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Tosello V, Grassi A, Rose D, Bao LC, Zulato E, Dalle Fratte C, Polano M, Del Bianco P, Pasello G, Guarneri V, Indraccolo S, Bonanno L. Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC. Sci Rep 2024; 14:18545. [PMID: 39122833 PMCID: PMC11316016 DOI: 10.1038/s41598-024-68229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Liquid biopsy has recently emerged as an important tool in clinical practice particularly for lung cancer patients. We retrospectively evaluated cell-free DNA analyses performed at our Institution by next generation sequencing methodology detecting the major classes of genetic alterations. Starting from the graphical representation of chromosomal alterations provided by the analysis software, we developed a support vector machine classifier to automatically classify chromosomal profiles as stable (SCP) or unstable (UCP). High concordance was found between our binary classification and tumor fraction evaluation performed using shallow whole genome sequencing. Among clinical features, UCP patients were more likely to have ≥ 3 metastatic sites and liver metastases. Longitudinal assessment of chromosomal profiles in 33 patients with lung cancer receiving immune checkpoint inhibitors (ICIs) showed that only patients that experienced early death or hyperprogressive disease retained or acquired an UCP within 3 weeks from the beginning of ICIs. UCP was not observed following ICIs among patients that experienced progressive disease or clinical benefit. In conclusion, our binary classification, applied to whole copy number alteration profiles, could be useful for clinical risk stratification during systemic treatment for non-small cell lung cancer patients.
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Affiliation(s)
- Valeria Tosello
- Basic and Translational Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Angela Grassi
- Clinical Research Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Dominic Rose
- Sequencing Solutions, Roche Diagnostics Deutschland GmbH, Mannheim, Germany
| | - Loc Carlo Bao
- Department of Surgery, Oncology, Gastroenterology, University of Padova, Padua, Italy
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Elisabetta Zulato
- Basic and Translational Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Chiara Dalle Fratte
- Basic and Translational Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano IRCCS, Aviano, Italy
| | - Paola Del Bianco
- Clinical Research Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Giulia Pasello
- Department of Surgery, Oncology, Gastroenterology, University of Padova, Padua, Italy
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Valentina Guarneri
- Department of Surgery, Oncology, Gastroenterology, University of Padova, Padua, Italy
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Stefano Indraccolo
- Basic and Translational Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy.
- Department of Surgery, Oncology, Gastroenterology, University of Padova, Padua, Italy.
| | - Laura Bonanno
- Department of Surgery, Oncology, Gastroenterology, University of Padova, Padua, Italy
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
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Lai HF, Wang SE, Chen SC, Shyr BS, Shyr YM, Shyr BU. The emerging role of cell-free DNA as a molecular marker for duodenal adenocarcinoma. J Chin Med Assoc 2024; 87:422-427. [PMID: 38391235 DOI: 10.1097/jcma.0000000000001079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Duodenal adenocarcinoma is rare and its prognostic factors remain controversial. In our study, the role of cell-free deoxyribonucleic acid (cfDNA) as prognostic factor in duodenal adenocarcinoma was evaluated. METHODS From June 2003 to July 2021, plasma samples were collected from 41 patients with duodenal adenocarcinoma. Plasma cfDNA was assessed in combination with clinicopathological and biochemical characteristics. Univariate and multivariate analyses were conducted to identify independent prognostic factors for overall survival with a Cox proportional hazards regression model. RESULTS The 1- and 5-year survival rates of the patients with high plasma cfDNA level (>9288 copies/mL) group were 58.7% and 17.6%, respectively, which were much lower than patients with low cfDNA level (≤9288 copies/mL), with 95.2% and 64.6%. In univariate analysis, high cfDNA level, lymph node involvement, lymphovascular invasion, and tumor stage were associated with decreased survival. When subjected to multivariate analysis, only high cfDNA level showed significance in influencing the overall survival of duodenal cancer. CONCLUSION cfDNA analysis is simple and noninvasive. High cfDNA level is a strong independent prognostic factor for decreased overall survival and it should be integrated into clinical care.
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Affiliation(s)
- Hon-Fan Lai
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital and National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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George NG, Rishi B, Singh A, Vishmaya S, Kumar R, Kushwaha N, Kaur M, Bhardwaj R, Jain A, Jain A, Chaudhry S, Misra A. Early prognosis prediction in acute myeloid and acute lymphoid leukemia patients using cell-free DNA concentration ratios. Front Mol Biosci 2024; 10:1333943. [PMID: 38317776 PMCID: PMC10840420 DOI: 10.3389/fmolb.2023.1333943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Background: Cell-free DNA (cfDNA) is a promising biomarker for disease prediction in many cancers, including acute leukemia (acute myeloid leukemia [AML] and acute lymphoblastic leukemia [ALL]). This study investigated the role of cfDNA in predicting relapse or unfavorable outcomes in acute leukemia patients upon initial diagnosis. Methods: Paired peripheral blood samples of 25 patients with ALL and AML were compared at baseline and induction/follow-up and clinically correlated with clinicopathological and outcome variables according to the risk category. cfDNA was isolated using commercial cfDNA extraction kits. The probability of poor outcomes in high-risk groups and a cut-off value for risk stratification minimal residual disease (MRD) positivity and outcome prediction were derived. Results: Twenty-five patients diagnosed with AML and ALL were risk-stratified based on NCI risk stratification, and of these 25 patients, 4 patients were of standard risk (SR) and 1 patient was of intermediate risk (IR), while a majority of patients (80%) were of high risk (HR). Of these, four HR patients passed away. The ratio of cfDNA reduction at baseline and the end of induction was a strong predictor of poor outcomes in high-risk patients, regardless of the MRD status. A cfDNA ratio score of 2.6 or higher at diagnosis/remission predicted poor outcomes, with higher accuracy than conventional MRD detection by flow cytometry. Conclusion: A higher cfDNA ratio at diagnosis/remission or at baseline predicts poor outcomes in acute leukemia patients. This pilot study suggests that cfDNA ratio scoring may be a useful tool for predicting prognosis in acute leukemia patients, regardless of the MRD status.
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Affiliation(s)
| | - Bhavika Rishi
- ICMR‐National Institute of Pathology, New Delhi, India
| | - Amitabh Singh
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sree Vishmaya
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Rakesh Kumar
- ICMR‐National Institute of Pathology, New Delhi, India
| | | | - Manpreet Kaur
- ICMR‐National Institute of Pathology, New Delhi, India
| | | | - Ankur Jain
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Aditi Jain
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sumita Chaudhry
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
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Park J, Chang ES, Kim JY, Chelakkot C, Sung M, Song JY, Jung K, Lee JH, Choi JY, Kim NY, Lee H, Kang MR, Kwon MJ, Shin YK, Park YH, Choi YL. c-MET-positive circulating tumor cells and cell-free DNA as independent prognostic factors in hormone receptor-positive/HER2-negative metastatic breast cancer. Breast Cancer Res 2024; 26:13. [PMID: 38238761 PMCID: PMC10797795 DOI: 10.1186/s13058-024-01768-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Endocrine therapy resistance in hormone receptor-positive/HER2-negative (HR+/HER2-) breast cancer (BC) is a significant clinical challenge that poses several unmet needs in the management of the disease. This study aimed to investigate the prognostic value of c-MET-positive circulating tumor cells (cMET+ CTCs), ESR1/PIK3CA mutations, and cell-free DNA (cfDNA) concentrations in patients with hormone receptor-positive (HR+) metastatic breast cancer (mBC). METHODS Ninety-seven patients with HR+ mBC were prospectively enrolled during standard treatment at Samsung Medical Center. CTCs were isolated from blood using GenoCTC® and EpCAM or c-MET CTC isolation kits. PIK3CA and ESR1 hotspot mutations were analyzed using droplet digital PCR. CfDNA concentrations were calculated using internal control copies from the ESR1 mutation test. Immunocytochemistry was performed to compare c-MET overexpression between primary and metastatic sites. RESULTS The proportion of c-MET overexpression was significantly higher in metastatic sites than in primary sites (p = 0.00002). Survival analysis showed that c-MET+ CTC, cfDNA concentration, and ESR1 mutations were significantly associated with poor prognosis (p = 0.0026, 0.0021, and 0.0064, respectively) in HR+/HER2- mBC. By contrast, EpCAM-positive CTC (EpCAM+ CTC) and PIK3CA mutations were not associated with progression-free survival (PFS) in HR+/HER2- mBC. Multivariate analyses revealed that c-MET+ CTCs and cfDNA concentration were independent predictors of PFS in HR+/HER2- mBC. CONCLUSIONS Monitoring c-MET+ CTC, rather than assessing c-MET expression in the primary BC site, could provide valuable information for predicting disease progression, as c-MET expression can change during treatment. The c-MET+ CTC count and cfDNA concentration could provide complementary information on disease progression in HR+ /HER2- mBC, highlighting the importance of integrated liquid biopsy.
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Grants
- HI19C0141 Ministry of Health & Welfare, South Korea
- HI19C0141 Ministry of Health & Welfare, South Korea
- HI19C0141 Ministry of Health & Welfare, South Korea
- HI19C0141 Ministry of Health & Welfare, South Korea
- HI19C0141 Ministry of Health & Welfare, South Korea
- 2022R1A2C2006322 Ministry of Science and ICT, South Korea
- 2022R1A2C2006322 Ministry of Science and ICT, South Korea
- 2022R1A2C2006322 Ministry of Science and ICT, South Korea
- 2022R1A2C2006322 Ministry of Science and ICT, South Korea
- 2022R1A2C2006322 Ministry of Science and ICT, South Korea
- 2022R1A2C2006322 Ministry of Science and ICT, South Korea
- #SMO1230021 Samsung Medical Center
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Affiliation(s)
- Jieun Park
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eun Sol Chang
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
- Laboratory of Molecular Pathology and Theranostics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Irwon-ro 81, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Chaithanya Chelakkot
- Technical Research Center, Genobio Corp., Seoul, Republic of Korea
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minjung Sung
- Laboratory of Molecular Pathology and Theranostics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ji-Young Song
- Laboratory of Molecular Pathology and Theranostics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyungsoo Jung
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Irwon-ro 81, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Ji Hye Lee
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | | | - Na Young Kim
- R&D Center, ABION Inc., Seoul, Republic of Korea
| | - Hyegyeong Lee
- Central Laboratory, LOGONE Bio-Convergence Research Foundation, Seoul, Republic of Korea
| | - Mi-Ran Kang
- R&D Center, Gencurix Inc., Seoul, Republic of Korea
| | - Mi Jeong Kwon
- Vessel-Organ Interaction Research Center (MRC), College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Young Kee Shin
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 08826, Republic of Korea.
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
- R&D Center, ABION Inc., Seoul, Republic of Korea.
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Irwon-ro 81, Gangnam-gu, Seoul, 06351, Republic of Korea.
| | - Yoon-La Choi
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.
- Laboratory of Molecular Pathology and Theranostics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Irwon-ro 81, Gangnam-gu, Seoul, 06351, Republic of Korea.
