1
|
Gressel GM, Maggi EC, Harmon BE, Ye KQ, Kuo DYS, Dolan SM, Montagna C. Low molecular weight serum cell-free DNA concentration is associated with clinicopathologic indices of poor prognosis in women with uterine cancer. J Transl Med 2020; 18:323. [PMID: 32854748 PMCID: PMC7457235 DOI: 10.1186/s12967-020-02493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Serum cell-free DNA (cfDNA) holds promise as a non-invasive cancer biomarker. The objective of this study was to evaluate the association of cfDNA concentration with clinicopathologic variables of poor prognosis and overall survival among women with uterine cancer compared to benign cancer-free controls. Methods cfDNA was extracted from the serum of 91 women with multiple uterine cancer histologies and 22 post-menopausal controls without cancer. Low molecular weight (LMW) cfDNA was separated from contaminating genomic high molecular weight cfDNA using paramagnetic bead purification and its concentration was measured using fluorometric quantification. Clinicopathologic data was abstracted from the electronic medical record. The association between serum cfDNA concentration, clinicopathologic variables, and overall survival was assessed using linear regression modelling, Cox proportional hazards modelling, and the Kaplan–Meier method. Results Median total serum cfDNA concentration for the cohort was 69.2 ng/mL (IQR 37.4, 132.3) and median LMW cfDNA concentration was 23.8 ng/mL (IQR 14.9, 44.4). There were no significant differences in total serum cfDNA concentration with any clinicopathologic variables. However, LMW cfDNA concentration was significantly higher in serum of women with cancer (25.8 ng/mL IQR 16.0, 49.6) compared to benign controls (15.5 ng/mL IQR 9.3, 25.8 ng/mL) (p < 0.01). It is also significantly higher among women with early stage cancer than benign controls (p < 0.01). There were also significant associations between LMW cfDNA concentration and stage of cancer (p = 0.01) and histology (p = 0.02). Patients with leiomyosarcoma and carcinosarcoma had higher cfDNA concentrations than those with endometrioid cancer. Over a median follow-up of 51.9 months, 75th percentile for overall survival for women with cancer was 24.0 months. Higher LMW cfDNA concentrations is associated with lower survival among women with cancer (p < 0.01). Conclusions Serum LMW cfDNA concentration is associated with overall survival in women with uterine cancer, and it is higher among women with uterine cancer compared to those of controls.
Collapse
Affiliation(s)
- Gregory M Gressel
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Elaine C Maggi
- Department of Genetics, Albert Einstein College of Medicine Price Center/Block Research Pavilion, Room 401, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Bryan E Harmon
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kenny Q Ye
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - D Y S Kuo
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Siobhan M Dolan
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine Price Center/Block Research Pavilion, Room 401, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
| |
Collapse
|
2
|
Widschwendter M, Evans I, Jones A, Ghazali S, Reisel D, Ryan A, Gentry-Maharaj A, Zikan M, Cibula D, Eichner J, Alunni-Fabbroni M, Koch J, Janni WJ, Paprotka T, Wittenberger T, Menon U, Wahl B, Rack B, Lempiäinen H. Methylation patterns in serum DNA for early identification of disseminated breast cancer. Genome Med 2017; 9:115. [PMID: 29268762 PMCID: PMC5740791 DOI: 10.1186/s13073-017-0499-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/22/2017] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Monitoring treatment and early detection of fatal breast cancer (BC) remains a major unmet need. Aberrant circulating DNA methylation (DNAme) patterns are likely to provide a highly specific cancer signal. We hypothesized that cell-free DNAme markers could indicate disseminated breast cancer, even in the presence of substantial quantities of background DNA. METHODS We used reduced representation bisulfite sequencing (RRBS) of 31 tissues and established serum assays based on ultra-high coverage bisulfite sequencing in two independent prospective serum sets (n = 110). The clinical use of one specific region, EFC#93, was validated in 419 patients (in both pre- and post-adjuvant chemotherapy samples) from SUCCESS (Simultaneous Study of Gemcitabine-Docetaxel Combination adjuvant treatment, as well as Extended Bisphosphonate and Surveillance-Trial) and 925 women (pre-diagnosis) from the UKCTOCS (UK Collaborative Trial of Ovarian Cancer Screening) population cohort, with overall survival and occurrence of incident breast cancer (which will or will not lead to death), respectively, as primary endpoints. RESULTS A total of 18 BC specific DNAme patterns were discovered in tissue, of which the top six were further tested in serum. The best candidate, EFC#93, was validated for clinical use. EFC#93 was an independent poor prognostic marker in pre-chemotherapy samples (hazard ratio [HR] for death = 7.689) and superior to circulating tumor cells (CTCs) (HR for death = 5.681). More than 70% of patients with both CTCs and EFC#93 serum DNAme positivity in their pre-chemotherapy samples relapsed within five years. EFC#93-positive disseminated disease in post-chemotherapy samples seems to respond to anti-hormonal treatment. The presence of EFC#93 serum DNAme identified 42.9% and 25% of women who were diagnosed with a fatal BC within 3-6 and 6-12 months of sample donation, respectively, with a specificity of 88%. The sensitivity with respect to detecting fatal BC was ~ 4-fold higher compared to non-fatal BC. CONCLUSIONS Detection of EFC#93 serum DNAme patterns offers a new tool for early diagnosis and management of disseminated breast cancers. Clinical trials are required to assess whether EFC#93-positive women in the absence of radiological detectable breast cancers will benefit from anti-hormonal treatment before the breast lesions become clinically apparent.
