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For: Ungerer V, Bronkhorst AJ, Van den Ackerveken P, Herzog M, Holdenrieder S. Serial profiling of cell-free DNA and nucleosome histone modifications in cell cultures. Sci Rep 2021;11:9460. [PMID: 33947882 PMCID: PMC8096822 DOI: 10.1038/s41598-021-88866-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Davidson BA, Miranda AX, Reed SC, Bergman RE, Kemp JDJ, Reddy AP, Pantone MV, Fox EK, Dorand RD, Hurley PJ, Croessmann S, Park BH. An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release. Commun Biol 2024;7:441. [PMID: 38600351 PMCID: PMC11006667 DOI: 10.1038/s42003-024-06129-1] [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: 08/22/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024]  Open
2
Das D, Avssn R, Chittela RK. A phenol-chloroform free method for cfDNA isolation from cell conditioned media: development, optimization and comparative analysis. Anal Biochem 2024;687:115454. [PMID: 38158107 DOI: 10.1016/j.ab.2023.115454] [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: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
3
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. [PMID: 38478957 DOI: 10.1139/bcb-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]  Open
4
Yagci ZB, Kelkar GR, Johnson TJ, Sen D, Keung AJ. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities. Methods Mol Biol 2024;2842:23-55. [PMID: 39012589 DOI: 10.1007/978-1-0716-4051-7_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] [Indexed: 07/17/2024]
5
Nel I, Münch C, Shamkeeva S, Heinemann ML, Isermann B, Aktas B. The Challenge to Stabilize, Extract and Analyze Urinary Cell-Free DNA (ucfDNA) during Clinical Routine. Diagnostics (Basel) 2023;13:3670. [PMID: 38132253 PMCID: PMC10743081 DOI: 10.3390/diagnostics13243670] [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: 11/23/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]  Open
6
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]
7
Kim J, Hong SP, Lee S, Lee W, Lee D, Kim R, Park YJ, Moon S, Park K, Cha B, Kim JI. Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids. Hum Genomics 2023;17:96. [PMID: 37898819 PMCID: PMC10613368 DOI: 10.1186/s40246-023-00533-0] [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: 05/10/2023] [Accepted: 09/11/2023] [Indexed: 10/30/2023]  Open
8
Mattox AK, Douville C, Wang Y, Popoli M, Ptak J, Silliman N, Dobbyn L, Schaefer J, Lu S, Pearlman AH, Cohen JD, Tie J, Gibbs P, Lahouel K, Bettegowda C, Hruban RH, Tomasetti C, Jiang P, Chan KA, Lo YMD, Papadopoulos N, Kinzler KW, Vogelstein B. The Origin of Highly Elevated Cell-Free DNA in Healthy Individuals and Patients with Pancreatic, Colorectal, Lung, or Ovarian Cancer. Cancer Discov 2023;13:2166-2179. [PMID: 37565753 PMCID: PMC10592331 DOI: 10.1158/2159-8290.cd-21-1252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/16/2022] [Accepted: 08/09/2023] [Indexed: 08/12/2023]
9
Roth S, Wernsdorf SR, Liesz A. The role of circulating cell-free DNA as an inflammatory mediator after stroke. Semin Immunopathol 2023:10.1007/s00281-023-00993-5. [PMID: 37212886 DOI: 10.1007/s00281-023-00993-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/03/2023] [Indexed: 05/23/2023]
10
Koval AP, Khromova AS, Blagodatskikh KA, Zhitnyuk YV, Shtykova YA, Alferov AA, Kushlinskii NE, Shcherbo DS. Application of PCR-based approaches for evaluation of cell-free DNA fragmentation in colorectal cancer. Front Mol Biosci 2023;10:1101179. [PMID: 37051326 PMCID: PMC10083340 DOI: 10.3389/fmolb.2023.1101179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/14/2023] [Indexed: 03/29/2023]  Open
11
