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Naser H, Munn K, Lawrence R, Wright R, Grewal E, Williams L, Doak S, Jenkins G. Human plasma can modulate micronucleus frequency in TK6 and OE33 cells in vitro. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 896:503766. [PMID: 38821668 DOI: 10.1016/j.mrgentox.2024.503766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
In this paper, we studied the potential genotoxic effects of human plasma from healthy volunteers, as well as patients with gastro-oesophageal reflux disease, Barrett's oesophagus (BO) and oesophageal adenocarcinoma (OAC) using the oesophageal adenocarcinoma cell line (OE33) and the lymphoblastoid cell line (TK6). Both TK6 and OE33 cells were treated with plasma (10 % volume, replacing foetal bovine serum (FBS) or horse serum (HS)) at different time points of 4 h (for the micronucleus (Mn) assay and the invasion assay) and 24 h (for the cell cycle studies). Plasma-induced effects on DNA damage levels, cell viability and the cell cycle were studied by the micronucleus assay, cytokinesis block proliferation index (CBPI) and flow cytometry respectively. The expression of IL-8 in supernatants of TK6 cells and IFN-β in OE33 cells was also analysed by enzyme-linked immunosorbent assay (ELISA). Finally, we carried out an assessment of cellular invasion of OE33 cells following plasma treatment. The results of the micronucleus assay confirmed the genotoxicity of direct plasma treatment from some participants through the increase in DNA damage in TK6 cells. Conversely, some individual patient plasma samples reduced background levels of TK6 cell Mn frequency, in an anti-genotoxic fashion. In TK6 cells, (on average) plasma samples from patients with Barrett's oesophagus induced higher micronucleus levels than healthy volunteers (p= 0.0019). There was little difference in Mn induction when using plasma versus serum to treat the cells in vitro. Cell cycle results showed that direct plasma treatment had a marked impact on OE33 cells at 24 h (p=0.0182 for BO and p=0.0320 for OAC) by decreasing the proportion of cells in the S phase, while plasma exposure was less impactful on the cell cycle of TK6 cells. Invasion of OE33 cells was also seen to be non-significantly affected by plasma treatment of OE33 cells. The addition of N-acetyl cysteine NAC in a dose-dependent matter did not alter the formation of Mn in TK6 cells, suggesting that reactive oxygen species (ROS) are not the root cause of plasma's genotoxicity. The concentration of IL-8 in TK6 cells and IFN-β in OE33 cells was significantly higher in cells treated with OAC-derived plasma than in the untreated negative control. Collectively, our results demonstrate that plasma-specific effects are detectable which helps us better understand some important aspects of the biology of blood-based biomarkers under development.
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Affiliation(s)
- Hamsa Naser
- Institute of Life Science, Faculty of Medicine, Health and Life Science, Swansea University, Singleton Park, Swansea SA2 8PP, UK.
| | - Kathryn Munn
- Institute of Life Science, Faculty of Medicine, Health and Life Science, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Rachel Lawrence
- Barts Cancer Centre, Charterhouse Square, London EC1M6AU, UK
| | - Rhiannon Wright
- Institute of Life Science, Faculty of Medicine, Health and Life Science, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Ethan Grewal
- Institute of Life Science, Faculty of Medicine, Health and Life Science, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Lisa Williams
- Department of Gastroenterology, Singleton Hospital, Swansea Bay University Health Board, Sketty Lane, Swansea SA28QA, UK
| | - Shareen Doak
- Institute of Life Science, Faculty of Medicine, Health and Life Science, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Gareth Jenkins
- Institute of Life Science, Faculty of Medicine, Health and Life Science, Swansea University, Singleton Park, Swansea SA2 8PP, UK
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Chimienti G, Russo F, Bianco A, Maqoud F, De Virgilio C, Galeano G, Orlando A, Riezzo G, D’Attoma B, Ignazzi A, Linsalata M, Prospero L, Franco I, Bagnato CB, Curci R, Coletta S. Effect of a 12-Week Walking Program Monitored by Global Physical Capacity Score (GPCS) on Circulating Cell-Free mtDNA and DNase Activity in Patients with Irritable Bowel Syndrome. Int J Mol Sci 2024; 25:4293. [PMID: 38673878 PMCID: PMC11050617 DOI: 10.3390/ijms25084293] [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: 03/27/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Irritable bowel syndrome (IBS) involves low-grade mucosal inflammation. Among the various approaches capable of managing the symptoms, physical activity is still under investigation. Despite its benefits, it promotes oxidative stress and inflammation. Mitochondria impacts gut disorders by releasing damage-associated molecular patterns, such as cell-free mtDNA (cf-mtDNA), which support inflammation. This study evaluated the effects of a 12-week walking program on the cf-mtDNA and DNase in 26 IBS and 17 non-IBS subjects. Pro- and anti-inflammatory cytokines were evaluated by ELISA. Digital droplet PCR was used to quantify cf-mtDNA; DNase activity was assessed using a single radial enzyme diffusion assay. PCR-RFLP was used to genotype DNASE1 rs1053874 SNP. Significantly lower IL-10 levels were found in IBS than in non-IBS individuals. Exercise reduced cf-mtDNA in non-IBS subjects but not in IBS patients. DNase activity did not correlate with the cf-mtDNA levels in IBS patients post-exercise, indicating imbalanced cf-mtDNA clearance. Different rs1053874 SNP frequencies were not found between groups. The study confirms the positive effects of regular moderate-intensity physical activity in healthy subjects and its role in cf-mtDNA release and clearance. Walking alone might not sufficiently reduce subclinical inflammation in IBS, based on imbalanced pro- and anti-inflammatory molecules. Prolonged programs are necessary to investigate their effects on inflammatory markers in IBS.
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Affiliation(s)
- Guglielmina Chimienti
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (G.C.); (C.D.V.)
| | - Francesco Russo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonella Bianco
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Fatima Maqoud
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Caterina De Virgilio
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (G.C.); (C.D.V.)
| | - Grazia Galeano
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonella Orlando
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Giuseppe Riezzo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Benedetta D’Attoma
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonia Ignazzi
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Michele Linsalata
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Laura Prospero
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Isabella Franco
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Claudia Beatrice Bagnato
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Ritanna Curci
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Sergio Coletta
- Core Facility Biobank, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy;
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Cepeda J, Racca ME, Rossetti MF, Cardozo MA, Gaydou L, Luque EH, Muñoz-de-Toro M, Milesi MM, Varayoud J, Ramos JG. A Reliable Method for Quantifying Plasma Cell-Free DNA Using an Internal Standard Strategy: Evaluation in a Cohort of Non-Pregnant and Pregnant Women. Reprod Sci 2024; 31:987-996. [PMID: 38030813 DOI: 10.1007/s43032-023-01403-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023]
Abstract
The use of plasma cell-free DNA (cfDNA) as a useful biomarker in obstetric clinical practice has been delayed due to the lack of reliable quantification protocols. We developed a protocol to quantify plasma cfDNA using an internal standard strategy to overcome difficulties posed by low levels and high fragmentation of cfDNA. cfDNA was isolated from plasma samples of non-pregnant (NP, n = 26) and pregnant (P, n = 26) women using a commercial kit and several elution volumes were evaluated. qPCR parameters were optimized for cfDNA quantification, and several quantities of a recombinant standard were evaluated as internal standard. Absolute quantification was performed using a standard curve and the quality of the complete method was evaluated. cfDNA was eluted in a 50-μl volume, actin-β (ACTB) was selected as the target gene, and qPCR parameters were optimized. The ACTB standard was constructed and 1000 copies were selected as internal standard. The standard curve showed R2 = 0.993 and E = 109.7%, and the linear dynamic range was defined between 102 and 106 ACTB copies/tube. Repeatability and reproducibility in terms of CV were 19% and up to 49.5% for ACTB copies per milliliter of plasma, respectively. The range of cfDNA levels was 428-18,851 copies/mL in NP women and 4031-2,019,363 copies/mL in P women, showing significant differences between the groups. We recommend the application of internal standard strategy for a reliable plasma cfDNA quantification. This methodology holds great potential for a future application in the obstetric field.
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Affiliation(s)
- Julieta Cepeda
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
| | - M Emilia Racca
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - M Florencia Rossetti
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
| | - M Alejandra Cardozo
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
- Laboratorios BLUT, Santa Fe, Argentina
| | - Luisa Gaydou
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Enrique H Luque
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Cátedra de Fisiología Humana, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Mónica Muñoz-de-Toro
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Cátedra de Patología Humana, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - M Mercedes Milesi
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Cátedra de Fisiología Humana, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Jorgelina Varayoud
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Cátedra de Fisiología Humana, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Jorge G Ramos
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina.
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina.
