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Giovanna Masala
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Giuseppe Gorini
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Marco Zappa
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Cristina Sani
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Laura Carrozzi
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, 56126 Pisa, Italy, (L.C.)
- Pulmonary Unit, Cardiothoracic and Vascular Department, Pisa University Hospital, 56124 Pisa, Italy
| | - Eugenio Paci
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Rudolf Kaaks
- Division of Cancer Epidemiology (C020), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; (R.K.); (M.M.)
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Francesca Maria Carozzi
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy; (S.B.); (G.P.); (G.C.); (G.M.); (G.G.); (M.Z.); (C.S.); (E.P.); (F.M.C.)
| | - Mario Mascalchi
- Division of Cancer Epidemiology (C020), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; (R.K.); (M.M.)
- Department of Clinical and Experimental Biomedical Sciences “Mario Serio”, University of Florence, 50121 Florence, Italy
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11
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Gerdes C, Basmanav FB. Intercellular transfer of plasmid DNA between in vitro cultured HEK293 cells following transient transfection. Plasmid 2024; 131-132:102729. [PMID: 38876373 DOI: 10.1016/j.plasmid.2024.102729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
Gene overexpression by transient transfection of in vitro cultured model cell lines with plasmid DNA is a commonly used method for studying molecular aspects of human biology and pathobiology. However, there is accumulating evidence suggesting that human cells may actively secrete fragments of DNA and the implications of this phenomenon for in vitro cultured cells transiently transfected with foreign nucleic acids has been overlooked. Therefore, in the current study we investigated whether a cell-to-cell transmission of acquired plasmid DNA takes place in a commonly used human cell line model. We transiently transfected HEK293 cells with EGFP encoding plasmids to serve as donor cells and either co-cultured these with stably mCherry expressing recipient cells in different set-ups or transferred their culture medium to the recipient cells. We found that recipient cells produced EGFP after being co-cultured with donor cells but not when they were exposed to their culture medium. The employment of different co-culture set-ups excluded that the observed effect stemmed from technical artefacts and provided evidence that an intercellular plasmid transfer takes place requiring physical proximity between living cells. This phenomenon could represent a significant biological artefact for certain studies such as those addressing protein transmissions in prion diseases.
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Affiliation(s)
- Christoph Gerdes
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, D-37073 Göttingen, Germany; Hannover Medical School, Department of Gastroenterology, Hepatology, Infectiology and Endocrinology, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - F Buket Basmanav
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, D-37073 Göttingen, Germany; Campus Laboratory for Advanced Imaging, Microscopy and Spectroscopy, University of Göttingen, D-37073 Göttingen, Germany; Institute of X-ray Physics, University of Göttingen, 37073 Göttingen, Germany; Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany.
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12
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Magbanua MJM, Ahmed Z, Sayaman RW, Swigart LB, Hirst GL, Yau C, Wolf DM, Li W, Delson AL, Perlmutter J, Pohlmann P, Symmans WF, Yee D, Hylton NM, Esserman LJ, DeMichele AM, Rugo HS, van ‘t Veer LJ. Cell-free DNA Concentration as a Biomarker of Response and Recurrence in HER2-Negative Breast Cancer Receiving Neoadjuvant Chemotherapy. Clin Cancer Res 2024; 30:2444-2451. [PMID: 38470545 PMCID: PMC11147708 DOI: 10.1158/1078-0432.ccr-23-2928] [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: 10/03/2023] [Revised: 12/08/2023] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
PURPOSE We previously demonstrated the clinical significance of circulating tumor DNA (ctDNA) in patients with HER2-negative breast cancer receiving neoadjuvant chemotherapy (NAC). Here, we compared its predictive and prognostic value with cell-free DNA (cfDNA) concentration measured in the same samples from the same patients. EXPERIMENTAL DESIGN 145 patients with hormone receptor (HR)-positive/HER2-negative and 138 triple-negative breast cancer (TNBC) with ctDNA data from a previous study were included in the analysis. Associations of serial cfDNA concentration with residual cancer burden (RCB) and distant recurrence-free survival (DRFS) were examined. RESULTS In TNBC, we observed a modest negative correlation between cfDNA concentration 3 weeks after treatment initiation and RCB, but none of the other timepoints showed significant correlation. In contrast, ctDNA was significantly positively correlated with RCB at all timepoints (all R > 0.3 and P < 0.05). In the HR-positive/HER2-negative group, cfDNA concentration did not associate with response to NAC, but survival analysis showed that high cfDNA shedders at pretreatment had a significantly worse DRFS than low shedders (hazard ratio, 2.12; P = 0.037). In TNBC, the difference in survival between high versus low cfDNA shedders at all timepoints was not statistically significant. In contrast, as previously reported, ctDNA at all timepoints was significantly correlated with DRFS in both subtypes. CONCLUSIONS In TNBC, cfDNA concentrations during therapy were not strongly correlated with response or prognosis. In the HR-positive/HER2-negative group, pretreatment cfDNA concentration was prognostic for DRFS. Overall, the predictive and prognostic value of cfDNA concentration was more limited than that of ctDNA.