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Khurram I, Khan MU, Ibrahim S, Saleem A, Khan Z, Mubeen M, Khawar A, Ali Q. Efficacy of cell-free DNA as a diagnostic biomarker in breast cancer patients. Sci Rep 2023; 13:15347. [PMID: 37715016 PMCID: PMC10504267 DOI: 10.1038/s41598-023-42726-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023] Open
Abstract
Breast cancer is the most prevalent and leading cause of mortality worldwide among women. Cell-free DNA (cfDNA) analysis is an alternative quantitative approach to conventional methods for cancer diagnosis. The current research project aimed to determine the efficacy of cfDNA as a diagnostic biomarker in breast cancer patients in Pakistan. Eighty-four female breast cancer patients were selected as cases, and 152 healthy females as controls. Immunohistochemistry was performed to identify tumor biomarkers along with clinical profiling. cfDNA was extracted from serum using the phenol-chloroform method. The cfDNA level in the serum was estimated using Agarose Gel Electrophoresis and Nanodrop. SPPS version 25.0 was used to perform statistical analyses. The results showed that the cancer biomarkers were significantly associated with breast cancer. The changes in hematological parameters were insignificant, whereas the biochemical parameter variations between the cases and controls were statistically significant. A significant association of cfDNA level with breast cancer was observed. Further cfDNA levels and cancer biomarkers were not statistically significant. A significant correlation was observed between cfDNA and biochemical parameters, except for creatinine, whereas hematological parameters showed no significant correlation.ROC analysis declared cfDNA as an authentic diagnostic marker for breast cancer. It was concluded that the level of cfDNA is significantly increased in breast cancer patients and can be utilized as a diagnostic biomarker.
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Affiliation(s)
- Iqra Khurram
- Faculty of Allied Health Sciences, University Institute of Medical Lab Technology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
| | - Saooda Ibrahim
- Faculty of Allied Health Sciences, University Institute of Medical Lab Technology, The University of Lahore, Lahore, Pakistan
| | - Ayman Saleem
- Faculty of Allied Health Sciences, University Institute of Medical Lab Technology, The University of Lahore, Lahore, Pakistan
| | - Zaman Khan
- Faculty of Allied Health Sciences, University Institute of Medical Lab Technology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Mubeen
- Faculty of Allied Health Sciences, University Institute of Medical Lab Technology, The University of Lahore, Lahore, Pakistan
| | - Arooj Khawar
- Faculty of Allied Health Sciences, University Institute of Medical Lab Technology, The University of Lahore, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
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Ning W, Zhang C, Tian Z, Wu M, Luo Z, Hu S, Pan H, Li Y. Ω-shaped fiber optic LSPR biosensor based on mismatched hybridization chain reaction and gold nanoparticles for detection of circulating cell-free DNA. Biosens Bioelectron 2023; 228:115175. [PMID: 36871422 DOI: 10.1016/j.bios.2023.115175] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Circulating cell-free DNA (cfDNA) is a promising biomarker of liquid biopsy, but it still faces some difficulties in achieving sensitive and convenient detection. Herein, an Ω-shaped fiber optic localized surface plasmon resonance (FO-LSPR) biosensor based on hybridization chain reaction (HCR) coupled with gold nanoparticles (AuNPs) was developed, and applied in simple and sensitive detection of cfDNA. Specifically, one-base mismatch was designed in HCR hairpins (H1 and H2) to obtain high reaction efficiency, and AuNPs was introduced onto H1 through poly-adenine to construct HCR coupled with AuNPs strategy. Meanwhile, target cfDNA was designed into two domains: one could trigger HCR to generate dsDNA concatemer carrying numerous AuNPs, and the other could hybridize with capture DNA on the surface of Ω-shaped fiber optic (FO) probes. Thus, the presence of target cfDNA would initiate HCR, and bring the formed dsDNA concatemer and AuNPs to approach the probe surface, resulting in dramatically amplified LSPR signal. Besides, HCR required simple isothermal and enzyme-free condition, and Ω-shaped FO probe with high refractive index sensitivity just needed to be immersed into HCR solution directly for signal monitoring. Benefiting from the synergetic amplification of mismatched HCR and AuNPs, the proposed biosensor exhibited high sensitivity with a limit of detection of 14.0 pM, and therefore could provide a potential strategy for biomedical analysis and disease diagnosis.
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Affiliation(s)
- Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuyan Zhang
- Medical Equipment Innovation Research Center, Precision Medicine Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongzhi Pan
- The Affiliated Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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Bortul M, Giudici F, Tierno D, Generali D, Scomersi S, Grassi G, Bottin C, Cappelletti MR, Zanconati F, Scaggiante B. A Case-Control Study by ddPCR of ALU 260/111 and LINE-1 266/97 Copy Number Ratio in Circulating Cell-Free DNA in Plasma Revealed LINE-1 266/97 as a Potential Biomarker for Early Breast Cancer Detection. Int J Mol Sci 2023; 24:ijms24108520. [PMID: 37239866 DOI: 10.3390/ijms24108520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND In Western countries, breast cancer (BC) is the most common cancer in women. Early detection has a positive impact on survival, quality of life, and public health costs. Mammography screening programs have increased early detection rates, but new approaches to more personalized surveillance could further improve diagnosis. Circulating cell-free DNA (cfDNA) in blood could provide a potential tool for early diagnosis by analyzing cfDNA quantity, circulating tumor DNA mutations, or cfDNA integrity (cfDI). METHODS Plasma was obtained from the blood of 106 breast cancer patients (cases) and 103 healthy women (controls). Digital droplet PCR was used for the determination of ALU 260/111 bp and LINE-1 266/97 bp copy number ratio and cfDI. cfDNA abundance was calculated using copies of the EEF1A2 gene. The accuracy of biomarker discrimination was analyzed with receiver operating characteristic curve (ROC). Sensitivity analyses were performed to account for age as a potential confounder. RESULTS Cases had significantly lower ALU 260/111 or LINE-1 266/97 copy number ratios (median; ALU 260/111 = 0.08, LINE-1 266/97 = 0.20), compared with control (median; ALU 260/111 = 0.10, LINE-1 266/97 = 0.28) (p < 0.001). ROC analysis showed that copy number ratio discriminated cases from controls (area under the curve, AUC = 0.69, 95% CI: 0.62-0.76 for ALU and 0.80, 95% CI: 0.73-0.86 for LINE-1). ROC from cfDI confirmed the better diagnostic performance of LINE-1 compared with ALU. CONCLUSIONS Analysis of LINE-1 266/97 copy number ratio or cfDI by ddPCR appears to be a useful noninvasive test that could aid in early BC detection. Further studies in a large cohort are needed to validate the biomarker.
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Affiliation(s)
- Marina Bortul
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Breast Unit, Azienda Sanitaria Universitaria Integrata Giuliano Isontina (ASUGI), 34149 Trieste, Italy
| | - Fabiola Giudici
- Cancer Epidemiologic Unit, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 33081 Aviano, Italy
| | - Domenico Tierno
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Daniele Generali
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Breast Cancer Unit and Translational Research Unit, Azienda Socio-Sanitaria Territoriale di Cremona-ASST, 26100 Cremona, Italy
| | - Serena Scomersi
- Breast Unit, Azienda Sanitaria Universitaria Integrata Giuliano Isontina (ASUGI), 34149 Trieste, Italy
| | - Gabriele Grassi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Cristina Bottin
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Maria Rosa Cappelletti
- Breast Cancer Unit and Translational Research Unit, Azienda Socio-Sanitaria Territoriale di Cremona-ASST, 26100 Cremona, Italy
| | - Fabrizio Zanconati
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Breast Unit, Azienda Sanitaria Universitaria Integrata Giuliano Isontina (ASUGI), 34149 Trieste, Italy
| | - Bruna Scaggiante
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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Zadran B, Sudhindar PD, Wainwright D, Bury Y, Luli S, Howarth R, McCain MV, Watson R, Huet H, Palinkas F, Berlinguer-Palmini R, Casement J, Mann DA, Oakley F, Lunec J, Reeves H, Faulkner GJ, Shukla R. Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation. Br J Cancer 2023; 128:1236-1248. [PMID: 36707636 PMCID: PMC10050422 DOI: 10.1038/s41416-023-02154-9] [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: 03/14/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Molecular characterisation of hepatocellular carcinoma (HCC) is central to the development of novel therapeutic strategies for the disease. We have previously demonstrated mutagenic consequences of Long-Interspersed Nuclear Element-1 (LINE1s/L1) retrotransposition. However, the role of L1 in HCC, besides somatic mutagenesis, is not well understood. METHODS We analysed L1 expression in the TCGA-HCC RNAseq dataset (n = 372) and explored potential relationships between L1 expression and clinical features. The findings were confirmed by immunohistochemical (IHC) analysis of an independent human HCC cohort (n = 48) and functional mechanisms explored using in vitro and in vivo model systems. RESULTS We observed positive associations between L1 and activated TGFβ-signalling, TP53 mutation, alpha-fetoprotein and tumour invasion. IHC confirmed a positive association between pSMAD3, a surrogate for TGFβ-signalling status, and L1 ORF1p (P < 0.0001, n = 32). Experimental modulation of L1 ORF1p levels revealed an influence of L1 ORF1p on key hepatocarcinogenesis-related pathways. Reduction in cell migration and invasive capacity was observed upon L1 ORF1 knockdown, both in vitro and in vivo. In particular, L1 ORF1p increased PIN1 cytoplasmic localisation. Blocking PIN1 activity abrogated L1 ORF1p-induced NF-κB-mediated inflammatory response genes while further activated TGFβ-signalling confirming differential alteration of PIN1 activity in cellular compartments by L1 ORF1p. DISCUSSION Our data demonstrate a causal link between L1 ORF1p and key oncogenic pathways mediated by PIN1, presenting a novel therapeutic avenue.
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Affiliation(s)
- Bassier Zadran
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Praveen Dhondurao Sudhindar
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Daniel Wainwright
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Yvonne Bury
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Saimir Luli
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Rachel Howarth
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Misti Vanette McCain
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Robyn Watson
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Hannah Huet
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Fanni Palinkas
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | | | - John Casement
- Bioinformatics Support Unit, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Derek A Mann
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
- Department of Gastroenterology and Hepatology, School of Medicine, Koç University, Istanbul, Turkey
| | - Fiona Oakley
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - John Lunec
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Helen Reeves
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
- Hepatopancreatobiliary Multidisciplinary Team, Freeman Hospital, Newcastle-upon-Tyne Hospitals NHS foundation, Newcastle-upon-Tyne, UK
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ruchi Shukla
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, NE1 8ST, UK.
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9
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Nair MG, Ramesh RS, Naidu CM, Mavatkar AD, V. P. S, Ramamurthy V, Somashekaraiah VM, C. E. A, Raghunathan K, Panigrahi A, Das M, Dhar SK, Prabhu JS. Estimation of ALU Repetitive Elements in Plasma as a Cost-Effective Liquid Biopsy Tool for Disease Prognosis in Breast Cancer. Cancers (Basel) 2023; 15:cancers15041054. [PMID: 36831397 PMCID: PMC9953974 DOI: 10.3390/cancers15041054] [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: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Liquid biopsy is widely recognized as an efficient diagnostic method in oncology for disease detection and monitoring. Though the examination of circulating tumor cells (CTC) is mostly implemented for the assessment of genomic aberrations, the need of complex methodologies for their detection has impeded its acceptance in low-resource settings. We evaluated cell-free DNA (cfDNA) as a liquid biopsy tool and investigated its utility in breast cancer patients. METHODS Total cell-free DNA was extracted from the plasma of breast cancer patients (n = 167) with a median follow-up of more than 5 years, at various stages of the disease. Quantitative PCR was performed to estimate the copy numbers of two fractions of ALU repetitive elements (ALU 115 and ALU 247), and DNA integrity (DI) was calculated as the ratio of ALU 247/115. Mutations in TP53 and PIK3CA in the cfDNA were estimated by next-gen sequencing (NGS) in a subset of samples. Associations of the levels of both the ALU fragments with various clinico-pathological factors and disease-free survival at various stages were examined. Nomogram models were constructed with clinical variables and ALU 247 levels to predict disease-free survival and the best performing model was evaluated by decision curve analysis. RESULTS DI and ALU 247 levels were significantly lower (p < 0.0001) in the post-operative plasma when compared to their pre-surgery levels. DI and ALU 247 were found to be significantly higher in patients with metastasis (p < 0.05). Patients with higher levels of ALU 247 in their post-operative plasma had significant poor disease-free survival (p = 0.005). Higher levels of ALU 247 in the circulation also correlated with low tumor-infiltrating lymphocytes (TIL) within their primary tumors in the ER-negative breast cancer subtype (p = 0.01). Cox proportional hazard analysis confirmed ALU 247 as an independent variable of disease-free survival both in univariate and multivariate analysis [HR 1.3 (95% CI 1.047 to 1.613, p = 0.017)]. The nomogram model showed that the addition of ALU 247 with other variables significantly improved (C-index 0.823) the predictive ability of the model. CONCLUSION Our results confirm the utility of cfDNA as an evolving liquid biopsy tool for molecular analysis. Evaluation of larger fragments of cfDNA estimated through ALU 247 can provide vital information concurrent with the pathological process of disease evolution in breast cancer and warrants expansion to other cancer types.