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Lin X, Li X, Li C, Wang H, Zou L, Pan J, Zhang X, He L, Rong X, Peng Y. Activation of STING signaling aggravates chronic alcohol exposure-induced cognitive impairment by increasing neuroinflammation and mitochondrial apoptosis. CNS Neurosci Ther 2024; 30:e14689. [PMID: 38516831 PMCID: PMC10958405 DOI: 10.1111/cns.14689] [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: 11/21/2023] [Revised: 02/18/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
AIMS Chronic alcohol exposure leads to persistent neurological disorders, which are mainly attributed to neuroinflammation and apoptosis. Stimulator of IFN genes (STING) is essential in the cytosolic DNA sensing pathway and is involved in inflammation and cellular death processes. This study was to examine the expression pattern and biological functions of STING signaling in alcohol use disorder (AUD). METHODS Cell-free DNA was extracted from human and mouse plasma. C57BL/6J mice were given alcohol by gavage for 28 days, and behavior tests were used to determine their mood and cognition. Cultured cells were treated with ethanol for 24 hours. The STING agonist DMXAA, STING inhibitor C-176, and STING-siRNA were used to intervene the STING. qPCR, western blot, and immunofluorescence staining were used to assess STING signaling, inflammation, and apoptosis. RESULTS Circulating cell-free mitochondrial DNA (mtDNA) was increased in individuals with AUD and mice chronically exposed to alcohol. Upregulation of STING signaling under alcohol exposure led to inflammatory responses in BV2 cells and mitochondrial apoptosis in PC12 cells. DMXAA exacerbated alcohol-induced cognitive impairment and increased the activation of microglia, neuroinflammation, and apoptosis in the medial prefrontal cortex (mPFC), while C-176 exerted neuroprotection. CONCLUSION Activation of STING signaling played an essential role in alcohol-induced inflammation and mitochondrial apoptosis in the mPFC. This study identifies STING as a promising therapeutic target for AUD.
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Affiliation(s)
- Xinrou Lin
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Nanhai Translational Innovation Center of Precision ImmunologySun Yat‐Sen Memorial HospitalFoshanChina
| | - Xiangpen Li
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Shenshan Medical Center, Sun Yat‐sen Memorial HospitalSun Yat‐sen UniversityShanweiChina
| | - Chenguang Li
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Hongxuan Wang
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Lubin Zou
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Nanhai Translational Innovation Center of Precision ImmunologySun Yat‐Sen Memorial HospitalFoshanChina
| | - Jingrui Pan
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Shenshan Medical Center, Sun Yat‐sen Memorial HospitalSun Yat‐sen UniversityShanweiChina
| | - Xiaoni Zhang
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Lei He
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Xiaoming Rong
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Ying Peng
- Department of Neurology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Nanhai Translational Innovation Center of Precision ImmunologySun Yat‐Sen Memorial HospitalFoshanChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
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Pru JK. Defining liquid biopsy parameters in postmenopausal women for disease diagnosis. Menopause 2024; 31:169-170. [PMID: 38385728 DOI: 10.1097/gme.0000000000002330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Affiliation(s)
- James K Pru
- From the Program in Reproductive Biology, University of Wyoming, Laramie, WY
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Fisher T, Powell E, Yuwono NL, Ford CE, Warton K. Circulating cell-free DNA is elevated in postmenopausal compared with pre- and perimenopausal women. Menopause 2024; 31:171-175. [PMID: 38385729 DOI: 10.1097/gme.0000000000002313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
OBJECTIVE With the rising use of circulating cell-free DNA (cirDNA) liquid biopsies for disease screening, it is important to understand biological differences that may impact the accuracy of cirDNA-based clinical tests. Although a number of biological factors have been researched, the relationship between menopause and cirDNA has not been thoroughly investigated. We aimed to compare plasma cirDNA concentration and DNA fragment integrity in healthy women pre- and postmenopause. METHODS Blood was collected from healthy female volunteers 40 years and older. cirDNA was extracted from plasma (n = 52) and quantified by quantitative polymerase chain reaction (n = 47; 26 premenopause, mean age-46 y; 21 postmenopause, mean age-59 y). cirDNA concentration was quantitated using an ALU repetitive sequence with a 115-base-pair (bp) product (ALU-115), and long cirDNA fragments were quantitated using an ALU repetitive sequence with a 247-bp product (ALU-247). cirDNA integrity was expressed as a ratio of ALU-247 over ALU-115. Mann-Whitney U test was used to compare pre- and postmenopause qPCR results, and a two-tailed, unpaired t test was undertaken to compare the integrity ratio between the two groups. RESULTS Postmenopause plasma samples were found to have a significantly higher cirDNA concentration (P < 0.0001, premenopause: mean, 3.10 ± 1.84 ng/mL; median, 2.90 ng/mL; postmenopause: mean, 5.28 ± 2.76 ng/mL; median, 4.56 ng/mL) and significantly higher concentration of long-stranded cirDNA fragments (P = 0.0033, premenopause: mean, 1.06 ± 0.48 ng/mL; median, 0.96 ng/mL; postmenopause: mean, 1.69 ± 0.89 ng/mL; median, 1.48 ng/mL). There was no significant difference in the integrity ratio between the groups (P = 0.1788). CONCLUSIONS Plasma cirDNA concentrations are higher in postmenopausal women. This has important implications in cirDNA liquid biopsy development and screening, especially for diseases such as cancer where the majority of cases are diagnosed postmenopause.
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Affiliation(s)
- Teagan Fisher
- From the Gynaecological Cancer Research Group, Adult Cancer Program, School of Clinical Medicine University of New South Wales, Sydney, Australia
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Verebi C, Nectoux J, Duriez P, Gorwood P, Ramoz N, Bienvenu T. The value of plasma cell-free DNA levels as biomarker in patients with eating disorders: A preliminary study. Psychoneuroendocrinology 2024; 160:106918. [PMID: 38065040 DOI: 10.1016/j.psyneuen.2023.106918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/02/2024]
Abstract
OBJECTIVE Circulating cell-free DNA (cfDNA) holds promise as a rapid and convenient biomarker for identifying individuals with eating disorders. To investigate this hypothesis, we measured plasma cfDNA in patients with different eating disorders. METHODS In this study, 110 participants (98 patients with eating disorders divided into 30 patients with bulimia nervosa, 33 patients with anorexia nervosa (AN) Restricting subtype, 35 patients with AN Binge-eating/purging subtype and 12 controls) were enrolled. We measured both cell-free nuclear DNA (cf-nDNA) and cell-free mitochondrial DNA (cf-mtDNA) from plasma using two specific droplet digital PCR assays each, referring to two amplicon sizes. RESULTS Levels of plasma cf-nDNA and cf-mtDNA showed no significant differences between control participants and those with eating disorders. However, we observed a higher proportion of long cf-nDNA fragments in patients with eating disorders, suggesting its potential as a biomarker for eating disorders. CONCLUSION This is the first study of cfDNA in patients with eating disorders. Our findings highlight the potential for qualitative exploration of cfDNA, although not of quantitative interest. Full characterization of cfDNA may serve as a valuable biomarker for eating disorders and provide some insights into the hidden mechanisms underlying the chronic development of these conditions. Future studies are needed to confirm or refute this hypothesis.
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Affiliation(s)
- Camille Verebi
- Service de Médecine Génomique des Maladies de Système et d'Organe, Fédération de Génétique et de Médecine Génomique, APHP, Centre - Université Paris Cité, Hôpital Cochin, Paris 75014, France; Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Gorwood Team, Paris 75014, France.
| | - Juliette Nectoux
- Service de Médecine Génomique des Maladies de Système et d'Organe, Fédération de Génétique et de Médecine Génomique, APHP, Centre - Université Paris Cité, Hôpital Cochin, Paris 75014, France
| | - Philibert Duriez
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Gorwood Team, Paris 75014, France; GHU Paris Psychiatrie et Neurosciences, CMME, Hôpital Sainte-Anne, Paris F-75014, France
| | - Philip Gorwood
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Gorwood Team, Paris 75014, France; GHU Paris Psychiatrie et Neurosciences, CMME, Hôpital Sainte-Anne, Paris F-75014, France
| | - Nicolas Ramoz
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Gorwood Team, Paris 75014, France; GHU Paris Psychiatrie et Neurosciences, CMME, Hôpital Sainte-Anne, Paris F-75014, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, Fédération de Génétique et de Médecine Génomique, APHP, Centre - Université Paris Cité, Hôpital Cochin, Paris 75014, France; Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Gorwood Team, Paris 75014, France
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Sawai A, Shida T, Hoshikawa Y, Hatanaka S, Ueda M, Kato Y, Tokinoya K, Natsui H, Kawakami Y, Takekoshi K. Effect of acute moderate-intensity cycling on cfDNA levels considering menstrual cycle phases. Front Sports Act Living 2024; 6:1322295. [PMID: 38348376 PMCID: PMC10859457 DOI: 10.3389/fspor.2024.1322295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Introduction We aimed to determine the effects of exercise on cell-free DNA (cfDNA) levels and concentration changes during the menstrual cycle in participants with regular menstrual cycles and no exercise habits. Methods Eleven sedentary female students with regular menstrual cycles and ovulation performed bicycle exercises at 60% VO2max for 30 min during the menstrual, ovulatory, and luteal phases. Blood samples were collected before (Pre), immediately after (Post 0), 30 min after (Post 30), and 60 min after (Post 60) exercise. Blood concentrations of ovarian hormones, cfDNA, prostaglandin F2a (PGF2α), interleukin-6 (IL-6), and aromatase were evaluated. Results Based on the concentration of ovarian hormones, seven individuals were finally analyzed. No significant phase difference was observed in cfDNA across all time points. cfDNA (menstrual phase: p = 0.028, ovulatory phase: p = 0.018, and luteal phase: p = 0.048) and aromatase concentrations (menstrual phase: p = 0.040, ovulatory phase: p = 0.039, and luteal phase: p = 0.045) significantly increased from Pre to Post 0 in all phases. Serum estradiol (E2) levels were significantly higher in the luteal phase at all time points than in the menstrual phase (Pre: p < 0.001, Post 0: p < 0.001, Post 30: p = 0.005, and Post 60: p = 0.011); however, serum progesterone (P4) levels were significantly higher in the luteal phase at all time points than in the menstrual (Pre: p < 0.001, Post 0: p < 0.001, Post 30: p < 0.001, and Post 60: p < 0.001) and ovulatory phases (Pre: p = 0.005, Post 0: p = 0.005, Post 30: p = 0.003, and Post 60: p = 0.003). E2 levels significantly increased from Pre to Post 0 in the ovulatory and luteal phases, whereas P4 levels increased in the luteal phase. Progesterone to estradiol level ratio (P4/E2) changes from Pre to Post 0 (%baseline) during the luteal phase were significantly negatively correlated (r = -0.82, p = 0.046) with the changes in cfDNA from Pre to Post 0. Furthermore, the repeated measures correlation between P4/E2 and cfDNA level showed a significant negative correlation in ovulatory and luteal phases. Discussion The results indicate that while resting cfDNA levels are unlikely to be affected by a woman's menstrual cycle, the increase in cfDNA after exercise is higher in the ovulatory phase (when only E2 increases) and lower in the luteal phase (when E2 and P4 increase with exercise) compared to that in the menstrual phase (when E2 and P4 are in low levels), suggesting the contribution of increased ovarian hormone levels after exercise.