Collapse
Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK.
| | - Iona Evans
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Shohreh Ghazali
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Andy Ryan
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Michal Zikan
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University Prague, Prague, Czech Republic
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University Prague, Prague, Czech Republic
| | | | - Marianna Alunni-Fabbroni
- Department of Gynaecology and Obstetrics, Klinikum Innenstadt, Ludwig-Maximilians Universitaet Muenchen, Maistrasse 11, 80337, Munich, Germany
| | - Julian Koch
- Department of Gynaecology and Obstetrics, Klinikum Innenstadt, Ludwig-Maximilians Universitaet Muenchen, Maistrasse 11, 80337, Munich, Germany
| | - Wolfgang J Janni
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Prittwitzstrasse 43, 89075, Ulm, Germany
| | - Tobias Paprotka
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | | | - Usha Menon
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Benjamin Wahl
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
- Boehringer Ingelheim Pharma, GmbH & Co. KG, Target Discovery Research, Biberach, Germany
| | - Brigitte Rack
- Department of Gynaecology and Obstetrics, Klinikum Innenstadt, Ludwig-Maximilians Universitaet Muenchen, Maistrasse 11, 80337, Munich, Germany
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Prittwitzstrasse 43, 89075, Ulm, Germany
| | | |
Collapse
|
3
|
Widschwendter M, Zikan M, Wahl B, Lempiäinen H, Paprotka T, Evans I, Jones A, Ghazali S, Reisel D, Eichner J, Rujan T, Yang Z, Teschendorff AE, Ryan A, Cibula D, Menon U, Wittenberger T. The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer. Genome Med 2017; 9:116. [PMID: 29268796 PMCID: PMC5740748 DOI: 10.1186/s13073-017-0500-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023] Open
Abstract
Background Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in DNA fragments shed by cancers into the bloodstream (i.e. cell-free DNA) can provide highly specific signals indicating cancer presence. Methods We analyzed 699 cancerous and non-cancerous tissues using a methylation array or reduced representation bisulfite sequencing to discover the most specific OC methylation patterns. A three-DNA-methylation-serum-marker panel was developed using targeted ultra-high coverage bisulfite sequencing in 151 women and validated in 250 women with various conditions, particularly in those associated with high CA125 levels (endometriosis and other benign pelvic masses), serial samples from 25 patients undergoing neoadjuvant chemotherapy, and a nested case control study of 172 UKCTOCS control arm participants which included serum samples up to two years before OC diagnosis. Results The cell-free DNA amount and average fragment size in the serum samples was up to ten times higher than average published values (based on samples that were immediately processed) due to leakage of DNA from white blood cells owing to delayed time to serum separation. Despite this, the marker panel discriminated high grade serous OC patients from healthy women or patients with a benign pelvic mass with specificity/sensitivity of 90.7% (95% confidence interval [CI] = 84.3–94.8%) and 41.4% (95% CI = 24.1–60.9%), respectively. Levels of all three markers plummeted after exposure to chemotherapy and correctly identified 78% and 86% responders and non-responders (Fisher’s exact test, p = 0.04), respectively, which was superior to a CA125 cut-off of 35 IU/mL (20% and 75%). 57.9% (95% CI 34.0–78.9%) of women who developed OC within two years of sample collection were identified with a specificity of 88.1% (95% CI = 77.3–94.3%). Sensitivity and specificity improved further when specifically analyzing CA125 negative samples only (63.6% and 87.5%, respectively). Conclusions Our data suggest that DNA methylation patterns in cell-free DNA have the potential to detect a proportion of OCs up to two years in advance of diagnosis and may potentially guide personalized treatment. The prospective use of novel collection vials, which stabilize blood cells and reduce background DNA contamination in serum/plasma samples, will facilitate clinical implementation of liquid biopsy analyses. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0500-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.