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Affiliation(s)
- Madhumathy G. Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
- Correspondence: (M.G.N.); (J.S.P.)
| | - Rakesh S. Ramesh
- Department of Surgical Oncology, St. John’s Medical College and Hospital, Bangalore 560034, India
| | - Chandrakala M. Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Apoorva D. Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Snijesh V. P.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Vishakha Ramamurthy
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Vidya M. Somashekaraiah
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Anupama C. E.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | | | - Anuradha Panigrahi
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Manjula Das
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Sujan K. Dhar
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Jyothi S. Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
- Correspondence: (M.G.N.); (J.S.P.)
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10
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Jiang XF, Zhang BM, Du FQ, Guo JN, Wang D, Li YE, Deng SH, Cui BB, Liu YL. Exploring biomarkers for prognosis and neoadjuvant chemosensitivity in rectal cancer: Multi-omics and ctDNA sequencing collaboration. Front Immunol 2022; 13:1013828. [PMID: 36569844 PMCID: PMC9780298 DOI: 10.3389/fimmu.2022.1013828] [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: 08/10/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction This study aimed to identified the key genes and sequencing metrics for predicting prognosis and efficacy of neoadjuvant chemotherapy (nCT) in rectal cancer (RC) based on genomic DNA sequencing in samples with different origin and multi-omics association database. Methods We collected 16 RC patients and obtained DNA sequencing data from cancer tissues and plasma cell-free DNA before and after nCT. Various gene variations were analyzed, including single nucleotide variants (SNV), copy number variation (CNV), tumor mutation burden (TMB), copy number instability (CNI) and mutant-allele tumor heterogeneity (MATH). We also identified genes by which CNV level can differentiate the response to nCT. The Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database were used to further evaluate the specific role of therapeutic relevant genes and screen out the key genes in multi-omics levels. After the intersection of the screened genes from differential expression analysis, survival analysis and principal components analysis dimensionality reduction cluster analysis, the key genes were finally identified. Results The genes CNV level of principal component genes in baseline blood and cancer tissues could significantly distinguish the two groups of patients. The CNV of HSP90AA1, EGFR, SRC, MTOR, etc. were relatively gained in the better group compared with the poor group in baseline blood. The CNI and TMB was significantly different between the two groups. The increased expression of HSP90AA1, EGFR, and SRC was associated with increased sensitivity to multiple chemotherapeutic drugs. The nCT predictive score obtained by therapeutic relevant genes could be a potential prognostic indicator, and the combination with TMB could further refine prognostic prediction for patients. After a series of analysis in multi-omics association database, EGFR and HSP90AA1 with significant differences in multiple aspects were identified as the key predictive genes related to prognosis and the sensitivity of nCT. Discussion This work revealed that effective combined application and analysis in multi-omics data are critical to search for predictive biomarkers. The key genes EGFR and HSP90AA1 could serve as an effective biomarker to predict prognose and neoadjuvant chemosensitivity.
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Affiliation(s)
- Xiu-Feng Jiang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bo-Miao Zhang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fen-Qi Du
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jun-Nan Guo
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dan Wang
- Department of Neurology, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, China
| | - Yi-En Li
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shen-Hui Deng
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bin-Bin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China,*Correspondence: Bin-Bin Cui, ; Yan-Long Liu,
| | - Yan-Long Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China,*Correspondence: Bin-Bin Cui, ; Yan-Long Liu,
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11
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Kumar S, Nadda N, Paul S, Gamanagatti S, Dash NR, Vanamail P, Saraya A, Shalimar, Nayak B. Evaluation of the cell-free DNA integrity index as a liquid biopsy marker to differentiate hepatocellular carcinoma from chronic liver disease. Front Mol Biosci 2022; 9:1024193. [PMID: 36483538 PMCID: PMC9723134 DOI: 10.3389/fmolb.2022.1024193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/08/2022] [Indexed: 08/19/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) occurs in the majority of patients with underlying chronic liver disease (CLD) of viral and non-viral etiologies, which requires screening for early HCC diagnosis. Liquid biopsy holds great promise now for early detection, prognosis, and assessment of response to cancer therapy. Cell-free DNA (cfDNA) as a liquid biopsy marker can be easily detected by a real-time quantitative PCR (RT-qPCR) assay for a change in its concentration, integrity, and fragmentation in cancer. Methods: Patients with HCC (n = 100), CLD (n = 100), and healthy (n = 30) controls were included in the study. The cfDNA was isolated from serum and real-time quantitative PCR (RT-qPCR) was carried out using primer pairs for large (>205 bp) and small (110 bp) fragments of repetitive elements (ALU and LINE1) and housekeeping genes (β-Actin and GAPDH). Total cfDNA concentrations and integrity index were determined by the absolute quantitation method (L/S ratio or cfDII-integrity). The cfDII as a measure of fragmentation was determined by comparative Ct (2-ΔΔCt) method of relative quantification (cfDII-fragmentation). Using a receiver operating characteristic (ROC) curve, cfDII-integrity and cfDII-fragmentation were used to differentiate HCC from CLD patients or healthy controls. Results: The total cfDNA concentrations in the sera of HCC (244 ng/ml) patients were significantly higher than those of CLD (33 ng/ml) patients and healthy (16.88 ng/ml) controls. HCC patients have shown poor DNA integrity or excess cfDNA fragmentation than CLD patients and healthy controls. The cfDII-integrity of GAPDH and ALU fragment significantly differentiate HCC from CLD at AUROC 0.72 and 0.67, respectively. The cfDII-fragmentation following normalization with cfDNA of healthy control has shown significant differential capabilities of HCC from CLD at AUROC 0.67 using GAPDH and 0.68 using the ALU element. The ROC curve of LINE1 and β-actin cfDII was not found significant for any of the above methods. The cfDII-fragmentation trend in HCC patients of different etiologies was similar indicating increased cfDNA fragmentation irrespective of its etiology. Conclusion: The cfDII measuring both DNA integrity (L/S ratio) and fragmentation of the Alu and GAPDH genes can differentiate HCC from CLD patients and healthy individuals.
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Affiliation(s)
- Sonu Kumar
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Neeti Nadda
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Shashi Paul
- Department of Radiodiagnosis, All India Institute of Medical Sciences, New Delhi, India
| | - Shivanand Gamanagatti
- Department of Radiodiagnosis, All India Institute of Medical Sciences, New Delhi, India
| | - Nihar Ranjan Dash
- Department of Gastrointestinal Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Perumal Vanamail
- Department of Biostatistics in Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi, India
- Trichy SRM Medical College Hospital & Research Centre, Tiruchirappalli, Tamil Nadu, India
| | - Anoop Saraya
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Baibaswata Nayak
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
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12
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Gianni C, Palleschi M, Merloni F, Di Menna G, Sirico M, Sarti S, Virga A, Ulivi P, Cecconetto L, Mariotti M, De Giorgi U. Cell-Free DNA Fragmentomics: A Promising Biomarker for Diagnosis, Prognosis and Prediction of Response in Breast Cancer. Int J Mol Sci 2022; 23:14197. [PMID: 36430675 PMCID: PMC9695769 DOI: 10.3390/ijms232214197] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
Identifying novel circulating biomarkers predictive of response and informative about the mechanisms of resistance, is the new challenge for breast cancer (BC) management. The integration of omics information will gradually revolutionize the clinical approach. Liquid biopsy is being incorporated into the diagnostic and decision-making process for the treatment of BC, in particular with the analysis of circulating tumor DNA, although with some relevant limitations, including costs. Circulating cell-free DNA (cfDNA) fragmentomics and its integrity index may become a cheaper, noninvasive biomarker that could provide significant additional information for monitoring response to systemic treatments in BC. The purpose of our review is to focus on the available research on cfDNA integrity and its features as a biomarker of diagnosis, prognosis and response to treatments in BC, highlighting new perspectives and critical issues for future applications.
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Affiliation(s)
- Caterina Gianni
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Michela Palleschi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Filippo Merloni
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Giandomenico Di Menna
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Marianna Sirico
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Samanta Sarti
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Alessandra Virga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Lorenzo Cecconetto
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Marita Mariotti
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Ugo De Giorgi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
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13
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Shen Q, Cen H, Jiang J, Cong Z, Zhou Y, Huang X, Zhu L, Jiang Q, Xue C. The level and integrity of plasma circulating cell-free DNA in patients with primary multiple myeloma. Transl Cancer Res 2022; 11:4137-4147. [PMID: 36523306 PMCID: PMC9745376 DOI: 10.21037/tcr-22-2416] [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] [Received: 09/21/2022] [Accepted: 11/16/2022] [Indexed: 09/10/2023]
Abstract
BACKGROUND To evaluate the clinical research related to the level and integrity of circulating free DNA (cfDNA) in the plasma of patients with multiple myeloma (MM). METHODS The plasma samples of 56 patients with newly diagnosed MM and 60 healthy volunteers were collected. ALU247 fragment and ALU115 fragment were used as target genes, and quantitative polymerase chain reaction (qPCR) was used to assess the plasma of the patient and healthy control groups. The cfDNA level in MM was analyzed, and the ALU247/ALU115 ratio was used to calculate the integrity of cfDNA. The correlation between the cfDNA level and integrity and the clinical characteristics of patients with primary MM was analyzed, and their value in efficacy monitoring and prognostic evaluation was evaluated. RESULTS The plasma concentrations of ALU247 and ALU115 and the integrity of cfDNA in patients with primary MM were significantly higher than those in the healthy controls (P<0.05). The ALU247 fragment concentration was markedly correlated with the Durie-Salmon (D-S), International Staging System (ISS), and Revised-International Staging System (R-ISS) stages (P<0.05). After three courses of induction chemotherapy, the levels of ALU247, ALU115, and cfDNA integrity in both groups were lower than those before chemotherapy (P<0.05). Patients with curative effects of CR, sCR, and VGPR were classified into the ≥ very good partial response (VGPR) group (n=38), while those with curative effects of PR and SD were allocated into the CONCLUSIONS CfDNA levels were significantly elevated in MM patients, and the ALU247 fragment concentration was remarkably correlated with multiple clinical features and had important clinical value for efficacy monitoring and prognostic assessment.