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Affiliation(s)
- Akemi Sawai
- Research Institute of Physical Fitness, Japan Women’s College of Physical Education, Setagaya City, Japan
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
| | - Takashi Shida
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
- Research Team for Promoting Independence and Mental Health, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi City, Japan
| | - Yoshihiro Hoshikawa
- Department of Sports Science, Japan Women’s College of Physical Education, Setagaya City, Japan
| | - Sho Hatanaka
- Research Team for Promoting Independence and Mental Health, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi City, Japan
| | - Mashiro Ueda
- Master’s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba City, Japan
| | - Yuri Kato
- Master’s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba City, Japan
| | - Katsuyuki Tokinoya
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
- Embodied Wisdom Division, Center for Liberal Education and Learning, Sophia University, Chiyoda City, Japan
| | - Hiroaki Natsui
- Department of Sports and Health Science, Japan Women’s College of Physical Education, Setagaya City, Japan
| | - Yasushi Kawakami
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
| | - Kazuhiro Takekoshi
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
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9
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Wong D, Luo P, Oldfield LE, Gong H, Brunga L, Rabinowicz R, Subasri V, Chan C, Downs T, Farncombe KM, Luu B, Norman M, Sobotka JA, Uju P, Eagles J, Pedersen S, Wellum J, Danesh A, Prokopec SD, Stutheit-Zhao EY, Znassi N, Heisler LE, Jovelin R, Lam B, Lujan Toro BE, Marsh K, Sundaravadanam Y, Torti D, Man C, Goldenberg A, Xu W, Veit-Haibach P, Doria AS, Malkin D, Kim RH, Pugh TJ. Early Cancer Detection in Li-Fraumeni Syndrome with Cell-Free DNA. Cancer Discov 2024; 14:104-119. [PMID: 37874259 PMCID: PMC10784744 DOI: 10.1158/2159-8290.cd-23-0456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
People with Li-Fraumeni syndrome (LFS) harbor a germline pathogenic variant in the TP53 tumor suppressor gene, face a near 100% lifetime risk of cancer, and routinely undergo intensive surveillance protocols. Liquid biopsy has become an attractive tool for a range of clinical applications, including early cancer detection. Here, we provide a proof-of-principle for a multimodal liquid biopsy assay that integrates a targeted gene panel, shallow whole-genome, and cell-free methylated DNA immunoprecipitation sequencing for the early detection of cancer in a longitudinal cohort of 89 LFS patients. Multimodal analysis increased our detection rate in patients with an active cancer diagnosis over uni-modal analysis and was able to detect cancer-associated signal(s) in carriers prior to diagnosis with conventional screening (positive predictive value = 67.6%, negative predictive value = 96.5%). Although adoption of liquid biopsy into current surveillance will require further clinical validation, this study provides a framework for individuals with LFS. SIGNIFICANCE By utilizing an integrated cell-free DNA approach, liquid biopsy shows earlier detection of cancer in patients with LFS compared with current clinical surveillance methods such as imaging. Liquid biopsy provides improved accessibility and sensitivity, complementing current clinical surveillance methods to provide better care for these patients. See related commentary by Latham et al., p. 23. This article is featured in Selected Articles from This Issue, p. 5.
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Affiliation(s)
- Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ping Luo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Leslie E. Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Haifan Gong
- The Hospital for Sick Children, Toronto, Canada
| | | | | | - Vallijah Subasri
- The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Clarissa Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Tiana Downs
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | - Beatrice Luu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Maia Norman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Julia A. Sobotka
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Precious Uju
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Jenna Eagles
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Stephanie Pedersen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Johanna Wellum
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Nadia Znassi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Bernard Lam
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Carina Man
- The Hospital for Sick Children, Toronto, Canada
| | - Anna Goldenberg
- The Hospital for Sick Children, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Patrick Veit-Haibach
- Joint Department of Medical Imaging, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada
| | | | - David Malkin
- The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Raymond H. Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- The Hospital for Sick Children, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
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10
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Leotta C, Hernandez L, Tothova L, Arefin S, Ciceri P, Cozzolino MG, Barany P, Chromek M, Stenvinkel P, Kublickiene K. Levels of Cell-Free DNA in Kidney Failure Patients before and after Renal Transplantation. Cells 2023; 12:2774. [PMID: 38132094 PMCID: PMC10741614 DOI: 10.3390/cells12242774] [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: 10/30/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has diverse applications in oncological, prenatal, toxicological, cardiovascular, and autoimmune diseases, diagnostics, and organ transplantation. In particular, mitochondrial cfDNA (mt-cfDNA) is associated with inflammation and linked to early vascular ageing (EVA) in end-stage kidney failure (ESKF), which could be a noninvasive marker for graft rejection and organ damage. Plasma samples from 44 ESKF patients, of whom half (n = 22) underwent either conservative therapy (non-HD) or hemodialysis (HD) before kidney transplantation (KT). These samples were analyzed at baseline and two years after KT. cfDNA was extracted from plasma and quantified using the fluorometric method. qPCR was used to quantify and differentiate the fractions of mt-cfDNA and nuclear cfDNA (nc-cfDNA). mt-cfDNA levels in KT patients decreased significantly from baseline to two years post-KT (p < 0.0268), while levels of total cfDNA and nc-cfDNA did not differ. Depending on therapy modality (HD vs. non-HD) before KT, total cfDNA levels were higher in HD patients at both baseline (p = 0.0133) and two years post-KT (p = 0.0421), while nc-cfDNA levels were higher in HD only at baseline (p = 0.0079). Males showed a nonsignificant trend of higher cfDNA levels. Patients with assessed vascular fibrosis (p = 0.0068), either alone or in combination with calcification plus fibrosis, showed reduced mt-cfDNA post-KT (p = 0.0195). Changes in mt-cfDNA levels suggests the impact of KT on the inflammatory state of ESKF, as evidenced via its correlation with high sensitivity C-reactive protein after KT. Further studies are warranted to assess if cfDNA could serve as a noninvasive method for monitoring the response to organ transplantation and even for amelioration of EVA status per se.
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Affiliation(s)
- Chiara Leotta
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
- Renal Division, Department of Health Sciences, ASST Santi Paolo e Carlo Hospital Milan, University of Milan, 20142 Milan, Italy (M.G.C.)
| | - Leah Hernandez
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
| | - Lubomira Tothova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Samsul Arefin
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
| | - Paola Ciceri
- Renal Division, Department of Health Sciences, ASST Santi Paolo e Carlo Hospital Milan, University of Milan, 20142 Milan, Italy (M.G.C.)
| | - Mario Gennaro Cozzolino
- Renal Division, Department of Health Sciences, ASST Santi Paolo e Carlo Hospital Milan, University of Milan, 20142 Milan, Italy (M.G.C.)
| | - Peter Barany
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
| | - Milan Chromek
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
- Division of Pediatrics, Clinical Science, Intervention and Technology (CLINTEC), Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Peter Stenvinkel
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
| | - Karolina Kublickiene
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
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11
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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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12
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [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: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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13
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Evrard C, Ingrand P, Rochelle T, Martel M, Tachon G, Flores N, Randrian V, Ferru A, Haineaux PA, Goujon JM, Karayan-Tapon L, Tougeron D. Circulating tumor DNA in unresectable pancreatic cancer is a strong predictor of first-line treatment efficacy: The KRASCIPANC prospective study. Dig Liver Dis 2023; 55:1562-1572. [PMID: 37308396 DOI: 10.1016/j.dld.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/08/2023] [Accepted: 03/27/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND There is no robust predictor of response to chemotherapy (CT) in unresectable pancreatic adenocarcinomas (UPA). The objective of the KRASCIPANC study was to analyze the kinetics of cell-free DNA (cfDNA)/circulating tumor DNA (ctDNA) as a predictor of response to CT in UPA. METHODS Blood samples were collected just before first CT and at day 28. The primary endpoint was the kinetics of KRAS-mutated ctDNA by digital droplet PCR between D0 and D28 as a predictor of progression-free survival (PFS). RESULTS We analyzed 65 patients with a KRAS-mutated tumor. A high level of cfDNA and KRAS-mutated ctDNA at D0, as well as the presence of KRAS-mutated ctDNA at D28, were strongly associated with lower centralized disease control rate (cDCR), shorter cPFS and OS in multivariate analysis. A score combining cfDNA level at diagnosis ≥ or <30 ng/mL and presence or not of KRAS-mutated ctDNA at D28 was an optimal predictor of cDCR (OR=30.7, IC95% 4.31-218 P=.001), PFS (HR=6.79, IC95% 2.76-16.7, P<.001) and OS (HR=9.98, IC95% 4.14-24.1, P<.001). CONCLUSION A combined score using cfDNA level at diagnosis and KRAS-mutated ctDNA at D28 is strongly associated with patient survival/response to chemotherapy in UPA. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04560270.