| | - Michal Zikan
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Benjamin Wahl
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | | | - Tobias Paprotka
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | - Iona Evans
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Shohreh Ghazali
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | | | - Tamas Rujan
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - Zhen Yang
- CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrew E Teschendorff
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.,CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andy Ryan
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Usha Menon
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | | |
Collapse
|
4
|
Ma Y, Lee JW, Park SJ, Yi ES, Choi YB, Yoo KH, Sung KW, Koo HH. Detection of MYCN Amplification in Serum DNA Using Conventional Polymerase Chain Reaction. J Korean Med Sci 2016; 31:1392-6. [PMID: 27510381 PMCID: PMC4974179 DOI: 10.3346/jkms.2016.31.9.1392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/03/2016] [Indexed: 01/11/2023] Open
Abstract
Neuroblastoma (NB) is the most common extra-cranial solid tumor of childhood and is characterized by a wide range of clinical behaviors. Amplification of MYCN is a well-known poor prognostic factor in NB patients. As the MYCN amplification status is usually tested using tumor specimens, lengthy and invasive procedures are unavoidable. To evaluate the possibility of detecting MYCN amplification without invasive procedure, we performed conventional polymerase chain reaction (PCR) analysis to identify MYCN amplification using the preserved serum DNA. PCR of serum DNA was done in 105 NB patients whose MYCN status had been confirmed by fluorescence in situ hybridization. MYCN amplification was evaluated as the ratio of signal intensities between MYCN and NAGK (M/N ratio). When regarding the tissue FISH results as a reference, 10 patients had MYCN-amplified (MNA) NB, and 95 had non-MNA NB. The M/N ratio of the MNA group (median 2.56, range 1.01-3.58) was significantly higher than that of the non-MNA group (median 0.97, range 0.67-5.18) (P < 0.001). In the receiver operating characteristic curve analysis, the area under the curve was 0.957 (95% confidence interval 0.898-1.000; P < 0.001), and it showed 90.9% sensitivity and 97.9% specificity with the selected cut-off value set as 1.6. The detection of MYCN amplification using conventional PCR analysis of serum samples seems to be a simple and promising method to evaluate the MYCN status of NB patients. Further study with a larger set of patients is needed to confirm the accuracy of this result.
Collapse
Affiliation(s)
- Youngeun Ma
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo Jin Park
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Eun Sang Yi
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Bae Choi
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ki Woong Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Hong Hoe Koo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
5
|
Abstract
AIM: To rapidly quantify hepatitis B virus (HBV) DNA by real-time PCR using efficient TaqMan probe and extraction methods of virus DNA.
METHODS: Three standards were prepared by cloning PCR products which targeted S, C and X region of HBV genome into pGEM-T vector respectively. A pair of primers and matched TaqMan probe were selected by comparing the copy number and the Ct values of HBV serum samples derived from the three different standard curves using certain serum DNA. Then the efficiency of six HBV DNA extraction methods including guanidinium isothiocyanate, proteinase K, NaI, NaOH lysis, alkaline lysis and simple boiling was analyzed in sample A, B and C by real-time PCR. Meanwhile, 8 clinical HBV serum samples were quantified.
RESULTS: The copy number of the same HBV serum sample originated from the standard curve of S, C and X regions was 5.7 × 104/mL, 6.3 × 102/mL and 1.6 × 103/mL respectively. The relative Ct value was 26.6, 31.8 and 29.5 respectively. Therefore, primers and matched probe from S region were chosen for further optimization of six extraction methods. The copy number of HBV serum samples A, B and C was 3.49 × 109/mL, 2.08 × 106/mL and 4.40 × 107/mL respectively, the relative Ct value was 19.9, 30 and 26.2 in the method of NaOH lysis, which was the efficientest among six methods. Simple boiling showed a slightly lower efficiency than NaOH lysis. Guanidinium isothiocyanate, proteinase K and NaI displayed that the copy number of HBV serum sample A, B and C was around 105/mL, meanwhile the Ct value was about 30. Alkaline failed to quantify the copy number of three HBV serum samples. Standard deviation (SD) and coefficient variation (CV) were very low in all 8 clinical HBV serum samples, showing that quantification of HBV DNA in triplicate was reliable and accurate.
CONCLUSION: Real-time PCR based on optimized primers and TaqMan probe from S region in combination with NaOH lysis is a simple, rapid and accurate method for quantification of HBV serum DNA.
Collapse
Affiliation(s)
- Yan-Qin Lu
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Key Laboratory of Ministry of Health for Biotech-Drugs, Jinan 250062, China
| | | | | | | | | | | |
Collapse
|