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Affiliation(s)
- Qian Shen
- Department of Hematology and Lymphoma, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Haiyan Cen
- Department of Hematology, Affiliated Hospital of Nantong University & Nantong Geriatric Rehabilitation Hospital, Nantong, China
| | - Jing Jiang
- Department of Radiology, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhirong Cong
- Department of Hematology and Lymphoma, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Ying Zhou
- Department of Hematology and Lymphoma, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Xiaoxiao Huang
- Department of Laboratory Medicine, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Li Zhu
- Department of Hematology and Lymphoma, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Qi Jiang
- Department of Hematology and Lymphoma, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Chenqi Xue
- Department of Interventional Radiology, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
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14
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Zhang S, Zhou D, Li S, Bai Y, Huang B, Han J, Xu M, Wang S, Deng G. Performance of ImproGene cfDNA blood collection tubes for mutation analysis in cancer patients. Scandinavian Journal of Clinical and Laboratory Investigation 2022; 82:378-384. [PMID: 35861435 DOI: 10.1080/00365513.2022.2100272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
With the widely application of liquid biopsy and the development of detection technology, the standardization of pre-analysis procedures is necessary. For controlling pre-analysis variation of circulating tumor DNA (ctDNA) in blood samples, the blood collection tubes for ctDNA preservation particularly contribute a lot. The objective of this study was to investigate whether ImproGene® Cell Free DNA Tube (ImproGene tube) can be used in sample collection, preservation and NGS based mutation detection for ctDNA. We investigated hemolysis and cell free DNA (cfDNA) concentration of blood samples stored in ImproGene tubes and detected β-actin, LINE1 and exogenous gene level by qPCR. We compared cfDNA and RNA quantity between samples in ImproGene tube and Streck Cell-Free DNA BCT® (Streck tube). And 10 gene mutations and three fusion mutations analysis were compared by sequencing. When stored at room temperature within 7 days in ImproGene tubes, blood samples had no visible hemolysis and the cfDNA concentration, levels of β-actin, LINE1 and exogenous gene remained stable which means no genomic DNA release and cfDNA was protected. There was no significant difference in cfDNA and RNA quantity between ImproGene tubes and Streck tubes. Furthermore, based on this limited data set, ImproGene tubes showed increased detection rates of low-level mutations. Therefore, ImproGene Cell Free DNA Tubes may have promising applications in sample collection, preservation and NGS based mutation detection for ctDNA by its good preservation performance.
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Affiliation(s)
- Shu Zhang
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Dongyao Zhou
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Siyun Li
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Yingming Bai
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Bo Huang
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Jianhong Han
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Mingfei Xu
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Sina Wang
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Guanhua Deng
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
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15
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Stein A, Paschold L, Tintelnot J, Goekkurt E, Henkes SS, Simnica D, Schultheiss C, Willscher E, Bauer M, Wickenhauser C, Thuss-Patience P, Lorenzen S, Ettrich T, Riera-Knorrenschild J, Jacobasch L, Kretzschmar A, Kubicka S, Al-Batran SE, Reinacher-Schick A, Pink D, Sinn M, Lindig U, Hiegl W, Hinke A, Hegewisch-Becker S, Binder M. Efficacy of Ipilimumab vs FOLFOX in Combination With Nivolumab and Trastuzumab in Patients With Previously Untreated ERBB2-Positive Esophagogastric Adenocarcinoma: The AIO INTEGA Randomized Clinical Trial. JAMA Oncol 2022; 8:1150-1158. [PMID: 35737383 DOI: 10.1001/jamaoncol.2022.2228] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Importance In metastatic esophagogastric adenocarcinoma (EGA), the addition of programmed cell death 1 (PD-1) inhibitors to chemotherapy has improved outcomes in selected patient populations. Objective To investigate the efficacy of trastuzumab and PD-1 inhibitors with cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) inhibitors or FOLFOX in first-line treatment of advanced ERBB2-positive EGA. Design, Setting, and Participants This phase 2 multicenter, outpatient, randomized clinical trial with 2 experimental arms compared with historical control individually was conducted between March 2018 and May 2020 across 21 German sites. The reported results are based on a median follow-up of 14.3 months. Patients with previously untreated, metastatic ERBB2-positive (local immunohistochemistry score of 3+ or 2+/in situ hybridization amplification positive) EGA, adequate organ function, and eligibility for immunotherapy were included. Data analysis was performed from June to September 2021. Interventions Patients were randomized to trastuzumab and nivolumab (1 mg/kg × 4/240 mg for up to 12 months) in combination with mFOLFOX6 (FOLFOX arm) or ipilimumab (3 mg/kg × 4 for up to 12 weeks) (ipilimumab arm). Main Outcomes and Measures The primary end point was survival improvement with a targeted increase of the 12-month overall survival rate from 55% (trastuzumab/chemotherapy-ToGA regimen) to 70% in each arm. Results A total of 97 patients were enrolled, and 88 were randomized (18 women, 70 men; median [range] age, 61 [41-80] years). Baseline Eastern Cooperative Oncology Group performance status was 0 in 54 patients (61%) and 1 in 34 patients (39%); 66 patients (75%) had EGA localized in the esophagogastric junction and 22 in the stomach (25%). Central post hoc biomarker analysis (84 patients) showed PD-1 ligand 1 (PD-L1) combined positive score of 1 or greater in 59 patients (72%) and 5 or greater in 46 patients (56%) and confirmed ERBB2 positivity in 76 patients. The observed overall survival rate at 12 months was 70% (95% CI, 54%-81%) with FOLFOX and 57% (95% CI, 41%-71%) with ipilimumab. Treatment-related grade 3 or greater adverse events (AEs) and serious AEs occurred in 29 and 15 patients in the FOLFOX arm and in 20 and 17 patients in the ipilimumab arm, respectively, with a higher incidence of autoimmune-related AEs in the ipilimumab arm and neuropathy in the FOLFOX arm. Liquid biopsy analyses showed strong correlation of early cell-free DNA increase with shorter progression-free and overall survival and emergence of truncating and epitope-loss ERBB2 resistance sequence variations with trastuzumab treatment. Conclusions and Relevance In this randomized clinical trial, trastuzumab, nivolumab, and FOLFOX showed favorable efficacy compared with historical data and trastuzumab, nivolumab, and ipilimumab in ERBB2-positive EGA. The ipilimumab arm yielded similar OS compared with the ToGA regimen. Trial Registration ClinicalTrials.gov Identifier: NCT03409848.
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Affiliation(s)
- Alexander Stein
- Hematology-Oncology Practice Eppendorf (HOPE), Hamburg, Germany.,University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lisa Paschold
- Department of Internal Medicine IV-Oncology/Hematology, University Hospital, Martin-Luther University, Halle, Germany
| | - Joseph Tintelnot
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eray Goekkurt
- Hematology-Oncology Practice Eppendorf (HOPE), Hamburg, Germany.,University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Svenja-Sibylla Henkes
- Department of Internal Medicine IV-Oncology/Hematology, University Hospital, Martin-Luther University, Halle, Germany
| | - Donjete Simnica
- Department of Internal Medicine IV-Oncology/Hematology, University Hospital, Martin-Luther University, Halle, Germany
| | - Christoph Schultheiss
- Department of Internal Medicine IV-Oncology/Hematology, University Hospital, Martin-Luther University, Halle, Germany
| | - Edith Willscher
- Department of Internal Medicine IV-Oncology/Hematology, University Hospital, Martin-Luther University, Halle, Germany
| | - Marcus Bauer
- Institute of Pathology, University Hospital, Martin-Luther University, Halle, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, University Hospital, Martin-Luther University, Halle, Germany
| | | | - Sylvie Lorenzen
- Rechts der Isar Hospital, Technical University of Munich, Munich, Germany
| | | | | | | | | | | | | | | | - Daniel Pink
- Klinik und Poliklinik für Innere Medizin C, University Greifswald, Greifswald, Germany.,Klinik für Hämatologie, Onkologie und Palliativmedizin, Sarkomzentrum Berlin-Brandenburg, HELIOS Klinikum Bad Saarow, Bad Saarow, Germany
| | - Marianne Sinn
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | | | - Mascha Binder
- Department of Internal Medicine IV-Oncology/Hematology, University Hospital, Martin-Luther University, Halle, Germany
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16
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The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies. Diagnostics (Basel) 2022; 12:diagnostics12061363. [PMID: 35741173 PMCID: PMC9221655 DOI: 10.3390/diagnostics12061363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy is a broad term that refers to the testing of body fluids for biomarkers that correlate with a pathological condition. While a variety of body-fluid components (e.g., circulating tumor cells, extracellular vesicles, RNA, proteins, and metabolites) are studied as potential liquid biopsy biomarkers, cell-free DNA (cfDNA) has attracted the most attention in recent years. The total cfDNA population in a typical biospecimen represents an immensely rich source of biological and pathological information and has demonstrated significant potential as a versatile biomarker in oncology, non-invasive prenatal testing, and transplant monitoring. As a significant portion of cfDNA is composed of repeat DNA sequences and some families (e.g., pericentric satellites) were recently shown to be overrepresented in cfDNA populations vs their genomic abundance, it holds great potential for developing liquid biopsy-based biomarkers for the early detection and management of patients with cancer. By outlining research that employed cell-free repeat DNA sequences, in particular the ALU and LINE-1 elements, we highlight the clinical potential of the repeat-element content of cfDNA as an underappreciated marker in the cancer liquid biopsy repertoire.
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Paschold L, Binder M. Circulating Tumor DNA in Gastric and Gastroesophageal Junction Cancer. Curr Oncol 2022; 29:1430-1441. [PMID: 35323320 PMCID: PMC8947276 DOI: 10.3390/curroncol29030120] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 12/21/2022] Open
Abstract
Tumor cells shed DNA into the plasma. “Liquid biopsy” analysis of mutations or other genomic alterations in circulating cell-free DNA (cfDNA) may provide us with a tool to detect minimal residual cancer, comprehensively profile the genomic tumor landscape in search of druggable targets, and monitor cancers non-invasively over time for treatment failure or emerging treatment-resistant tumor subclones. While liquid biopsies have not yet entered routine clinical management in patients with gastric and gastroesophageal junction cancers, this group of diseases may benefit from such advanced diagnostic tools due to their pronounced genetic spatiotemporal heterogeneity and limitations in imaging sensitivity. Moreover, as the armamentarium of targeted treatment approaches and immunotherapies expands, cfDNA analyses may reveal their utility not only as a biomarker of response but also for precision monitoring. In this review, we discuss the different applications of cfDNA analyses in patients with gastric and gastroesophageal junction cancer and the technical challenges that such liquid biopsies have yet to overcome.
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Affiliation(s)
| | - Mascha Binder
- Correspondence: ; Tel.: +49-345-557-4972; Fax: +49-345-557-2950
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18
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Cell-Free DNA Variables including Gene Mutations in CA15-3 Normal Breast Cancer Reflect Prognosis. DISEASE MARKERS 2022; 2022:5470166. [PMID: 35251373 PMCID: PMC8894049 DOI: 10.1155/2022/5470166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/16/2022] [Accepted: 01/31/2022] [Indexed: 11/22/2022]
Abstract
Background Cell-free DNA (cfDNA) has attracted considerable attention in precision medicine. However, few data are available regarding to the prognostic value of cfDNA variables in CA15-3 normal breast cancer (BC) patients. Here, we aimed at investigating the prognostic value of cfDNA variables including gene mutations in CA15-3 normal BC patients. Methods A total of 68 BC patients with normal CA15-3 levels were enrolled. cfDNA concentration and integrity were assessed based on qPCR. cfDNA gene mutations were conducted by using next gene sequencing (NGS). The association between cfDNA variables and the prognosis of patients was analyzed. Results cfDNA concentration was related to tumor stage (P = 0.002), metastases (P = 0.001), and distant metastases (P < 0.001). The elevated copy number variants (CNV) were found in distant metastasis patients compared with patients without distant metastases (P = 0.008). Nineteen mutant genes were validated in enrolled CA15-3 normal BC patients. Thirty-two patients (47.0%) had single nucleotide variants (SNV), and 13 (19.1%) patients had TP53 mutations (TP53mut). SNV (P = 0.033) was related to tumor stage, and TP53mut was related to metastases (P = 0.016) and distant metastases (P = 0.006). In multivariate logistic analysis, cfDNA concentration was associated with metastases (OR = 3.404, 95% CI: 1.074-10.788, P = 0.037) and distant metastases (OR = 13.750, 95% CI: 1.473-128.358, P = 0.021). Cases with high cfDNA levels (>15.6 ng/ml), SNV, and TP53mut showed worse DFS compared with patients with low cfDNA levels (P < 0.001), without SNV (P = 0.002) and with TP53 wildtype (P < 0.001), respectively. In the multivariate Cox proportional hazard model, cfDNA concentration was an independent predictor of poor survival (HR = 5.786, 95% CI: 1.101-30.407, P = 0.038). Conclusions Assessment of cfDNA concentration, CNV, SNV, and TP53mut could be useful in predicting prognosis for CA15-3 normal BC patients. The cfDNA concentration was an independent predictor prognostic factor in CA15-3 normal BC patients.