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Affiliation(s)
- Camille Evrard
- Medical Oncology Department, Poitiers University Hospital, Poitiers 86000, France; ProDicET, UR 24144, University of Poitiers, Poitiers 86000, France.
| | - Pierre Ingrand
- Department of Statistics, Faculty of Medicine, University of Poitiers, Poitiers 86000, France
| | - Tristan Rochelle
- Cancer Biology Department, Poitiers University Hospital, Poitiers 86000, France
| | - Marine Martel
- Cancer Biology Department, Poitiers University Hospital, Poitiers 86000, France
| | - Gaëlle Tachon
- Cancer Biology Department, Poitiers University Hospital, Poitiers 86000, France; Cancer Biology Department, Centre Léon Bérard, Lyon 69000, France
| | - Nicolas Flores
- Department of Imaging, University Hospital of Poitiers, Poitiers 86000, France
| | - Violaine Randrian
- ProDicET, UR 24144, University of Poitiers, Poitiers 86000, France; Hepato-Gastroenterology Department, Poitiers University Hospital, Poitiers, France
| | - Aurélie Ferru
- Medical Oncology Department, Poitiers University Hospital, Poitiers 86000, France
| | - Paul-Arthur Haineaux
- Hepato-Gastroenterology Department, Poitiers University Hospital, Poitiers, France; Hepato-Gastroenterology Department, Poitiers University Hospital, Châtellerault Hospital, Poitiers 86106, France
| | - Jean-Michel Goujon
- Department of Pathology, Poitiers University Hospital, Poitiers 86000, France
| | - Lucie Karayan-Tapon
- ProDicET, UR 24144, University of Poitiers, Poitiers 86000, France; Cancer Biology Department, Poitiers University Hospital, Poitiers 86000, France
| | - David Tougeron
- ProDicET, UR 24144, University of Poitiers, Poitiers 86000, France; Hepato-Gastroenterology Department, Poitiers University Hospital, Poitiers, France.
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14
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Hovhannisyan G, Harutyunyan T, Aroutiounian R, Liehr T. The Diagnostic, Prognostic, and Therapeutic Potential of Cell-Free DNA with a Special Focus on COVID-19 and Other Viral Infections. Int J Mol Sci 2023; 24:14163. [PMID: 37762464 PMCID: PMC10532175 DOI: 10.3390/ijms241814163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-free DNA (cfDNA) in human blood serum, urine, and other body fluids recently became a commonly used diagnostic marker associated with various pathologies. This is because cfDNA enables a much higher sensitivity than standard biochemical parameters. The presence of and/or increased level of cfDNA has been reported for various diseases, including viral infections, including COVID-19. Here, we review cfDNA in general, how it has been identified, where it can derive from, its molecular features, and mechanisms of release and clearance. General suitability of cfDNA for diagnostic questions, possible shortcomings and future directions are discussed, with a special focus on coronavirus infection.
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Affiliation(s)
- Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, 07747 Jena, Germany
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15
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Shen Y, Zhang X, Zhang L, Zhang Z, Lyu B, Lai Q, Li Q, Zhang Y, Ying J, Song J. Performance evaluation of a CRISPR Cas9-based selective exponential amplification assay for the detection of KRAS mutations in plasma of patients with advanced pancreatic cancer. J Clin Pathol 2023:jcp-2023-208974. [PMID: 37679033 DOI: 10.1136/jcp-2023-208974] [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: 05/22/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
AIMS Pancreatic ductal adenocarcinoma (PDAC) is highly malignant, with shockingly mortality rates. KRAS oncoprotein is the main molecular target for PDAC. Liquid biopsies, such as the detection of circulating tumour DNA (ctDNA), offer a promising approach for less invasive diagnosis. In this study, we aim to evaluate the precision and utility of programmable enzyme-based selective exponential amplification (PASEA) assay for rare mutant alleles identification. METHODS PASEA uses CRISPR-Cas9 to continuously shear wild-type alleles during recombinase polymerase amplification, while mutant alleles are exponentially amplified, ultimately reaching a level detectable by Sanger sequencing. We applied PASEA to detect KRAS mutations in plasma ctDNA. A total of 153 patients with stage IV PDAC were enrolled. We investigated the relationship between ctDNA detection rates with various clinical factors. RESULTS Our results showed 91.43% vs 44.83% detection rate in patients of prechemotherapy and undergoing chemotherapy. KRAS ctDNA was more prevalent in patients with liver metastases and patients did not undergo surgical resection. Patients with liver metastases prior to chemotherapy showed a sensitivity of 95.24% (20/21) with PASEA. Through longitudinal monitoring, we found ctDNA may be a more accurate biomarker for monitoring chemotherapy efficacy in PDAC than CA19-9. CONCLUSIONS Our study sheds light on the potential of ctDNA as a valuable complementary biomarker for precision targeted therapy, emphasising the importance of considering chemotherapy status, metastatic sites and surgical history when evaluating its diagnostic potential in PDAC. PASEA technology provides a reliable, cost-effective and minimally invasive method for detecting ctDNA of PDAC.
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Affiliation(s)
- Yue Shen
- School of life sciences, Tianjin University, Tianjin, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xiaoling Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Liyi Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zuoying Zhang
- School of life sciences, Tianjin University, Tianjin, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Bao Lyu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qian Lai
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qinglin Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yuhua Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jieer Ying
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jinzhao Song
- School of life sciences, Tianjin University, Tianjin, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
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16
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Meriranta L, Pitkänen E, Leppä S. Blood has never been thicker: Cell-free DNA fragmentomics in the liquid biopsy toolbox of B-cell lymphomas. Semin Hematol 2023; 60:132-141. [PMID: 37455222 DOI: 10.1053/j.seminhematol.2023.06.006] [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: 03/20/2023] [Revised: 05/30/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Liquid biopsies utilizing plasma circulating tumor DNA (ctDNA) are anticipated to revolutionize decision-making in cancer care. In the field of lymphomas, ctDNA-based blood tests represent the forefront of clinically applicable tools to harness decades of genomic research for disease profiling, quantification, and detection. More recently, the discovery of nonrandom fragmentation patterns in cell-free DNA (cfDNA) has opened another avenue of liquid biopsy research beyond mutational interrogation of ctDNA. Through examination of structural features, nucleotide content, and genomic distribution of massive numbers of plasma cfDNA molecules, the study of fragmentomics aims at identifying new tools that augment existing ctDNA-based analyses and discover new ways to profile cancer from blood tests. Indeed, the characterization of aberrant lymphoma ctDNA fragment patterns and harnessing them with powerful machine-learning techniques are expected to unleash the potential of nonmutant molecules for liquid biopsy purposes. In this article, we review cfDNA fragmentomics as an emerging approach in the ctDNA research of B-cell lymphomas. We summarize the biology behind the formation of cfDNA fragment patterns and discuss the preanalytical and technical limitations faced with current methodologies. Then we go through the advances in the field of lymphomas and envision what other noninvasive tools based on fragment characteristics could be explored. Last, we place fragmentomics as one of the facets of ctDNA analyses in emerging multiview and multiomics liquid biopsies. We pay attention to the unknowns in the field of cfDNA fragmentation biology that warrant further mechanistic investigation to provide rational background for the development of these precision oncology tools and understanding of their limitations.
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Affiliation(s)
- Leo Meriranta
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Esa Pitkänen
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), HILIFE, Helsinki, Finland
| | - Sirpa Leppä
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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17
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Michelson J, Rausser S, Peng A, Yu T, Sturm G, Trumpff C, Kaufman BA, Rai AJ, Picard M. MitoQuicLy: A high-throughput method for quantifying cell-free DNA from human plasma, serum, and saliva. Mitochondrion 2023; 71:26-39. [PMID: 37172669 PMCID: PMC10524316 DOI: 10.1016/j.mito.2023.05.001] [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: 01/04/2023] [Revised: 04/12/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
Circulating cell-free mitochondrial DNA (cf-mtDNA) is an emerging biomarker of psychobiological stress and disease which predicts mortality and is associated with various disease states. To evaluate the contribution of cf-mtDNA to health and disease states, standardized high-throughput procedures are needed to quantify cf-mtDNA in relevant biofluids. Here, we describe MitoQuicLy: Mitochondrial DNA Quantification in cell-free samples by Lysis. We demonstrate high agreement between MitoQuicLy and the commonly used column-based method, although MitoQuicLy is faster, cheaper, and requires a smaller input sample volume. Using 10 µL of input volume with MitoQuicLy, we quantify cf-mtDNA levels from three commonly used plasma tube types, two serum tube types, and saliva. We detect, as expected, significant inter-individual differences in cf-mtDNA across different biofluids. However, cf-mtDNA levels between concurrently collected plasma, serum, and saliva from the same individual differ on average by up to two orders of magnitude and are poorly correlated with one another, pointing to different cf-mtDNA biology or regulation between commonly used biofluids in clinical and research settings. Moreover, in a small sample of healthy women and men (n = 34), we show that blood and saliva cf-mtDNAs correlate with clinical biomarkers differently depending on the sample used. The biological divergences revealed between biofluids, together with the lysis-based, cost-effective, and scalable MitoQuicLy protocol for biofluid cf-mtDNA quantification, provide a foundation to examine the biological origin and significance of cf-mtDNA to human health.
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Affiliation(s)
- Jeremy Michelson
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Shannon Rausser
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Amanda Peng
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Temmie Yu
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Gabriel Sturm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Brett A Kaufman
- Center for Metabolism and Mitochondrial Medicine and the Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, USA
| | - Alex J Rai
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA.