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Affiliation(s)
- Mark Jesus M. Magbanua
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Ziad Ahmed
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Rosalyn W. Sayaman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Lamorna Brown Swigart
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Gill L. Hirst
- Department of Surgery, University of California San Francisco, San Francisco, USA
| | - Christina Yau
- Department of Surgery, University of California San Francisco, San Francisco, USA
| | - Denise M. Wolf
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Wen Li
- Department of Radiology, University of California San Francisco, San Francisco, USA
| | - Amy L. Delson
- Breast Science Advocacy Core, University of California San Francisco, San Francisco, USA
| | - Jane Perlmutter
- Breast Science Advocacy Core, University of California San Francisco, San Francisco, USA
| | - Paula Pohlmann
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - W. Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Douglas Yee
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, USA
| | - Nola M. Hylton
- Department of Radiology, University of California San Francisco, San Francisco, USA
| | - Laura J. Esserman
- Department of Surgery, University of California San Francisco, San Francisco, USA
| | - Angela M. DeMichele
- Division of Hematology/Oncology, University of Pennsylvania, Philadelphia, USA
| | - Hope S. Rugo
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, USA
| | - Laura J. van ‘t Veer
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
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13
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Kudriavtsev A, Pastor B, Mirandola A, Pisareva E, Gricourt Y, Capdevila X, Thierry AR, Cuvillon P. Association of the immediate perioperative dynamics of circulating DNA levels and neutrophil extracellular traps formation in cancer patients. PRECISION CLINICAL MEDICINE 2024; 7:pbae008. [PMID: 38699382 PMCID: PMC11062027 DOI: 10.1093/pcmedi/pbae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 05/05/2024] Open
Abstract
Objectives Elevated circulating DNA (cirDNA) concentrations were found to be associated with trauma or tissue damage which suggests involvement of inflammation or cell death in post-operative cirDNA release. We carried out the first prospective, multicenter study of the dynamics of cirDNA and neutrophil extracellular trap (NETs) markers during the perioperative period from 24 h before surgery up to 72 h after curative surgery in cancer patients. Methods We examined the plasma levels of two NETs protein markers [myeloperoxidase (MPO) and neutrophil elastase (NE)], as well as levels of cirDNA of nuclear (cir-nDNA) and mitochondrial (cir-mtDNA) origin in 29 colon, prostate, and breast cancer patients and in 114 healthy individuals (HI). Results The synergistic analytical information provided by these markers revealed that: (i) NETs formation contributes to post-surgery conditions; (ii) post-surgery cir-nDNA levels were highly associated with NE and MPO in colon cancer [r = 0.60 (P < 0.001) and r = 0.53 (P < 0.01), respectively], but not in prostate and breast cancer; (iii) each tumor type shows a specific pattern of cir-nDNA and NETs marker dynamics, but overall the pre- and post-surgery median values of cir-nDNA, NE, and MPO were significantly higher in cancer patients than in HI. Conclusion Taken as a whole, our work reveals the association of NETs formation with the elevated cir-nDNA release during a cancer patient's perioperative period, depending on surgical procedure or cancer type. By contrast, cir-mtDNA is poorly associated with NETs formation in the studied perioperative period, which would appear to indicate a different mechanism of release or suggest mitochondrial dysfunction.