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Shaban S, Al‑Rahim A, Suleiman A. ALU repeat as potential molecular marker in the detection and prognosis of different cancer types: A systematic review. Mol Clin Oncol 2022; 16:86. [PMID: 35251637 PMCID: PMC8892463 DOI: 10.3892/mco.2022.2519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/13/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer is a major health issue worldwide. cfDNA integrity has been reported as a potential diagnostic molecular marker for different types of cancer, identifying the importance of liquid biopsy. The aim of this review was to evaluate the prognostic and diagnostic performance of Arthrobacter luteus (ALU) repeat in tumor. Following a thorough review of the literature published from January, 2000 to September 2021, 36 studies were included. All of the study descriptions were analyzed. According to several studies, there were increased concentrations of ALU repetitive elements in cancer patients, while these concentrations were decreased in control, benign, different cancer stage, and other diseases. The total ALU (115 and 247) sequence levels are potential biomarkers for the purpose of investigations and cancer prognosis.
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Affiliation(s)
- Semaa Shaban
- Department of Biology, College of Sciences, Tikrit University, Tikrit, Saladin 34001, Iraq
| | - Aya Al‑Rahim
- Department of Molecular and Medical Biotechnology, College of Biotechnology, Al‑Nahrain University, Baghdad 64074, Iraq
| | - Ahmed Suleiman
- Department of Biotechnology, Science College, University of Anbar, Ramadi, Anbar 46006, Iraq
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Lamminaho M, Kujala J, Peltonen H, Tengström M, Kosma VM, Mannermaa A. High Cell-Free DNA Integrity Is Associated with Poor Breast Cancer Survival. Cancers (Basel) 2021; 13:cancers13184679. [PMID: 34572906 PMCID: PMC8467852 DOI: 10.3390/cancers13184679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 01/16/2023] Open
Abstract
Simple Summary A recent point of focus in breast cancer (BC) research has been the utilization of cell-free DNA and its concentration (cfDConc) and integrity (cfDI) as potential biomarkers. Though the association of cfDConc and BC survival is already recognized, studies on the prognostic value of cfDI have had contradictory results. The aim of this study was to investigate the prognostic potential of cfDConc and cfDI in Eastern Finnish BC cases with a non-metastatic disease. While the prognostic value of cfDConc remained non-significant in our analyses, high cfDI was an independent prognostic factor for poor overall survival (OS) and breast cancer-specific survival (BCSS). Inclusion of cfDI in the multivariate logistic regression model improved the predictive performance of the model, thus suggesting that the combined use of traditional tumor features and liquid biopsy could help to discriminate BC patients with poor OS and BCSS more accurately at the time of diagnosis. Abstract Background: A recent point of focus in breast cancer (BC) research has been the utilization of cell-free DNA (cfDNA) and its concentration (cfDConc) and integrity (cfDI) as potential biomarkers. Though the association of cfDConc and poor survival is already recognized, studies on the prognostic value of cfDI have had contradictory results. Here, we provide further evidence to support the use of cfDI as a potential biomarker. Methods: We selected 204 Eastern Finnish BC cases with non-metastatic disease and isolated cfDNA from the serum collected at the time of diagnosis before any treatment was given. The cfDConc and cfDI were measured with a fluorometer and electrophoresis and analyzed with 25 years of survival data. Results: High cfDConc was not an independent prognostic factor in our analyses while high cfDI was found to be an independent prognostic factor for poor OS (p = 0.020, hazard ratio (HR) = 1.57, 95% confidence interval (CI) 1.07–2.29, Cox) and BCSS (p = 0.006, HR = 1.93, 95% CI 1.21–3.08)). Inclusion of cfDI in the multivariate logistic regression model improved the predictive performance. Conclusions: Our results show high cfDI is an independent prognostic factor for poor OS and BCSS and improves the predictive performance of logistic regression models, thus supporting its prognostic potential.
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Affiliation(s)
- Maria Lamminaho
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland; (M.L.); (J.K.); (H.P.); (V.-M.K.)
| | - Jouni Kujala
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland; (M.L.); (J.K.); (H.P.); (V.-M.K.)
| | - Hanna Peltonen
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland; (M.L.); (J.K.); (H.P.); (V.-M.K.)
| | - Maria Tengström
- Cancer Center, Kuopio University Hospital, FI-70029 Kuopio, Finland;
| | - Veli-Matti Kosma
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland; (M.L.); (J.K.); (H.P.); (V.-M.K.)
- Department of Clinical Pathology, Kuopio University Hospital, FI-70029 Kuopio, Finland
- Multidisciplinary Cancer Research Community (RC Cancer), University of Eastern Finland, FI-70211 Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, FI-70029 Kuopio, Finland
| | - Arto Mannermaa
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland; (M.L.); (J.K.); (H.P.); (V.-M.K.)
- Multidisciplinary Cancer Research Community (RC Cancer), University of Eastern Finland, FI-70211 Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, FI-70029 Kuopio, Finland
- Correspondence:
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21
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Barcenas CH, Song J, Murthy RK, Raghavendra AS, Li Y, Hsu L, Carlson RW, Tripathy D, Hortobagyi GN. Prognostic Model for De Novo and Recurrent Metastatic Breast Cancer. JCO Clin Cancer Inform 2021; 5:789-804. [PMID: 34351787 PMCID: PMC8807018 DOI: 10.1200/cci.21.00020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Metastatic breast cancer (MBC) has a heterogeneous clinical course. We sought to develop a prognostic model for overall survival (OS) that incorporated contemporary tumor and clinical factors for estimating individual prognosis. METHODS We identified patients with MBC from our institution diagnosed between 1998 and 2017. We developed OS prognostic models by Cox regression using demographic, tumor, and treatment variables. We assessed model predictive accuracy and estimated annual OS probabilities. We evaluated model discrimination and prediction calibration using an external validation data set from the National Comprehensive Cancer Network. RESULTS We identified 10,655 patients. A model using age at diagnosis, race or ethnicity, hormone receptor and human epidermal growth factor receptor 2 subtype, de novo versus recurrent MBC categorized by metastasis-free interval, Karnofsky performance status, organ involvement, frontline biotherapy, frontline hormone therapy, and the interaction between variables significantly improved predictive accuracy (C-index, 0.731; 95% CI, 0.724 to 0.739) compared with a model with only hormone receptor and human epidermal growth factor receptor 2 status (C-index, 0.617; 95% CI, 0.609 to 0.626). The extended Cox regression model consisting of six independent models, for < 3, 3-14, 14-20, 20-33, 33-61, and ≥ 61 months, estimated up to 5 years of annual OS probabilities. The selected multifactor model had good discriminative ability but suboptimal calibration in the group of 2,334 National Comprehensive Cancer Network patients. A recalibration model that replaced the baseline survival function with the average of those from the training and validation data improved predictions across both data sets. CONCLUSION We have generated and validated a robust prognostic OS model for MBC. This model can be used in clinical decision making and stratification in clinical trials.
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Affiliation(s)
- Carlos H Barcenas
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Juhee Song
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rashmi K Murthy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Akshara S Raghavendra
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yisheng Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Limin Hsu
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Robert W Carlson
- National Comprehensive Cancer Network (NCCN), Plymouth Meeting, PA.,Division of Medical Oncology, Department of Medicine, Stanford University Medical Center, Stanford, CA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gabriel N Hortobagyi
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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Shen Z, Chen C, Sun J, Huang J, Liu S. The status of WIF1 methylation in cell-free DNA is associated with the insusceptibility for gefitinib in the treatment of lung cancer. J Cancer Res Clin Oncol 2021; 147:2239-2248. [PMID: 34037837 DOI: 10.1007/s00432-021-03640-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/10/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Targeted cancer therapy has shed light on the treatment of tumor, especially for patients with non-small cell lung cancer. However, only a limited portion of NSCLC patients carrying specific mutations showed an ideal drug response. In addition, DNA methylation status showed a great potential for cancer detection and prognosis prediction. METHODS Bisulfite sequencing was performed to analyze the DNA methylation of WIF1 promoter in cfDNA and tumor tissue samples collected from NSCLC patients. PFS and OS analyses were carried out to evaluate the prognosis of gefitinib treatment in patients with differential levels of WIF1 DNA methylation. Quantitative real-time PCR was used to analyze the expression of WIF1 mRNA, while immunohistochemistry was performed to assess the expression of WIF1 protein. Furthermore, ELISA was carried out to evaluate the WIF1 activity in plasma. RESULTS The DNA methylation level of WIF1 promoter was lower in the cfDNA of NSCLC patients with a complete or partial response to gefitinib, and NSCLC patients with hypomethylated WIF1 showed better PFS and OS. The DNA methylation of WIF1 promoter in the resected tumor tissues was consistent with WIF1 DNA methylation in cfDNA, indicating that cfDNA was mainly derived from lung cancer tissues. As a result, the expression of WIF1 in tissue samples and the WIF1 activity in plasma was inhibited in patients with hypermethylated WIF1. Moreover, the cell viability of gefitinib-resistant cells was decreased by the suppressed WIF1 methylation in vitro. And the expression level of WIF1 mRNA was higher in gefitinib-resistant cells overexpressing ALKBH5, a known suppressor of WIF1 methylation. CONCLUSION In summary, the findings of this study demonstrated that the level of WIF1 methylation in cfDNA was associated with the insusceptibility of gefitinib in the treatment of lung cancer.
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Affiliation(s)
- Zhijun Shen
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.,Department of Clinical Laboratory, Hubei No. 3 People's Hospital of Jianghan University, No. 26 Zhongshan Avenue, Wuhan, 430033, Hubei, China
| | - Chen Chen
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Jianhai Sun
- Department of Oncology, Hubei No. 3 People's Hospital of Jianghan University, Wuhan, 430033, Hubei, China
| | - Jingsong Huang
- Department of Transfusion, School of Medicine, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen, 361101, Fujian, China.
| | - Shiguo Liu
- Department of Clinical Laboratory, Hubei No. 3 People's Hospital of Jianghan University, No. 26 Zhongshan Avenue, Wuhan, 430033, Hubei, China.