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18
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Verebi C, Nectoux J, Gorwood P, Le Strat Y, Duriez P, Ramoz N, Bienvenu T. A systematic literature review and meta-analysis of circulating nucleic acids as biomarkers in psychiatry. Prog Neuropsychopharmacol Biol Psychiatry 2023; 125:110770. [PMID: 37068545 DOI: 10.1016/j.pnpbp.2023.110770] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
Common mental disorders (CMDs) such as depression, anxiety and post-traumatic stress disorders account for 40% of the global burden of disease. In most psychiatric disorders, both diagnosis and monitoring can be challenging, frequently requiring long-term investigation and follow-up. The discovery of better methods to facilitate accurate and fast diagnosis and monitoring of psychiatric disorders is therefore crucial. Circulating nucleic acids (CNAs) are among these new tools. CNAs (DNA or RNA) can be found circulating in body biofluids, and can be isolated from biological samples such as plasma. They can serve as biomarkers for diagnosis and prognoses. They appear to be promising for disorders (such as psychiatric disorders) that involve organs or structures that are difficult to assess. This review presents an accurate assessment of the current literature about the use of plasma and serum cell-free DNA (cfDNA) as biomarkers for several aspects of psychiatric disorders: diagnosis, prognosis, treatment response, and monitor disease progression. For each psychiatric disorder, we examine the effect sizes to give insights on the efficacy of CNAs as biomarkers. The global effect size for plasma nuclear and mitochondrial cfDNA studies was generally moderate for psychiatric disorders. In addition, we discuss future applications of CNAs and particularly cfDNA as non-invasive biomarkers for these diseases.
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Affiliation(s)
- Camille Verebi
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France; INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France
| | - Juliette Nectoux
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France
| | - Philip Gorwood
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France; Université Paris Cité, GHU Paris Psychiatrie et Neurosciences (CMME), Paris, France
| | - Yann Le Strat
- AP-HP, Department of Psychiatry, Louis Mourier Hospital, Université Paris Cité, Faculté de Médecine, Colombes, France
| | - Philibert Duriez
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France; Université Paris Cité, GHU Paris Psychiatrie et Neurosciences (CMME), Paris, France
| | - Nicolas Ramoz
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France; INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France.
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19
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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20
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Martínez de Toda I, González-Sánchez M, Díaz-Del Cerro E, Valera G, Carracedo J, Guerra-Pérez N. Sex differences in markers of oxidation and inflammation. Implications for ageing. Mech Ageing Dev 2023; 211:111797. [PMID: 36868323 DOI: 10.1016/j.mad.2023.111797] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
Sexual dimorphism is a key factor to consider in the ageing process given the impact that it has on life expectancy. The oxidative-inflammatory theory of ageing states that the ageing process is the result of the establishment of oxidative stress which, due to the interplay of the immune system, translates into inflammatory stress, and that both processes are responsible for the damage and loss of function of an organism. We show that there are relevant gender differences in a number of oxidative and inflammatory markers and propose that they may account for the differential lifespan between sexes, given that males display, in general, higher oxidation and basal inflammation. In addition, we explain the significant role of circulating cell-free DNA as a marker of oxidative damage and an inductor of inflammation, connecting both processes and having the potential to become a useful ageing marker. Finally, we discuss how oxidative and inflammatory changes take place differentially with ageing in each sex, which could also have an impact on the sex-differential lifespan. Further research including sex as an essential variable is needed to understand the grounds of sex differences in ageing and to better comprehend ageing itself.
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Affiliation(s)
- Irene Martínez de Toda
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Mónica González-Sánchez
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Estefanía Díaz-Del Cerro
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Gemma Valera
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Julia Carracedo
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Natalia Guerra-Pérez
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
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21
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Nguyen THH, Lu YT, Le VH, Bui VQ, Nguyen LH, Pham NH, Phan TH, Nguyen HT, Tran VS, Bui CV, Vo VK, Nguyen PTN, Dang HHP, Pham VD, Cao VT, Nguyen TD, Nguyen LHD, Phan NM, Nguyen TH, Nguyen VTC, Pham TMQ, Tran VU, Le MP, Vo DH, Tran TMT, Nguyen MN, Nguyen TT, Tieu BL, Nguyen HTP, Truong DYA, Cao CTT, Nguyen VT, Le TLQ, Luong TLA, Doan TKP, Dao TT, Phan CD, Nguyen TX, Pham NT, Nguyen BT, Pham TTT, Le HL, Truong CT, Jasmine TX, Le MC, Phan VB, Truong QB, Tran THL, Huynh MT, Tran TQ, Nguyen ST, Tran V, Tran VK, Nguyen HN, Nguyen DS, Nguyen TQT, Phan TV, Do TTT, Truong DK, Tang HS, Phan MD, Giang H, Nguyen HN, Tran LS. Clinical validation of a ctDNA-Based Assay for Multi-Cancer Detection: An Interim Report from a Vietnamese Longitudinal Prospective Cohort Study of 2795 Participants. Cancer Invest 2023; 41:1-17. [PMID: 36719061 DOI: 10.1080/07357907.2023.2173773] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023]
Abstract
The SPOT-MAS assay "Screening for the Presence Of Tumor by Methylation And Size" detects the five most common cancers in Vietnam by evaluating circulating tumor DNA in the blood. Here, we validated its performance in a prospective multi-center clinical trial, K-DETEK. Our analysis of 2795 participants from 14 sites across Vietnam demonstrates its ability to detect cancers in asymptomatic individuals with a positive predictive value of 60%, with 83.3% accuracy in detecting tumor location. We present a case report to support further using SPOT-MAS as a complementary method to achieve early cancer detection and provide the opportunity for early treatment.
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Affiliation(s)
- Thi Hue Hanh Nguyen
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Y-Thanh Lu
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Medical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Van Hoi Le
- Department of General Planning and General Affaire, National Cancer Hospital, Hanoi, Vietnam
| | - Vinh Quang Bui
- Department of Radiation Therapy, Hanoi Oncology Hospital, Hanoi, Vietnam
| | - Lan Hieu Nguyen
- Department of Cardiology, Hanoi Medical University, Hanoi, Vietnam
| | - Nhu Hiep Pham
- Gastroenterology Department, Hue Central Hospital, Hue, Vietnam
| | - Thanh Hai Phan
- Director Board, Medic Medical Center, Ho Chi Minh, Vietnam
| | - Huu Thinh Nguyen
- Out-patient health care services department, University Medical Center HCM, Ho Chi Minh, Vietnam
| | - Van Song Tran
- Director Board, People's Hospital 115, Ho Chi Minh, Vietnam
| | - Chi Viet Bui
- Board of Management, Xuyen A General Hospital, Ho Chi Minh, Vietnam
| | - Van Kha Vo
- Director of Cantho Oncology Hospital, Vietnam, Cantho Oncology Hospital, Can Tho, Vietnam
| | | | - Ha Huu Phuoc Dang
- Interventional Cardiology Department, Dongnai General Hospital, Dong Nai, Vietnam
| | - Van Dung Pham
- Director Board, Thong Nhat Dongnai General Hospital, Dong Nai, Vietnam
| | - Van Thinh Cao
- Department of Cardiology, Le Van Thinh Hospital, Ho Chi Minh, Vietnam
| | - Thanh Dat Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Data Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Luu Hong Dang Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Medical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Ngoc Minh Phan
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Medical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Trong Hieu Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Data Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Van Thien Chi Nguyen
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Mong Quynh Pham
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Vu Uyen Tran
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Minh Phong Le
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Dac Ho Vo
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Minh Thu Tran
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Minh Nguyen Nguyen
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Thanh Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Medical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Ba Linh Tieu
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Medical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Huu Tam Phuc Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Clinical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Dinh Yen An Truong
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Clinical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Chi Thuy Tien Cao
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Clinical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Van Tung Nguyen
- Breast Cancer Department, National Cancer Hospital, Hanoi, Vietnam
| | - Thi Le Quyen Le
- Lung Cancer Department, Hanoi Oncology Hospital, Hanoi, Vietnam
| | - Thi Lan Anh Luong
- Center of clinical genetics and genomics Vietnam, Hanoi Medical University, Hanoi, Vietnam
| | - Thi Kim Phuong Doan
- Center of clinical genetics and genomics Vietnam, Hanoi Medical University, Hanoi, Vietnam
| | - Thi Trang Dao
- Center of clinical genetics and genomics Vietnam, Hanoi Medical University, Hanoi, Vietnam
| | - Canh Duy Phan
- Oncology Department, Hue Central hospital, Hue, Vietnam
| | | | | | - Bao Toan Nguyen
- Laboratory Department, Medic Medical Center, Ho Chi Minh, Vietnam
| | | | - Huu Linh Le
- Respiratory Clinic, Medic Medical Center, Ho Chi Minh, Vietnam
| | | | | | - Minh Chi Le
- Health care services Department, University Medical Center HCM, Ho Chi Minh, Vietnam
| | - Van Bau Phan
- Board of Management, People's Hospital 115, Ho Chi Minh, Vietnam
| | - Quang Binh Truong
- Cardiology Center, University Medical Center HCM, Ho Chi Minh, Vietnam
| | - Thi Huong Ly Tran
- General Planning Department, Cantho Oncology Hospital, Can Tho, Vietnam
| | - Minh Thien Huynh
- General Planning Department, Cantho Oncology Hospital, Can Tho, Vietnam
| | - Tu Quy Tran
- General Surgery Department, Danang Oncology Hospital, Da Nang, Vietnam
| | - Si Tuan Nguyen
- Microbiology Department, Thong Nhat Dongnai General Hospital, Dong Nai, Vietnam
| | - Vu Tran
- Oncology Department, Thong Nhat Dongnai General Hospital, Dong Nai, Vietnam
| | - Van Khanh Tran
- Director Board, Le Van Thinh Hospital, Ho Chi Minh, Vietnam
| | - Huu Nguyen Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Director Board, Gene Solutions, Ho Chi Minh, Vietnam
| | - Duy Sinh Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Medical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | | | - Thi Van Phan
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Clinical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | | | - Dinh-Kiet Truong
- Director Board, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Hung Sang Tang
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Medical Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Minh Duy Phan
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Data Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Data Department, Gene Solutions, Ho Chi Minh, Vietnam
| | - Hoai Nghia Nguyen
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Le Son Tran
- Research and Development Department, Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh, Vietnam
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22
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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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction Natural antibody (NAb) derived from CD5+ B-1 cells maintains tissue homeostasis, controls inflammation, aids in establishing long-term protective responses against pathogens, and provides immediate protection from infection. CD5+ B-1 cell NAbs recognize evolutionarily fixed epitopes, such as phosphatidylcholine (PtC), found on bacteria and senescent red blood cells. Anti-PtC antibodies are essential in protection against bacterial sepsis. CD5+ B-1 cell-derived NAbs have a unique germline-like structure that lacks N-additions, a feature critical for providing protection against infection. Previously, we demonstrated the repertoire and germline status of PtC+CD5+ B-1 cell IgM obtained from male mice changes with age depending on the anatomical location of the B-1 cells. More recently, we demonstrated serum antibody from aged female mice maintains protection against pneumococcal infection, whereas serum antibody from male mice does not provide protection. Results Here, we show that aged female mice have significantly more splenic PtC+CD5+ B-1 cells and more PtC specific serum IgM than aged male mice. Furthermore, we find both age and biological sex related repertoire differences when comparing B cell receptor (BCR) sequencing results of PtC+CD5+ B-1 cells. While BCR germline status of PtC+CD5+ B-1 cells from aged male and female mice is similar in the peritoneal cavity, it differs significantly in the spleen, where aged females retain germline configuration and aged males do not. Nucleic acid sensing toll-like receptors are critical in the maintenance of PtC+ B-1 cells; therefore, to begin to understand the mechanism of differences observed between the male and female PtC+CD5+ B-1 cell repertoire, we analyzed levels of cell-free nucleic acids and found increases in aged females. Conclusion Our results suggest the antigenic milieu differs between aged males and females, leading to differential selection of antigen-specific B-1 cells over time. Further elucidation of how biological sex differences influence the maintenance of B-1 cells within the aging environment will be essential to understand sex and age-related disparities in the susceptibility to bacterial infection and will aid in the development of more effective vaccination and/or therapeutic strategies specific for males and females.