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Affiliation(s)
- Andrei Kudriavtsev
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Brice Pastor
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
- Institut régional du Cancer de Montpellier, Montpellier 34298, France
| | - Alexia Mirandola
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Ekaterina Pisareva
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Yann Gricourt
- Department of Anaesthesiology and Pain Management, Centre Hospitalo-Universitaire (CHU) Carémeau, Place du Professeur Debré,Nîmes 30400, France
- University of Montpellier, Montpellier 34298, France
| | - Xavier Capdevila
- Division of Anaesthesia Intensive Care, Pain and Emergency Medicine, Montpellier University Hospital, Montpellier 34090, France
- Montpellier NeuroSciences Institute, INSERM U1298, University of Montpellier, Montpellier 34295, France
| | - Alain R Thierry
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
- Institut régional du Cancer de Montpellier, Montpellier 34298, France
| | - Philippe Cuvillon
- Department of Anaesthesiology and Pain Management, Centre Hospitalo-Universitaire (CHU) Carémeau, Place du Professeur Debré,Nîmes 30400, France
- University of Montpellier, Montpellier 34298, France
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14
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Filatova AA, Alekseeva LA, Sen’kova AV, Savin IA, Sounbuli K, Zenkova MA, Mironova NL. Tumor- and Fibroblast-Derived Cell-Free DNAs Differently Affect the Progression of B16 Melanoma In Vitro and In Vivo. Int J Mol Sci 2024; 25:5304. [PMID: 38791341 PMCID: PMC11120878 DOI: 10.3390/ijms25105304] [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: 03/28/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
It is widely postulated that the majority of pathologically elevated extracellular or cell-free DNA (cfDNA) in cancer originates from tumor cells; however, evidence has emerged regarding the significant contributions of other cells from the tumor microenvironment. Here, the effect of cfDNA originating from murine B16 melanoma cells and L929 fibroblasts on B16 cells was investigated. It was found that cfDNAL929 increased the viability and migration properties of B16 cells in vitro and their invasiveness in vivo. In contrast, cfDNAB16 exhibited a negative effect on B16 cells, reducing their viability and migration in vitro, which in vivo led to decreased tumor size and metastasis number. It was shown that cell treatment with both cfDNAs resulted in an increase in the expression of genes encoding DNases and the oncogenes Braf, Kras, and Myc. cfDNAL929-treated cells were shown to experience oxidative stress. Gene expression changes in the case of cfDNAB16 treatment are well correlated with the observed decrease in proliferation and migration of B16 cells. The obtained data may indicate the possible involvement of fibroblast DNA in the tumor microenvironment in tumor progression and, potentially, in the formation of new tumor foci due to the transformation of normal cells.
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Affiliation(s)
- Alina A. Filatova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila A. Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Aleksandra V. Sen’kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Innokenty A. Savin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Khetam Sounbuli
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Nadezhda L. Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
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15
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Xu C, Zhang L, Xu S, Wang Z, Han Q, Lv Y, Wang X, Zhang X, Zhang Q, Zhang Y, He S, Yuan Q, Bian Y, Li C, Wang J, Xu F, Cao Y, Pang J, Chen Y. Neutrophil ALDH2 is a new therapeutic target for the effective treatment of sepsis-induced ARDS. Cell Mol Immunol 2024; 21:510-526. [PMID: 38472357 PMCID: PMC11061144 DOI: 10.1038/s41423-024-01146-w] [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: 10/03/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Acetaldehyde dehydrogenase 2 (ALDH2) mutations are commonly found in a subgroup of the Asian population. However, the role of ALDH2 in septic acute respiratory distress syndrome (ARDS) remains unknown. Here, we showed that human subjects carrying the ALDH2rs671 mutation were highly susceptible to developing septic ARDS. Intriguingly, ALDH2rs671-ARDS patients showed higher levels of blood cell-free DNA (cfDNA) and myeloperoxidase (MPO)-DNA than ALDH2WT-ARDS patients. To investigate the mechanisms underlying ALDH2 deficiency in the development of septic ARDS, we utilized Aldh2 gene knockout mice and Aldh2rs671 gene knock-in mice. In clinically relevant mouse sepsis models, Aldh2-/- mice and Aldh2rs671 mice exhibited pulmonary and circulating NETosis, a specific process that releases neutrophil extracellular traps (NETs) from neutrophils. Furthermore, we discovered that NETosis strongly promoted endothelial destruction, accelerated vascular leakage, and exacerbated septic ARDS. At the molecular level, ALDH2 increased K48-linked polyubiquitination and degradation of peptidylarginine deiminase 4 (PAD4) to inhibit NETosis, which was achieved by promoting PAD4 binding to the E3 ubiquitin ligase CHIP. Pharmacological administration of the ALDH2-specific activator Alda-1 substantially alleviated septic ARDS by inhibiting NETosis. Together, our data reveal a novel ALDH2-based protective mechanism against septic ARDS, and the activation of ALDH2 may be an effective treatment strategy for sepsis.