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Poulet G, Garlan F, Garrigou S, Zonta E, Benhaim L, Carrillon MJ, Didelot A, Le Corre D, Mulot C, Nizard P, Ginot F, Boutonnet-Rodat A, Blons H, Bachet JB, Taïeb J, Zaanan A, Geromel V, Pellegrina L, Laurent-Puig P, Wang-Renault SF, Taly V. Characterization of Plasma Cell-Free DNA Integrity Using Droplet-Based Digital PCR: Toward the Development of Circulating Tumor DNA-Dedicated Assays. Front Oncol 2021; 11:639675. [PMID: 34094923 PMCID: PMC8174096 DOI: 10.3389/fonc.2021.639675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/16/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Cellular-cell free-DNA (ccfDNA) is being explored as a diagnostic and prognostic tool for various diseases including cancer. Beyond the evaluation of the ccfDNA mutational status, its fragmentation has been investigated as a potential cancer biomarker in several studies. However, probably due to a lack of standardized procedures dedicated to preanalytical and analytical processing of plasma samples, contradictory results have been published. Methods: ddPCR assays allowing the detection of KRAS wild-type and mutated sequences (KRAS p.G12V, pG12D, and pG13D) were designed to target different fragments sizes. Once validated on fragmented and non-fragmented DNA extracted from cancer cell lines, these assays were used to investigate the influence of the extraction methods on the non-mutated and mutated ccfDNA integrity reflected by the DNA integrity index (DII). The DII was then analyzed in two prospective cohorts of metastatic colorectal cancer patients (RASANC study n = 34; PLACOL study n = 12) and healthy subjects (n = 49). Results and Discussion: Our results demonstrate that ccfDNA is highly fragmented in mCRC patients compared with healthy individuals. These results strongly suggest that the characterization of ccfDNA integrity hold great promise toward the development of a universal biomarker for the follow-up of mCRC patients. Furthermore, they support the importance of standardization of sample handling and processing in such analysis.
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Affiliation(s)
- Geoffroy Poulet
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Eurofins-Biomnis, Specialized Medical Biology Laboratory, Lyon, France
| | - Fanny Garlan
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Sonia Garrigou
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Eleonora Zonta
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Leonor Benhaim
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Visceral and Surgical Oncology, Gustave Roussy, Villejuif, France
| | - Marie-Jennifer Carrillon
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Audrey Didelot
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Delphine Le Corre
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,CIC-EC4 URC, HEGP, Hôpitaux Universitaires Paris Ouest AP-HP, Paris, France
| | - Philippe Nizard
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | | | | | - Helene Blons
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Jean-Baptiste Bachet
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Sorbonne Universités, UPMC Université, Paris, France.,Department of Hepato-gastroenterology, Groupe Hospitalier Pitié Salpêtrière, Paris, France.,AGEO (Association des Gastroentérologues Oncologues), Paris, France
| | - Julien Taïeb
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France.,AGEO (Association des Gastroentérologues Oncologues), Paris, France
| | - Aziz Zaanan
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Vanna Geromel
- Eurofins-Biomnis, Specialized Medical Biology Laboratory, Lyon, France
| | | | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Shu-Fang Wang-Renault
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
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Sim SH, Yang HN, Jeon SY, Lee KS, Park IH. Mutation analysis using cell-free DNA for endocrine therapy in patients with HR+ metastatic breast cancer. Sci Rep 2021; 11:5566. [PMID: 33692409 PMCID: PMC7946916 DOI: 10.1038/s41598-021-84999-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/24/2021] [Indexed: 11/09/2022] Open
Abstract
We prospectively evaluated the utility of ESR1 and PIK3CA mutation analysis with cell-free DNA (cfDNA) using droplet digital PCR (ddPCR) for the efficacy of endocrine therapy (ET) in hormone receptive positive (HR+) metastatic breast cancer (MBC) patients. CfDNA was analyzed just before the start of ET for MBC. E380Q, Y537N, Y537S, and D538G were assessed for ESR1 mutations and H1047R, E545K, and E542K were assessed for PIK3CA mutations. A total of 75 patients were enrolled. Of those, 31 (41.3%) received letrozole with palbociclib, and 28 (37.3%) received exemestane and everolimus (EverX). ESR1 mutations were found in 36 (48.0%) patients, of which 16 (21.3%) had more than one variant. Seventeen (23.6%) patients had one PIK3CA mutation and 8 (11.1%) had two. In the total population, time to progression of the first ET after enrollment (TTP1) decreased significantly as the number of ESR1 mutations increased (p < 0.001). PIK3CA mutations were also significantly associated with shorter TTP1 (median TTP1: 16.2 months vs. 10.9 months, p = 0.03). In contrast, PIK3CA mutations were significantly associated with longer TTP in patients receiving EverX treatment (median TTP of EverX: 15.9 months vs. 5.2 months, p = 0.01) and remained a significant factor in multivariable analysis for TTP of EverX in this subgroup (hazard ratio = 0.2, 95% CI = 0.1- 0.8, p = 0.03). ESR1 and PIK3CA mutations in cfDNA were associated with clinical efficacies of ET in HR+ MBC patients.
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Affiliation(s)
- Sung Hoon Sim
- Translational Cancer Research Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea.,Center for Breast Cancer, National Cancer Center Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Han Na Yang
- Translational Cancer Research Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Su Yeon Jeon
- Translational Cancer Research Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Keun Seok Lee
- Center for Breast Cancer, National Cancer Center Hospital, National Cancer Center, Goyang, Republic of Korea
| | - In Hae Park
- Translational Cancer Research Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea. .,Center for Breast Cancer, National Cancer Center Hospital, National Cancer Center, Goyang, Republic of Korea. .,Division of Hematology/Oncology, Department of Internal Medicine, Korea University College of Medicine, Guro Hospital, 148, Gurodongro, Gurogu, Seoul, 08308, Republic of Korea.
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25
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Wang YF, Wang XJ, Lu Z, Liu SR, Jiang Y, Wan XQ, Cheng CC, Shi LH, Wang LH, Ding Y. Overexpression of Stat3 increases circulating cfDNA in breast cancer. Breast Cancer Res Treat 2021; 187:69-80. [PMID: 33630196 DOI: 10.1007/s10549-021-06142-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE Current studies on circulating cell-free DNA (cfDNA) have been focusing on its potential as biomarkers in liquid biopsy by detecting its content or genetic and epigenetic changes for the evaluation of tumor burden and therapeutic efficacy. However, the regulatory mechanism of cfDNA release remains unclear. Stat3 has been documented as an oncogene for the development and metastasis of breast cancer cells. In this study, we investigated whether Stat3 affects the release of cfDNA into blood and its association with the number of circulating tumor cells (CTCs). METHODS The cfDNA level in plasma of patients with breast cancer and healthy volunteers were determined by quantitative real-time PCR. Three mouse breast cancer models with different Stat3 expression were generated and used to established three breast cancer orthotopic animal models to examine the effect of Stat3 on cfDNA release in vivo. Stat3 mediated Epithelial-mesenchymal phenotype transition of CTCs was determined by immunofluorescence assay and Western blot assay. RESULTS The data showed that Stat3 increased circulating cfDNA, which is correlated with the increased volume of primary tumors and number of CTCs, accompanied with the dynamic EMT changes regulated by Snail induction. Furthermore, the high level of total circulating cfDNA and Stat3-cfDNA in patients with breast cancer were detected by quantitative real-time PCR using GAPDH and Stat3 primers. CONCLUSION Our results suggested that Stat3 increases the circulating cfDNA and CTCs in breast cancer.
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Affiliation(s)
- Yi-Fei Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xue-Jian Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Zhong Lu
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Shu-Rong Liu
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Yu Jiang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xiao-Qing Wan
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China
| | - Cong-Cong Cheng
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Li-Hong Shi
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Li-Hua Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Yi Ding
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China. .,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China.
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Yan YY, Guo QR, Wang FH, Adhikari R, Zhu ZY, Zhang HY, Zhou WM, Yu H, Li JQ, Zhang JY. Cell-Free DNA: Hope and Potential Application in Cancer. Front Cell Dev Biol 2021; 9:639233. [PMID: 33693004 PMCID: PMC7938321 DOI: 10.3389/fcell.2021.639233] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Cell-free DNA (cfDNA) is easily accessible in peripheral blood and can be used as biomarkers for cancer diagnostics, prognostics, and therapeutics. The applications of cfDNA in various areas of cancer management are attracting attention. In this review article, we discuss the potential relevance of using cfDNA analysis in clinical oncology, particularly in cancer screening, early diagnosis, therapeutic evaluation, monitoring disease progression; and determining disease prognosis.
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Affiliation(s)
- Yan-Yan Yan
- School of Medicine, Shanxi Datong University, Datong, China.,Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qiao-Ru Guo
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Feng-Hua Wang
- Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Rameshwar Adhikari
- Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur, Nepal
| | - Zhuang-Yan Zhu
- School of Medicine, Shanxi Datong University, Datong, China
| | - Hai-Yan Zhang
- School of Medicine, Shanxi Datong University, Datong, China
| | - Wen-Min Zhou
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hua Yu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, Avenida da Universidade, Taipa, China
| | - Jing-Quan Li
- The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Jian-Ye Zhang
- School of Medicine, Shanxi Datong University, Datong, China.,Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,The First Affiliated Hospital, Hainan Medical University, Haikou, China
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Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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van Poppelen NM, de Bruyn DP, Bicer T, Verdijk R, Naus N, Mensink H, Paridaens D, de Klein A, Brosens E, Kiliҫ E. Genetics of Ocular Melanoma: Insights into Genetics, Inheritance and Testing. Int J Mol Sci 2020; 22:E336. [PMID: 33396957 PMCID: PMC7795687 DOI: 10.3390/ijms22010336] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/04/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Ocular melanoma consists of posterior uveal melanoma, iris melanoma and conjunctival melanoma. These malignancies derive from melanocytes in the uveal tract or conjunctiva. The genetic profiles of these different entities differ from each other. In uveal melanoma, GNAQ and GNA11 gene mutations are frequently found and prognosis is based on mutation status of BAP1, SF3B1 and EIF1AX genes. Iris melanoma, also originating from the uvea, has similarities to the genetic makeups of both posterior uveal melanoma (UM) and conjunctival melanoma since mutations in GNAQ and GNA11 are less common and genes involved in conjunctival melanoma such as BRAF have been described. The genetic spectrum of conjunctival melanoma, however, includes frequent mutations in the BRAF, NRAS and TERT promoter genes, which are found in cutaneous melanoma as well. The BRAF status of the tumor is not correlated to prognosis, whereas the TERT promoter gene mutations are. Clinical presentation, histopathological characteristics and copy number alterations are associated with survival in ocular melanoma. Tissue material is needed to classify ocular melanoma in the different subgroups, which creates a need for the use of noninvasive techniques to prognosticate patients who underwent eye preserving treatment.