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Affiliation(s)
- Sarah E. Webster
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Naomi L. Tsuji
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Michael J. Clemente
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States,Flow Cytometry and Imaging Core, Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Nichol E. Holodick
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States,Flow Cytometry and Imaging Core, Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States,*Correspondence: Nichol E. Holodick,
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23
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Michelson J, Rausser S, Peng A, Yu T, Sturm G, Trumpff C, Kaufman BA, Rai AJ, Picard M. MitoQuicLy: a high-throughput method for quantifying cell-free DNA from human plasma, serum, and saliva. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522744. [PMID: 36711938 PMCID: PMC9882007 DOI: 10.1101/2023.01.04.522744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Circulating cell-free mitochondrial DNA (cf-mtDNA) is an emerging biomarker of psychobiological stress and disease which predicts mortality and is associated with various disease states. To evaluate the contribution of cf-mtDNA to health and disease states, standardized high-throughput procedures are needed to quantify cf-mtDNA in relevant biofluids. Here, we describe MitoQuicLy: Mito chondrial DNA Qu antification in c ell-free samples by Ly sis. We demonstrate high agreement between MitoQuicLy and the commonly used column-based method, although MitoQuicLy is faster, cheaper, and requires a smaller input sample volume. Using 10 µL of input volume with MitoQuicLy, we quantify cf-mtDNA levels from three commonly used plasma tube types, two serum tube types, and saliva. We detect, as expected, significant inter-individual differences in cf-mtDNA across different biofluids. However, cf-mtDNA levels between concurrently collected plasma, serum, and saliva from the same individual differ on average by up to two orders of magnitude and are poorly correlated with one another, pointing to different cf-mtDNA biology or regulation between commonly used biofluids in clinical and research settings. Moreover, in a small sample of healthy women and men (n=34), we show that blood and saliva cf-mtDNAs correlate with clinical biomarkers differently depending on the sample used. The biological divergences revealed between biofluids, together with the lysis-based, cost-effective, and scalable MitoQuicLy protocol for biofluid cf-mtDNA quantification, provide a foundation to examine the biological origin and significance of cf-mtDNA to human health.
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Affiliation(s)
- Jeremy Michelson
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Shannon Rausser
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Amanda Peng
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Temmie Yu
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Gabriel Sturm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Brett A. Kaufman
- Center for Metabolism and Mitochondrial Medicine and the Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine
| | - Alex J. Rai
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA,Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA,New York State Psychiatric Institute, New York, NY, USA,Corresponding author: 1051 Riverside Drive, Kolb 4, New York, NY 10032, United States; (646) 774-5026;
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24
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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
Abstract
Cell-free DNA (cfDNA) is of growing clinical and research significance. In vitro cfDNA models are a useful tool in cfDNA research; however, artifacts in these models may have implications for the interpretation of new and published data. This report aimed to establish how endogenous cfDNA in fetal bovine serum (FBS) may influence in vitro cfDNA measurements. Three commercial cell culture media, supplemented with 10% FBS, were analyzed for the presence of cfDNA, with and without culture with ovarian cancer cell lines. cfDNA from FBS was identified with all three commercial media and contributed a major portion of 167-bp cfDNA. Future studies should account for bovine cfDNA in FBS-supplemented media when conducting in vitro cfDNA research.
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25
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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
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease in children and adolescents, increasing the risk of its progression toward nonalcoholic steatohepatitis (NASH), cirrhosis, and cancer. There is an urgent need for noninvasive early diagnostic and prognostic tools such as epigenetic marks (epimarks), which would replace liver biopsy in the future. We used plasma samples from 67 children with biopsy-proven NAFLD, and as controls we used samples from 20 children negative for steatosis by ultrasound. All patients were genotyped for patatin-like phospholipase domain containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), membrane bound O-acyltransferase domain containing 7 (MBOAT7), and klotho-β (KLB) gene variants, and data on anthropometric and biochemical parameters were collected. Furthermore, plasma cell-free DNA (cfDNA) methylation was quantified using a commercially available kit, and ImageStream(X) was used for the detection of free circulating histone complexes and variants. We found a significant enrichment of the levels of histone macroH2A1.2 in the plasma of children with NAFLD compared to controls, and a strong correlation between cfDNA methylation levels and NASH. Receiver operating characteristic curve analysis demonstrated that combination of cfDNA methylation, PNPLA3 rs738409 variant, coupled with either high-density lipoprotein cholesterol or alanine aminotransferase levels can strongly predict the progression of pediatric NAFLD to NASH with area under the curve >0.87. Conclusion: Our pilot study combined epimarks and genetic and metabolic markers for a robust risk assessment of NAFLD development and progression in children, offering a promising noninvasive tool for the consistent diagnosis and prognosis of pediatric NAFLD. Further studies are necessary to identify their pathogenic origin and function.