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Affiliation(s)
- Changchang Xu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Lin Zhang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Shaoyu Xu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Zichen Wang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Qi Han
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Ying Lv
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xingfang Wang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xiangxin Zhang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Qingju Zhang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Ying Zhang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Simeng He
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Qiuhuan Yuan
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Yuan Bian
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Chuanbao Li
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Jiali Wang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Feng Xu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Yihai Cao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, 171 65, Sweden
| | - Jiaojiao Pang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China.
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China.
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China.
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China.
| | - Yuguo Chen
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China.
- Chest Pain Center, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China.
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China.
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China.
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16
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Flory A, Wilson-Robles H. Noninvasive Blood-Based Cancer Detection in Veterinary Medicine. Vet Clin North Am Small Anim Pract 2024; 54:541-558. [PMID: 38195361 DOI: 10.1016/j.cvsm.2023.12.008] [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: 01/11/2024]
Abstract
The past decade has seen incredible advances in blood-based cancer detection in people and in dogs - yet this represents only a glimpse of the benefits these tests can provide to patients. The clinical uses of this technology range from screening asymptomatic individuals for early detection to use as an aid in diagnosis when cancer is suspected, to cancer monitoring both during and after treatment. This article summarizes the benefits of early cancer detection and examines use cases and methods of blood-based cancer detection in dogs, including quantitative, qualitative, and alternative approaches.
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Affiliation(s)
- Andi Flory
- PetDx, 9310 Athena Circle, Suite 230, La Jolla, CA 92037, USA.
| | - Heather Wilson-Robles
- Volition Veterinary Diagnostics Development, LLC 1489 West Warm Springs Road Suite 110, Henderson, NV 89014, USA; Ethos Discovery, 10435 Sorrento Valley Road, San Diego, CA 92121, USA; The Oncology Service, United Veterinary Health, 6651 Backlick Road, Springfield, VA 22150, USA
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17
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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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18
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Satir S, Kaya DI, Ozsoy SC. Effect of tobacco use on cadmium accumulation in the oral keratinized mucosa. BMC Oral Health 2024; 24:257. [PMID: 38378541 PMCID: PMC10877838 DOI: 10.1186/s12903-024-04001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND This cross-sectional study aimed to evaluate the effect of tobacco use on the accumulation of cadmium (Cd), a carcinogenic element, in the oral keratinized mucosa (OKM). METHODS OKM samples were obtained by standard punch biopsy from nonsmokers (n = 19) and smokers (n = 21). Cd analysis was performed using inductively coupled plasma optical emission spectroscopy (ICP-OES). The calibration curve R2 values for three wavelengths (214,439, 226,502, and 228,802 nm) were at the level of 0.9999. The frequency of consumption of foods that are Cd sources, such as seafood, rice, and vegetables, was assessed in all patients. The age, sex, and nutritional habits of all patients and the frequency of tobacco consumption by smokers were recorded. The independent t-test, Mann-Whitney U test, Fisher's exact test, and Spearman correlation test were used for the statistical analyses, and p < 0.05 was considered significant. RESULTS Although the Cd levels in nonsmokers were higher than those in smokers, no statistically significant difference was found (p > 0.05). In smokers, a positive correlation was found between age and Cd level (r = 0.574, p = 0.006). No significant relationship was found between the groups in terms of nutrition or between the frequency of tobacco consumption and Cd accumulation. CONCLUSION The OKM may not have the characteristic cumulative accumulation in terms of toxic elements. Changes in the turnover rate, keratinization, and apoptotic mechanisms in the OKM with the thermal/chemical effects of tobacco may be responsible for the difference in Cd accumulation. TRIAL REGISTRATION NUMBER TCTR20230206001/06 Feb 2023 (TCTR: Thai Clinical Trials Registry).
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Affiliation(s)
- Samed Satir
- Faculty of Dentistry, Oral and Maxillofacial Radiology, Karamanoglu Mehmetbey University, Karaman, 70200, Turkey.
| | - Dogan Ilgaz Kaya
- Faculty of Dentistry, Oral and Maxillofacial Surgery, Karamanoglu Mehmetbey University, Karaman, Turkey, 70200
| | - Sumeyye Celik Ozsoy
- Faculty of Dentistry, Oral and Maxillofacial Radiology, Karamanoglu Mehmetbey University, Karaman, 70200, Turkey
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Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
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Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
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