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Affiliation(s)
- Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Daniël P. de Bruyn
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Tolga Bicer
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Ophthalmology, University of Health Sciences Diskapi Training and Research Hospital, Ankara 06330, Turkey
| | - Rob Verdijk
- Department of Pathology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands;
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Nicole Naus
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
| | - Hanneke Mensink
- Department of Ophthalmic Oncology, The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Ophthalmic Oncology, The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Emine Kiliҫ
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
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Clatot F, Perdrix A, Beaussire L, Lequesne J, Lévy C, Emile G, Bubenheim M, Lacaille S, Calbrix C, Augusto L, Guillemet C, Alexandru C, Fontanilles M, Sefrioui D, Burel L, Guénot S, Richard D, Sarafan-Vasseur N, Di Fiore F. Risk of early progression according to circulating ESR1 mutation, CA-15.3 and cfDNA increases under first-line anti-aromatase treatment in metastatic breast cancer. Breast Cancer Res 2020; 22:56. [PMID: 32466779 PMCID: PMC7254698 DOI: 10.1186/s13058-020-01290-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Background Endocrine therapy is recommended as a first-line treatment for hormone receptor-positive metastatic breast cancer (HR+MBC) patients. No biomarker has been validated to predict tumor progression in that setting. We aimed to prospectively compare the risk of early progression according to circulating ESR1 mutations, CA-15.3, and circulating cell-free DNA in MBC patients treated with a first-line aromatase inhibitor (AI). Methods Patients with MBC treated with a first-line AI were prospectively included. Circulating biomarker assessment was performed every 3 months. The primary objective was to determine the risk of progression or death at the next follow-up visit (after 3 months) in case of circulating ESR1 mutation detection among patients treated with a first-line AI for HR+MBC. Results Overall, 103 patients were included, and 70 (68%) had progressive disease (PD). Circulating ESR1 mutations were detected in 22/70 patients with PD and in 0/33 patients without progression (p < 0.001). Among the ESR1-mutated patients, 18/22 had a detectable mutation prior to progression, with a median delay of 110 days from first detection to PD. The detection of circulating ESR1 mutations was associated with a 4.9-fold (95% CI 3.0–8.0) increase in the risk of PD at 3 months. Using a threshold value of 25% or 100%, a CA-15.3 increase was also correlated with progression (p < 0.001 and p = 0.003, respectively). In contrast to ESR1, the CA-15.3 increase occurred concomitantly with PD in most cases, in 27/47 (57%) with a 25% threshold and in 21/25 (84%) with a 100% threshold. Using a threshold value of either 25% or 100%, cfDNA increase was not correlated with progression. Conclusion The emergence of circulating ESR1 mutations is associated with a 4.9-fold increase in the risk of early PD during AI treatment in HR+MBC. Our results also highlighted that tracking circulating ESR1 mutations is more relevant than tracking CA-15.3 or cfDNA increase to predict progression in this setting. Trial registration ClinicalTrials.gov, NCT02473120. Registered 16 June 2015—retrospectively registered after one inclusion (first inclusion 1 June 2015)
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Affiliation(s)
- Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France. .,Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
| | - Anne Perdrix
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Biopathology, Centre Henri Becquerel, Rouen, France
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Christelle Lévy
- Institut Normand du Sein, Centre François Baclesse, Caen, France
| | - George Emile
- Institut Normand du Sein, Centre François Baclesse, Caen, France
| | - Michael Bubenheim
- Department of Clinical Research and Innovation, Rouen University Hospital, Rouen, France
| | - Sigrid Lacaille
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Céline Calbrix
- Department of Biopathology, Centre Henri Becquerel, Rouen, France
| | - Laetitia Augusto
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Cécile Guillemet
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | | | - Maxime Fontanilles
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France.,Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Lucie Burel
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Sabine Guénot
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Doriane Richard
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Frédéric Di Fiore
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France.,Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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Delmonico L, Alves G, Bines J. Cell free DNA biology and its involvement in breast carcinogenesis. Adv Clin Chem 2020; 97:171-223. [PMID: 32448434 DOI: 10.1016/bs.acc.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid biopsy represents a procedure for minimally invasive analysis of non-solid tissue, blood and other body fluids. It comprises a set of analytes that includes circulating tumor cells (CTCs) and circulating free DNA (cfDNA), RNA, long noncoding RNA (lncRNA) and micro RNA (miRNA), as well as extracellular vesicles. These novel analytes represent an alternative tool to complement diagnosis and monitor and predict response to treatment of the tumoral process and may be used for other disease processes such viral and parasitic infection. This review focuses on the biologic and molecular characteristics of cfDNA in general and the molecular changes (mutational and epigenetic) proven useful in oncologic practice for diagnosis, monitoring and treatment of breast cancer specifically.
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Affiliation(s)
- Lucas Delmonico
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Gilda Alves
- Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - José Bines
- Instituto Nacional de Câncer (INCA-HCIII), Rio de Janeiro, Brazil
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31
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Liao H, Li H. Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer. Cancer Manag Res 2020; 12:3547-3560. [PMID: 32547192 PMCID: PMC7244344 DOI: 10.2147/cmar.s249041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) represents the most commonly diagnosed cancer among females worldwide. Although targeted therapy has greatly improved the efficacy of treating BC, a large proportion of BC patients eventually develop recurrence or metastasis. Traditional invasive tumor tissue biopsy is short of comprehensiveness in tumor assessment due to heterogeneity. Liquid biopsy, an attractive non-invasive approach mainly including circulating tumor cell and circulating tumor DNA (ctDNA), has been widely utilized in a variety of cancers with the advances of sequencing technologies in recent years. The ctDNA that is found circulating in body fluids refers to DNA released from tumor cells and has shown clinical utility in metastatic breast cancer (MBC). With the results of genomic variants detection, ctDNA could be used to predict clinical outcomes, monitor disease progression, and guide treatment for patients with MBC. Moreover, the drug resistance problem may be addressed by ctDNA detection. In this review, we summarized the technological developments and clinical applications of ctDNA in MBC.
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Affiliation(s)
- Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
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32
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Plasma cell-free DNA is a prognostic biomarker for survival in patients with aggressive non-Hodgkin lymphomas. Ann Hematol 2020; 99:1293-1302. [DOI: 10.1007/s00277-020-04008-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/19/2020] [Indexed: 12/17/2022]
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33
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Ren S, Ren XD, Guo LF, Qu XM, Shang MY, Dai XT, Huang Q. Urine cell-free DNA as a promising biomarker for early detection of non-small cell lung cancer. J Clin Lab Anal 2020; 34:e23321. [PMID: 32281142 PMCID: PMC7439414 DOI: 10.1002/jcla.23321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/26/2022] Open
Abstract
Background While blood‐derived cell‐free DNA has been shown to be a candidate biomarker able to provide diagnostic and prognostic insight in cancer patients, little is known regarding the potential application of urine cell‐free DNA (ucfDNA) in diagnosis of cancer. Thus, the aim of this study was to investigate ucfDNA concentration and integrity index as potential biomarkers for early detection of non‐small‐cell lung cancer (NSCLC). Methods Urine samples were collected from 35 healthy controls and 55 NSCLC patients at various tumor node metastasis (TNM) stages. Two long interspersed nuclear element 1 (LINE1) fragments (LINE1‐97 and 266 bp) were quantified via quantitative real‐time PCR (qPCR). DNA integrity index was calculated as the ratio of LINE1‐266/LINE‐97. Results LINE1 fragments concentrations of ucfDNA (LINE1‐97, 266 bp) were significantly higher in NSCLC patients with stage III/IV than in stage I/II and in healthy controls. The receiver operating characteristic (ROC) curves for discriminating patients with stage III/IV from healthy controls had areas under the curves (AUC) of 0.84 and 0.886, respectively. Moreover, ucfDNA integrity LINE1‐266/97 was significantly higher in patients with stage III/IV than in stage I/II and in healthy controls. The AUC of ROC curve for discriminating patients with stage III/IV from healthy controls was 0.800. Furthermore, LINE1‐266 fragment concentration was significantly higher in lymph node metastasis (LNM)‐positive patients relative to LNM‐negative patients. The ROC curve for discriminating LNM‐positive from LNM‐negative patients had an AUC of 0.822. Conclusion UcfDNA could serve as a promising biomarker for early detection of NSCLC.
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Affiliation(s)
- Sai Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Li-Fang Guo
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xue-Mei Qu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiao-Tian Dai
- Department of Pulmonology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
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Tuchalska-Czuroń J, Lenart J, Augustyniak J, Durlik M. Clinical value of tissue DNA integrity index in pancreatic cancer. Surgeon 2020; 18:269-279. [PMID: 32156475 DOI: 10.1016/j.surge.2019.10.008] [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: 06/25/2019] [Revised: 10/08/2019] [Accepted: 10/28/2019] [Indexed: 10/24/2022]
Abstract
BACKGROUND DNA integrity index as a blood biomarker is associated with the prognosis of cancer patients. AIMS The primary goal of the study was to examine tissue DNA integrity index (DII) in a group of pancreatic cancer (PC) tumor tissues and control adjacent pancreatic tissues. We also aimed to test the relationship between the tumor tissue DII and the clinicopathological parameters and the overall survival. METHODS In the prospective study, DII was calculated using: the Alu 247/115 ratio, the LINE1 300/79 ratio and the average of the above values, based on the data obtained by real-time PCR. The tumors samples (n = 42) originated from the patients with pathologically confirmed pancreatic ductal adenocarcinoma and the control adjacent pancreatic tissue specimens (n = 32) were received from surgical margins. RESULTS Specimens from the tumors pathologically marked as R1 (microscopic residual tumor) had a significantly higher LINE1 300/79 ratio values than specimens from adjacent normal pancreatic tissue (P<0.05). ROC curve analysis revealed that LINE1 300/79 ratio is a good parameter to distinguish between R0 and R1 tumors (AUC = 0.703, P<0.05). CONCLUSIONS This is the first study exploring the tissue DNA integrity index (DII) in pancreatic cancer. LINE1 DII can be used as auxiliary parameter for objective evaluation of margin status.
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Affiliation(s)
- Julia Tuchalska-Czuroń
- Department of Surgical Research and Transplantology, Medical Research Centre Polish Academy of Sciences, Warsaw, Poland; Diagnostic Radiology Department, Central Clinical Hospital of the MSWiA in Warsaw, Poland.
| | - Jacek Lenart
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Justyna Augustyniak
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Durlik
- Department of Surgical Research and Transplantology, Medical Research Centre Polish Academy of Sciences, Warsaw, Poland; Department of Gastroenterological Surgery and Transplantation Medicine, Centre of Postgraduate Medical Education, Warsaw, Poland; Clinical Department of Gastroenterological Surgery and Transplantation Medicine, Central Clinical Hospital of the MSWiA in Warsaw, Poland
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35
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Wu X, Li J, Gassa A, Buchner D, Alakus H, Dong Q, Ren N, Liu M, Odenthal M, Stippel D, Bruns C, Zhao Y, Wahba R. Circulating tumor DNA as an emerging liquid biopsy biomarker for early diagnosis and therapeutic monitoring in hepatocellular carcinoma. Int J Biol Sci 2020; 16:1551-1562. [PMID: 32226301 PMCID: PMC7097921 DOI: 10.7150/ijbs.44024] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023] Open
Abstract
As one of the most common malignant tumors worldwide, hepatocellular carcinoma (HCC) is known for its poor prognosis due to diagnosis only in advanced stages. Nearly 50% of the patients with the first diagnosis of HCC die within a year. Currently, the advancements in the integration of omics information have begun to transform the clinical management of cancer patients. Molecular profiling for HCC patients is in general obtained from resected tumor materials or biopsies. However, the resected tumor tissue is limited and can only be obtained through surgery, so that dynamic monitoring of patients cannot be performed. Compared to invasive procedures, circulating tumor DNA (ctDNA) has been proposed as an alternative source to perform molecular profiling of tumor DNA in cancer patients. The detection of abnormal forms of circulating cell-free DNA (cfDNA) that originate from cancer cells (ctDNA) provides a novel tool for cancer detection and disease monitoring. This may also be an opportunity to optimize the early diagnosis of HCC. In this review, we summarized the updated methods, materials, storage of sampling, detection techniques for ctDNA and the comparison of the applications among different biomarkers in HCC patients. In particular, we analyzed ctDNA studies dealing with copy number variations, gene integrity, mutations (RAS, TERT, CTNNB1, TP53 and so on), DNA methylation alterations (DBX2, THY1, TGR5 and so on) for the potential utility of ctDNA in the diagnosis and management of HCC. The biological functions and correlated signaling pathways of ctDNA associated genes (including MAPK/RAS pathway, p53 signaling pathway and Wnt-β catenin pathway) are also discussed and highlighted. Thus, exploration of ctDNA/cfDNA as potential biomarkers may provide a great opportunity in future liquid biopsy applications for HCC.