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Affiliation(s)
- Diana Buzova
- Department of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
| | - Maria Rita Braghini
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Salvatore Daniele Bianco
- Laboratory of BioinformaticsFondazione IRCCS Casa Sollievo della SofferenzaSan Giovanni Rotondo (FG)Italy
| | - Oriana Lo Re
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic,Department of Translational Stem Cell BiologyResearch Institute of the Medical University of VarnaVarnaBulgaria
| | - Marco Raffaele
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Jan Frohlich
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Antoniya Kisheva
- Department of Internal Diseases IMedical University of VarnaVarnaBulgaria
| | - Annalisa Crudele
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Antonella Mosca
- Hepatology, Gastroenterology and Nutrition UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Maria Rita Sartorelli
- Hepatology, Gastroenterology and Nutrition UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Clara Balsano
- Department of LifeHealth & Environmental Sciences‐ MESVA‐School of Emergency and Urgency Medicine, University of L'AquilaL'AquilaItaly
| | - Jan Cerveny
- Department of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
| | - Tommaso Mazza
- Laboratory of BioinformaticsFondazione IRCCS Casa Sollievo della SofferenzaSan Giovanni Rotondo (FG)Italy
| | - Anna Alisi
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Manlio Vinciguerra
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic,Department of Translational Stem Cell BiologyResearch Institute of the Medical University of VarnaVarnaBulgaria,Liverpool Center for Cardiovascular ScienceLiverpool Johns Moore UniversityLiverpoolUK
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26
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Yuwono NL, Alonso A, Abbott J, Houshdaran S, Henry CE, Rodgers R, Ford CE, Warton K. Circulating cell-free endometrial DNA level is unaltered during menstruation and in endometriosis. Hum Reprod 2022; 37:2560-2569. [PMID: 36166696 DOI: 10.1093/humrep/deac198] [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: 01/13/2022] [Revised: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
STUDY QUESTION Is circulating cell-free DNA (cirDNA) from the endometrium elevated during menstruation and in endometriosis? SUMMARY ANSWER Endometrial cirDNA does not increase during menstruation and is not elevated in endometriosis. WHAT IS KNOWN ALREADY Changes in cirDNA associated with common benign conditions are a potential source of false positives in cancer diagnostic applications, but also present an opportunity for biomarker development for diseases such as endometriosis. Elevated cirDNA has been reported in endometriosis patients compared to healthy community controls, but no difference in total or endometrial cirDNA has been found between patients with endometriosis and patients with other gynaecological conditions. Likewise, menstruation is a potential driver of changes in cirDNA levels and tissue profile, but total and endothelial cirDNA do not increase during menstruation. STUDY DESIGN, SIZE, DURATION For endometriosis comparisons, 59 participants with surgically confirmed endometriosis and 27 laparoscopic patients without endometriosis (hospital controls) were prospectively recruited, while 25 healthy community participants (healthy controls) were recruited in a university setting. Total and endometrial cirDNA and cirDNA fragmentation were measured across the three groups. For menstrual comparisons, 36 matched non-menstruating and menstruating samples were collected from healthy women recruited within a university setting, and the endometrial cirDNA was compared between the two groups. PARTICIPANTS/MATERIALS, SETTING, METHODS cirDNA was extracted from venous blood plasma then quantitated by quantitative PCR of ALU repetitive element (115 bp) and TP53 gene sequence (105 bp) for total concentration. cirDNA derived from the endometrium was quantitated by methylation-specific droplet digital PCR of a FAM101A region (69 bp) after bisulfite conversion of the DNA. A cirDNA size fragmentation ratio was obtained by quantifying a long segment of ALU repetitive element (247 bp) and expressing the amount relative to the 115 bp ALU target. MAIN RESULTS AND THE ROLE OF CHANCE No differences in cirDNA level were found in any comparison populations in this study. Mean total cirDNA was unchanged between healthy controls (ALU-115-3.31 ng/ml; TP53-2.73 ng/ml), hospital controls (ALU-115-3.47 ng/ml; TP53-2.83 ng/ml) and endometriosis patients (ALU-115-3.35 ng/ml; TP53-2.66 ng/ml). Likewise, endometrial cirDNA was unchanged between healthy controls (18.3 copies/ml), hospital controls (20.6 copies/ml) and endometriosis patients (22 copies/ml). Endometrial cirDNA did not change during menstruation (non-menstruating: 38 copies/ml; menstruating: 33 copies/ml). Irrespective of endometriosis diagnosis, blood from patients undergoing laparoscopy (hospital controls: 0.77; endometriosis patients: 0.79), had a significantly higher cirDNA size ratio than community-recruited healthy controls (0.64), indicating increased abundance of long cirDNA fragments. LIMITATIONS, REASONS FOR CAUTION It was not possible to completely match the age, BMI and parity between the three cohorts investigated, however of these, only age has been shown to influence circulating DNA levels and not within the age range of our cohort. Blood from community-recruited healthy women and women undergoing laparoscopy was collected via antecubital vein venepuncture (processed within 3 h) and with either peripheral cannula or venepuncture (processed within 6 h), respectively, which could potentially impact the size distribution of circulating DNA fragments. For the collection of non-menstruating phase blood samples, we did not differentiate between follicular phase, ovulation and luteal phase. Thus, only the mensturating samples were collected at a consistent phase, and any fluctuations in cirDNA that occur at the other phases may have obscured small changes during menstruation. WIDER IMPLICATIONS OF THE FINDINGS There is no evidence that cirDNA has potential as a diagnostic biomarker for endometriosis. Endometriosis, representing a common benign gynaecological condition, and menstruation, representing a normal physiological occurrence in women, should not affect methylation-based diagnostics in other disease areas, including oncology. STUDY FUNDING/COMPETING INTEREST(S) N.L.Y.: Australian Government Research Training Program (RTP) Stipend through The University of New South Wales, Translational Cancer Research Network PhD Scholarship Top-Up Award via the Cancer Institute NSW, Beth Yarrow Memorial Award in Medical Science, UNSW Completion Scholarship; C.E.H.: Gynaecological Oncology Fund of the Royal Hospital for Women; K.W.: Ovarian Cancer Research Foundation and CAMILLA AND MARC. C.E.F.: UNSW Women's Wellbeing Academy and the Australian Human Rights Institute. We declare the following competing interest: K.W. holds stock in Guardant Health, Exact Sciences and Epigenomics AG. No other authors have competing interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- N L Yuwono
- Department of Obstetrics and Gynaecology, Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - A Alonso
- Department of Obstetrics and Gynaecology, Gynaecological Research and Clinical Evaluation (GRACE) Unit, Royal Hospital for Women, Sydney, NSW, Australia.,Department of Obstetrics and Gynaecology, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - J Abbott
- Department of Obstetrics and Gynaecology, Gynaecological Research and Clinical Evaluation (GRACE) Unit, Royal Hospital for Women, Sydney, NSW, Australia.,Department of Obstetrics and Gynaecology, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - S Houshdaran
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - C E Henry
- Department of Obstetrics and Gynaecology, Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - R Rodgers
- Department of Obstetrics and Gynaecology, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.,Department of Gynaecology and Reproductive Medicine, Royal Hospital for Women, Sydney, NSW, Australia
| | - C E Ford
- Department of Obstetrics and Gynaecology, Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - K Warton
- Department of Obstetrics and Gynaecology, Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
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27
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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: 15] [Impact Index Per Article: 7.5] [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
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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28
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Kananen L, Hurme M, Bürkle A, Moreno-Villanueva M, Bernhardt J, Debacq-Chainiaux F, Grubeck-Loebenstein B, Malavolta M, Basso A, Piacenza F, Collino S, Gonos ES, Sikora E, Gradinaru D, Jansen EHJM, Dollé MET, Salmon M, Stuetz W, Weber D, Grune T, Breusing N, Simm A, Capri M, Franceschi C, Slagboom E, Talbot D, Libert C, Raitanen J, Koskinen S, Härkänen T, Stenholm S, Ala-Korpela M, Lehtimäki T, Raitakari OT, Ukkola O, Kähönen M, Jylhä M, Jylhävä J. Circulating cell-free DNA in health and disease - the relationship to health behaviours, ageing phenotypes and metabolomics. GeroScience 2022; 45:85-103. [PMID: 35864375 PMCID: PMC9886738 DOI: 10.1007/s11357-022-00590-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/06/2022] [Indexed: 02/03/2023] Open
Abstract
Circulating cell-free DNA (cf-DNA) has emerged as a promising biomarker of ageing, tissue damage and cellular stress. However, less is known about health behaviours, ageing phenotypes and metabolic processes that lead to elevated cf-DNA levels. We sought to analyse the relationship of circulating cf-DNA level to age, sex, smoking, physical activity, vegetable consumption, ageing phenotypes (physical functioning, the number of diseases, frailty) and an extensive panel of biomarkers including blood and urine metabolites and inflammatory markers in three human cohorts (N = 5385; 17-82 years). The relationships were assessed using correlation statistics, and linear and penalised regressions (the Lasso), also stratified by sex.cf-DNA levels were significantly higher in men than in women, and especially in middle-aged men and women who smoke, and in older more frail individuals. Correlation statistics of biomarker data showed that cf-DNA level was higher with elevated inflammation (C-reactive protein, interleukin-6), and higher levels of homocysteine, and proportion of red blood cells and lower levels of ascorbic acid. Inflammation (C-reactive protein, glycoprotein acetylation), amino acids (isoleucine, leucine, tyrosine), and ketogenesis (3-hydroxybutyrate) were included in the cf-DNA level-related biomarker profiles in at least two of the cohorts.In conclusion, circulating cf-DNA level is different by sex, and related to health behaviour, health decline and metabolic processes common in health and disease. These results can inform future studies where epidemiological and biological pathways of cf-DNA are to be analysed in details, and for studies evaluating cf-DNA as a potential clinical marker.