Webster SE, Tsuji NL, Clemente MJ, Holodick NE. Age-related changes in antigen-specific natural antibodies are influenced by sex. Front Immunol 2023;13:1047297. [PMID: 36713434 PMCID: PMC9878317 DOI: 10.3389/fimmu.2022.1047297] [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: 09/17/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023]  Open
12
Cell-Free DNA Fragmentomics: A Promising Biomarker for Diagnosis, Prognosis and Prediction of Response in Breast Cancer. Int J Mol Sci 2022;23:ijms232214197. [PMID: 36430675 PMCID: PMC9695769 DOI: 10.3390/ijms232214197] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]  Open
13
Endogenous cell-free DNA in fetal bovine serum introduces artifacts to in vitro cell-free DNA models. Biotechniques 2022;73:219-226. [DOI: 10.2144/btn-2022-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
14
Buzova D, Braghini MR, Bianco SD, Lo Re O, Raffaele M, Frohlich J, Kisheva A, Crudele A, Mosca A, Sartorelli MR, Balsano C, Cerveny J, Mazza T, Alisi A, Vinciguerra M. Profiling of cell-free DNA methylation and histone signatures in pediatric NAFLD: A pilot study. Hepatol Commun 2022;6:3311-3323. [PMID: 36264206 PMCID: PMC9701487 DOI: 10.1002/hep4.2082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/19/2022] [Accepted: 08/10/2022] [Indexed: 01/21/2023]  Open
15
New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022;12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022]  Open
16
Cell-Free DNA Fragmentation Patterns in a Cancer Cell Line. Diagnostics (Basel) 2022;12:diagnostics12081896. [PMID: 36010246 PMCID: PMC9406536 DOI: 10.3390/diagnostics12081896] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 12/20/2022]  Open
17
Oberhofer A, Bronkhorst AJ, Uhlig C, Ungerer V, Holdenrieder S. Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures. Diagnostics (Basel) 2022;12:diagnostics12081834. [PMID: 36010184 PMCID: PMC9406971 DOI: 10.3390/diagnostics12081834] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022]  Open
18
Kim PJ, Olymbios M, Siu A, Wever Pinzon O, Adler E, Liang N, Swenerton R, Sternberg J, Kaur N, Ahmed E, Chen YA, Fehringer G, Demko ZP, Billings PR, Stehlik J. A novel donor-derived cell-free DNA assay for the detection of acute rejection in heart transplantation. J Heart Lung Transplant 2022;41:919-927. [PMID: 35577713 PMCID: PMC9670834 DOI: 10.1016/j.healun.2022.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/06/2022] [Accepted: 04/04/2022] [Indexed: 01/25/2023]  Open
19
Ronchetti L, Terrenato I, Ferretti M, Corrado G, Goeman F, Donzelli S, Mandoj C, Merola R, Zampa A, Carosi M, Blandino G, Conti L, Lobascio AM, Iacobelli M, Vizza E, Piaggio G, Gurtner A. Circulating cell free DNA and citrullinated histone H3 as useful biomarkers of NETosis in endometrial cancer. J Exp Clin Cancer Res 2022;41:151. [PMID: 35449078 PMCID: PMC9027343 DOI: 10.1186/s13046-022-02359-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/06/2022] [Indexed: 12/18/2022]  Open
20
Boniface CT, Spellman PT. Blood, Toil, and Taxoteres: Biological Determinates of Treatment-Induce ctDNA Dynamics for Interpreting Tumor Response. Pathol Oncol Res 2022;28:1610103. [PMID: 35665409 PMCID: PMC9160182 DOI: 10.3389/pore.2022.1610103] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022]
21
Sipos F, Bohusné Barta B, Simon Á, Nagy L, Dankó T, Raffay RE, Petővári G, Zsiros V, Wichmann B, Sebestyén A, Műzes G. Survival of HT29 Cancer Cells Is Affected by IGF1R Inhibition via Modulation of Self-DNA-Triggered TLR9 Signaling and the Autophagy Response. Pathol Oncol Res 2022;28:1610322. [PMID: 35651701 PMCID: PMC9148969 DOI: 10.3389/pore.2022.1610322] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023]
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