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Affiliation(s)
- Laura Kananen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. .,Faculty of Social Sciences (Health Sciences), and Gerontology Research Center, Tampere University, Tampere, Finland. .,Faculty of Medicine and Health Technology, and Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Mikko Hurme
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, and Gerontology Research Center, Tampere University, Tampere, Finland
| | - Alexander Bürkle
- grid.9811.10000 0001 0658 7699Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Maria Moreno-Villanueva
- grid.9811.10000 0001 0658 7699Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | | | - Florence Debacq-Chainiaux
- grid.6520.10000 0001 2242 8479URBC-Narilis, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Beatrix Grubeck-Loebenstein
- grid.5771.40000 0001 2151 8122Research Institute for Biomedical Aging Research, University of Innsbruck, Rennweg, 10, 6020 Innsbruck, Austria
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Andrea Basso
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Sebastiano Collino
- grid.5333.60000000121839049Nestlé Research, Nestlé Institute of Health Sciences, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | - Efstathios S. Gonos
- grid.22459.380000 0001 2232 6894Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ewa Sikora
- grid.419305.a0000 0001 1943 2944Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur street, 02-093 Warsaw, Poland
| | - Daniela Gradinaru
- grid.8194.40000 0000 9828 7548Department of Biochemistry, Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Eugene H. J. M. Jansen
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Centre for Health Protection, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Martijn E. T. Dollé
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Centre for Health Protection, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Michel Salmon
- grid.425994.7Straticell, Science Park Crealys, Rue Jean Sonet 10, 5032 Les Isnes, Belgium
| | - Wolfgang Stuetz
- grid.9464.f0000 0001 2290 1502Institute of Nutritional Sciences (140), University of Hohenheim, 70593 Stuttgart, Germany
| | - Daniela Weber
- grid.418213.d0000 0004 0390 0098Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - Tilman Grune
- grid.418213.d0000 0004 0390 0098Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany ,grid.10420.370000 0001 2286 1424Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria ,grid.9464.f0000 0001 2290 1502Institute of Nutritional Medicine (180), University of Hohenheim, 70593 Stuttgart, Germany
| | - Nicolle Breusing
- grid.9464.f0000 0001 2290 1502Institute of Nutritional Medicine (180), University of Hohenheim, 70593 Stuttgart, Germany
| | - Andreas Simm
- grid.461820.90000 0004 0390 1701Department of Cardiothoracic Surgery, University Hospital Halle, Ernst-Grube Str. 40, 06120 Halle (Saale), Germany
| | - Miriam Capri
- grid.6292.f0000 0004 1757 1758DIMES- Department of Experimental, Diagnostic and Specialty Medicine,
Interdepartmental Center “Alma Mater Research Institute On Global Challenges and Climate Change (Alma Climate)”,
Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Claudio Franceschi
- grid.6292.f0000 0004 1757 1758DIMES- Department of Experimental, Diagnostic and Specialty Medicine,
Interdepartmental Center “Alma Mater Research Institute On Global Challenges and Climate Change (Alma Climate)”,
Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Eline Slagboom
- grid.10419.3d0000000089452978Section of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Duncan Talbot
- Unilever Science and Technology, Beauty and Personal Care, Sharnbrook, UK
| | - Claude Libert
- grid.11486.3a0000000104788040Center for Inflammation Research, VIB, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jani Raitanen
- grid.502801.e0000 0001 2314 6254Faculty of Social Sciences (Health Sciences), and Gerontology Research Center, Tampere University, Tampere, Finland
| | - Seppo Koskinen
- grid.14758.3f0000 0001 1013 0499National Institute for Health and Welfare, Helsinki, Finland
| | - Tommi Härkänen
- grid.14758.3f0000 0001 1013 0499National Institute for Health and Welfare, Helsinki, Finland
| | - Sari Stenholm
- grid.1374.10000 0001 2097 1371Department of Public Health, University of Turku and Turku University Hospital, Turku, Finland ,grid.1374.10000 0001 2097 1371Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Mika Ala-Korpela
- grid.10858.340000 0001 0941 4873Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland ,grid.10858.340000 0001 0941 4873Center for Life Course Health Research, University of Oulu, Oulu, Finland ,grid.9668.10000 0001 0726 2490NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Terho Lehtimäki
- grid.502801.e0000 0001 2314 6254Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Cardiovascular Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland ,grid.511163.10000 0004 0518 4910Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Olli T. Raitakari
- grid.1374.10000 0001 2097 1371Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland ,grid.1374.10000 0001 2097 1371Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XDepartment of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Olavi Ukkola
- grid.10858.340000 0001 0941 4873Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Mika Kähönen
- grid.502801.e0000 0001 2314 6254Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Cardiovascular Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland ,grid.412330.70000 0004 0628 2985Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Marja Jylhä
- grid.502801.e0000 0001 2314 6254Faculty of Social Sciences (Health Sciences), and Gerontology Research Center, Tampere University, Tampere, Finland
| | - Juulia Jylhävä
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden ,grid.502801.e0000 0001 2314 6254Faculty of Social Sciences (Health Sciences), and Gerontology Research Center, Tampere University, Tampere, Finland
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29
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Temraz S, Nasr R, Mukherji D, Kreidieh F, Shamseddine A. Liquid Biopsy Derived Circulating Tumor Cells and Circulating Tumor DNA as Novel Biomarkers in Hepatocellular Carcinoma. Expert Rev Mol Diagn 2022; 22:507-518. [PMID: 35758097 DOI: 10.1080/14737159.2022.2094706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The diagnosis of hepatocellular carcinoma (HCC) is made at a relatively advanced stage resulting in poor prognosis. Alpha-fetoprotein and liver ultrasound have limited accuracy as biomarkers in HCC. Liver biopsy provides information on tumor biology; however, it is invasive and holds high threat of tumor seeding. Thus, more accurate and less invasive approaches are needed. AREAS COVERED Highly sensitive liquid biopsy assays have made possible the detection and analysis of cells or organelles such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and tumor-derived exosomes. Here, we focus on CTCs and ctDNA components of liquid biopsy and their clinical application as diagnostic, prognostic and predictive biomarkers in HCC. Unlike tissue biopsy, liquid biopsy involves attaining a sample at several time frames in an easy and a non-invasive manner. They have been efficacious in detecting and classifying cancer, in predicting treatment response, in monitoring disease relapse and in identifying mechanisms of resistance to targeted therapies. EXPERT OPINION Although interesting and highly promising, liquid biopsy techniques still have many obstacles to overcome before their wide spread clinical application sees the light. It is expected that these techniques will be incorporated into traditional methodologies for better diagnostic, predictive and prognostic results.
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Affiliation(s)
- Sally Temraz
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiology, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Deborah Mukherji
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Firas Kreidieh
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Ali Shamseddine
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
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Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12040870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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Transcending Blood—Opportunities for Alternate Liquid Biopsies in Oncology. Cancers (Basel) 2022; 14:cancers14051309. [PMID: 35267615 PMCID: PMC8909855 DOI: 10.3390/cancers14051309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Cell-free DNA—DNA that has been expelled from cells and can be isolated from blood plasma and other body fluids—is a useful tool in medicine, with applications as a biomarker in diagnosis, prognosis, disease profiling, and treatment selection. In oncology, the ease of access to the tumour genome is a major advantage of cell-free DNA, but while this has led to significant research in blood, other body fluids have not received equal attention. This review article summarises the current research into cell-free DNA in non-blood body fluids, highlighting its values and limitations, and suggesting the direction of future studies. We conclude that cell-free DNA from non-blood body fluids may provide additional information to supplement traditional biopsies, allowing informative and improved patient care across many cancer types. Abstract Cell-free DNA (cfDNA) is a useful molecular biomarker in oncology research and treatment, but while research into its properties in blood has flourished, there remains much to be discovered about cfDNA in other body fluids. The cfDNA from saliva, sputum, cerebrospinal fluid, urine, faeces, pleural effusions, and ascites has unique advantages over blood, and has potential as an alternative ‘liquid biopsy’ template. This review summarises the state of current knowledge and identifies the gaps in our understanding of non-blood liquid biopsies; where their advantages lie, where caution is needed, where they might fit clinically, and where research should focus in order to accelerate clinical implementation. An emphasis is placed on ascites and pleural effusions, being pathological fluids directly associated with cancer. We conclude that non-blood fluids are viable sources of cfDNA in situations where solid tissue biopsies are inaccessible, or only accessible from dated archived specimens. In addition, we show that due to the abundance of cfDNA in non-blood fluids, they can outperform blood in many circumstances. We demonstrate multiple instances in which DNA from various sources can provide additional information, and thus we advocate for analysing non-blood sources as a complement to blood and/or tissue. Further research into these fluids will highlight opportunities to improve patient outcomes across cancer types.
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Zhao G, Dai P, Wang C, Liu L, Zhao X, Kong X. Clinical Application of Noninvasive Prenatal Testing for Sex Chromosome Aneuploidies in Central China. Front Med (Lausanne) 2022; 8:672211. [PMID: 35155454 PMCID: PMC8825788 DOI: 10.3389/fmed.2021.672211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 12/07/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The relatively high incidence and the clinical symptoms of sex chromosome aneuploidies (SCAs) make prenatal screening of SCAs an attractive option for pregnant women. However, limited studies have assessed the clinical performance of noninvasive prenatal testing (NIPT) for screening SCAs. This study was performed to evaluate the clinical performance of NIPT for SCAs in singleton pregnancies in central China. METHODS Noninvasive prenatal testing was performed using next-generation sequencing. Standard Z-score analysis was used to identify fetal SCAs. NIPT-positive results were confirmed by invasive prenatal diagnosis (IPD). RESULTS A total of 42,164 pregnant women with singleton pregnancies were recruited in this study. They were divided into the following five groups with different clinical indications: with ultrasound soft index abnormalities (9.23%, 3,892/42,164); with advanced maternal age (22.14%, 9,336/42,164); with high risk for maternal serum screening (MSS) (18.35%, 7,738/42,164); with an intermediate risk for MSS (26.6%, 11,215/42,164); and with low risk (23.68%, 9,983/42,164). In all, 223 women had a high risk for SCAs by NIPT with a positive rate of 0.53%. There was no significant difference associated with the five groups in the positive rate. Of all of the positive results, 89 were 45,X (39.91%), 38 were 47,XXX (17.04%), 31 were 46,XY,del(X) (13.90%), 50 were 47,XXY (22.42%,), and 15 were 47,XYY (6.73%). Finally, 147 participants (65.92%) chose to undergo IPD, and 47 cases were confirmed. The combined positive predictive value (PPV) of NIPT for SCA was 31.97% (47/147). PPV was high for 47,XYY (100%, 11/11), moderate for 47,XXX (42.86%, 9/21) and 47,XXY (45.45%, 15/33), but low for 45,X (16.13%, 10/62) and 46,XY,del(X) (10%, 2/20). The termination rates of Turner syndrome and 47,XXY syndrome were higher than 47,XXX and 47,XYY syndromes. CONCLUSION In this relatively large cohort, we evaluated the value of NIPT for SCAs. Our data showed that with informed consent and subsequent professional genetical consulting, NIPT can be a useful method to screen SCAs.
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Affiliation(s)
- Ganye Zhao
- Department of Obstetrics and Gynecology, The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peng Dai
- Department of Obstetrics and Gynecology, The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Conghui Wang
- Department of Obstetrics and Gynecology, The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lina Liu
- Department of Obstetrics and Gynecology, The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuechao Zhao
- Department of Obstetrics and Gynecology, The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Department of Obstetrics and Gynecology, The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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