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Affiliation(s)
- Xiaolin Wu
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Jiahui Li
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Asmae Gassa
- Department of Cardiothoracic Surgery, Heart Center, University Hospital of Cologne, Germany, Kerpener Straße 62, 5.937 Cologne, Germany
| | - Denise Buchner
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Qiongzhu Dong
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R. China
| | - Ning Ren
- Liver Cancer Institute & Zhongshan Hospital; Department of Surgery, Institute of Fudan-Minhang Academic Health System, Minhang Branch, Zhongshan Hospital, Fudan University, 200032, Shanghai, P.R. China
| | - Ming Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University; Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, 510095, Guangzhou, P.R. China
| | - Margarete Odenthal
- Institute of Pathology, University Hospital of Cologne, 50937, Cologne, Germany
| | - Dirk Stippel
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Yue Zhao
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany
- Department of General, Visceral und Vascular Surgery, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Roger Wahba
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937, Cologne, Germany
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Abstract
In only few years, circulating tumor DNA (ctDNA) in breast cancer has moved from purely fundamental research to nearby daily use for treatment selection and drug-resistance assessment. Indeed, technical advances and widespread use of next-generation sequencing or digital PCR allowed for detection of very low amount of tumor DNA in bloodstream. The use of ctDNA as liquid biopsy able either to monitor tumor burden under treatment or to overcome tumor heterogeneity and identify potential targetable drivers. Time has come to define how ctDNA can be implemented for early or metastatic breast cancer management. Data from retrospective analyses of prospective trials have recently highlighted the potential advantages but also the limitations of ctDNA, in particular for patients under endocrine therapy.
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Affiliation(s)
- Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, 1 rue d'Amiens, 76038, Rouen Cedex 1, France.
- Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France.
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Progress in quantitative technique of circulating cell free DNA and its role in cancer diagnosis and prognosis. Cancer Genet 2019; 239:75-84. [PMID: 31639530 DOI: 10.1016/j.cancergen.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/24/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023]
Abstract
The interest in the potential application value of circulating cell free DNA (ccfDNA) has increased rapidly in recent years, as numerous researchers have demonstrated that the change of its level in the blood is associated with many diseases. Its potential role in cancer management is of particular concern. In comparison with traditional invasive tissue biopsy, quantitative analysis of ccfDNA level for the detection of cancer is advantageous due to the non-invasiveness of blood collection. Moreover, its clinical significance in prognosis prediction and dynamic monitoring of disease progression in cancer patients is equally worthy of attention. At the same time, quantitative detection of ccfDNA is being improved to pursue higher sensitivity due to its low concentration in the blood sample. In this review, we will summarize the progress in quantitative technology of ccfDNA and describe the possible relationship between ccfDNA level and cancer diagnosis and prognosis prediction.
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Basal-like Breast Cancers: From Pathology to Biology and Back Again. Stem Cell Reports 2019; 10:1676-1686. [PMID: 29874626 PMCID: PMC6117459 DOI: 10.1016/j.stemcr.2018.04.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/17/2022] Open
Abstract
Human breast cancers referred to as "basal-like" are of interest because they lack effective therapies and their biology is poorly understood. The term basal-like derives from studies demonstrating tumor gene expression profiles that include some transcripts characteristic of the basal cells of the normal adult human mammary gland and others associated with a subset of normal luminal cells. Elucidating the mechanisms responsible for the profiles of basal-like tumors is an active area of investigation. More refined molecular analysis of patients' samples and genetic strategies to produce breast cancers de novo from defined populations of normal mouse mammary cells have served as complementary approaches to identify relevant pathway alterations. However, both also have limitations. Here, we review some of the underlying reasons, including the unifying concept that some normal luminal cells have both luminal and basal features, as well as some emerging new avenues of investigation.
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Cervena K, Vodicka P, Vymetalkova V. Diagnostic and prognostic impact of cell-free DNA in human cancers: Systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:100-129. [DOI: 10.1016/j.mrrev.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
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40
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Viller Tuxen I, Barlebo Ahlborn L, Mau-Soerensen M, Staal Rohrberg K, Cilius Nielsen F, Oestrup O, Westmose Yde C, Richter Vogelius I, Lassen U. Plasma total cell-free DNA is a prognostic biomarker of overall survival in metastatic solid tumour patients. Br J Cancer 2019; 121:125-130. [PMID: 31186525 PMCID: PMC6738043 DOI: 10.1038/s41416-019-0491-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/09/2019] [Accepted: 05/16/2019] [Indexed: 02/06/2023] Open
Abstract
Background Selecting patients for early clinical trials is a challenging process and clinicians lack sufficient tools to predict overall survival (OS). Circulating cell-free DNA (cfDNA) has recently been shown to be a promising prognostic biomarker. The aim of this study was to investigate whether baseline cfDNA measurement could improve the prognostic information of the Royal Marsden Hospital (RMH) score. Methods Solid tumour patients referred for phase I trials were included in the Copenhagen Personalized Oncology (CoPPO) programme. Baseline characteristics were collected prospectively, including the RMH prognostic score, Eastern Cooperative Oncology Group (ECOG) performance status and concentration of cfDNA per millilitre plasma. Cox proportional hazards model was used to assess the prognostic value of baseline variables. Results Plasma cfDNA concentration was quantifiable in 302 patients out of a total of 419 included in the study period of 2 years and 5 months. The RMH score was confirmed to be associated with OS. Cell-free DNA was shown to be an independent prognostic marker of OS and improved the risk model, including RMH, performance status and age. Furthermore, both plasma cfDNA concentration and RMH score were associated with treatment allocation (p < 0.00001). Conclusion Our model based on RMH score, age, ECOG performance status and cfDNA improved prediction of OS and constitutes a clinically valuable tool when selecting patients for early clinical trials. An interactive version of the prognostic model is published on http://bit.ly/phase1survival.
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Affiliation(s)
- Ida Viller Tuxen
- The Phase I Unit, Department of Oncology, Copenhagen University, Rigshospitalet, Copenhagen, Denmark
| | - Lise Barlebo Ahlborn
- The Phase I Unit, Department of Oncology, Copenhagen University, Rigshospitalet, Copenhagen, Denmark.,Center for Genomic Medicine, Copenhagen University, Rigshospitalet, Copenhagen, Denmark
| | - Morten Mau-Soerensen
- The Phase I Unit, Department of Oncology, Copenhagen University, Rigshospitalet, Copenhagen, Denmark
| | - Kristoffer Staal Rohrberg
- The Phase I Unit, Department of Oncology, Copenhagen University, Rigshospitalet, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Copenhagen University, Rigshospitalet, Copenhagen, Denmark
| | - Olga Oestrup
- Center for Genomic Medicine, Copenhagen University, Rigshospitalet, Copenhagen, Denmark
| | | | - Ivan Richter Vogelius
- Section of Radiotherapy, Department of Oncology, Copenhagen University, Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Lassen
- The Phase I Unit, Department of Oncology, Copenhagen University, Rigshospitalet, Copenhagen, Denmark.
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Jiang Y, Zong W, Ju S, Jing R, Cui M. Promising member of the short interspersed nuclear elements ( Alu elements): mechanisms and clinical applications in human cancers. J Med Genet 2019; 56:639-645. [PMID: 30852527 DOI: 10.1136/jmedgenet-2018-105761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 12/11/2022]
Abstract
Alu elements are one of most ubiquitous repetitive sequences in human genome, which were considered as the junk DNA in the past. Alu elements have been found to be associated with human diseases including cancers via events such as amplification, insertion, recombination or RNA editing, which provide a new perspective of oncogenesis at both DNA and RNA levels. Due to the prevalent distribution, Alu elements are widely used as target molecule of liquid biopsy. Alu-based cell-free DNA shows feasible application value in tumour diagnosis, postoperative monitoring and adjuvant therapy. In this review, the special tumourigenesis mechanism of Alu elements in human cancers is discussed, and the application of Alu elements in various tumour liquid biopsy is summarised.
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Affiliation(s)
- Yun Jiang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Wei Zong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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42
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Su Y, Wang L, Wang X, Yue Z, Xing T, Zhao W, Zhao Q, Duan C, Huang C, Han Y, Qiu L, Cheng X, Liu Y, Ma X. Dynamic alterations of plasma cell free DNA in response to chemotherapy in children with neuroblastoma. Cancer Med 2019; 8:1558-1566. [PMID: 30793512 PMCID: PMC6488154 DOI: 10.1002/cam4.2045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 01/11/2019] [Accepted: 02/02/2019] [Indexed: 12/23/2022] Open
Abstract
Background To improve cure rates for neuroblastoma (NB), it is important and necessary to evaluate therapy response. Our investigation focuses on using plasma cell free DNA (cfDNA) as a biomarker to determine tumor burden and minimal residual disease (MRD) of NB patients during chemotherapy. Methods Total 58 NB patients were recruited from July 2016 to December 2017. Therapy regime and risk classification were based on COG standard and BCH‐NB‐2007 protocol. RECIST study was used to judge response to therapy at the end of fourth cycle of chemotherapy (CC4) and maintenance stage (MS) respectively. Serial quantifications of cfDNA, NSE, and LDH were examined at four stages, including newly diagnosed, second and CC4, and maintenance. Results During early chemotherapy, 65.5% of NB kids responded well. Consistently, cfDNA, NSE, and LDH levels were down‐regulated in NB patients with partial remission (PR) compared to those with stable disease (SD). In both training and predicting sets, the levels of cfDNA were significantly comparable between PR and SD only at CC4 stage. To predict the insufficient response to early chemotherapy, the optimal AUC value of cfDNA was 0.732 and 0.747 in training and predicting sets respectively, with a sensitivity of 63.2% and 80% specificity at 11.59 ng/ml and a sensitivity of 68.4% and 90% specificity at 10.35 ng/ml. At MS, responded NB patients were slightly increased up to 70%. This evaluation was confirmed by further decrease in cfDNA and NSE levels during intermediate chemotherapy in comparison with early stage. Conclusion The dynamic change of cfDNA was considered as a surrogate biomarker to evaluate tumor burden and MRD of NB during early and intermediate therapy periods.
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Affiliation(s)
- Yan Su
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lijun Wang
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company limited, Beijing, China
| | - Xisi Wang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhixia Yue
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tianyu Xing
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wen Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Qian Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chao Duan
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Cheng Huang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yi Han
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company limited, Beijing, China
| | - Lihua Qiu
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company limited, Beijing, China
| | - Xianfeng Cheng
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company limited, Beijing, China
| | - Yi Liu
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company limited, Beijing, China
| | - Xiaoli Ma
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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Qi J, Chen LY, Shen XJ, Ju SQ. Analytical Value of Cell-Free DNA Based on Alu in Psychiatric Disorders. Front Psychiatry 2019; 10:992. [PMID: 32038328 PMCID: PMC6985436 DOI: 10.3389/fpsyt.2019.00992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 11/17/2022] Open
Abstract
Psychiatric disorders impose a huge burden on individuals, families, and society. The Alu repeat sequence is a member of the short interspersed nuclear element (SINE) family of mammalian genomes, however, its expression pattern and role in psychiatric disorders is unclear. The current paper aimed at determining the concentrations of Alu in patients with schizophrenia (SZ), major depressive disorder (MDD), and alcohol-induced psychotic disorder (AIPD), and to further define the role and value of Alu as a potential biomarker in psychiatric disorders. In this work, we found that the concentration of Alu was considerably incremented in patients with SZ, and a significant difference existed between patients diagnosed with SZ and MDD or AIPD. ROC analysis also indicated that Alu was effective in the complementary diagnosis of SZ, and differentially diagnosed between SZ patients and patients with MDD or AIPD. In addition, we found a positive relationship between the Alu concentrations and interleukin-1β (IL-1β) in patients with SZ, MDD, and AIPD, and between the concentrations of Alu and interleukin-18 (IL-18) in patients with SZ. Overall, the present work indicates that Alu might be an innovative biomarker for diagnosing psychiatric disorders, and provides the basis for hypotheses about the pathophysiology of psychiatric disorders.
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Affiliation(s)
- Jing Qi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Ling-Yun Chen
- Center of Laboratory Medicine, Nantong Mental Health Center, Nantong, China
| | - Xian-Juan Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Shao-Qing Ju
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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da Silva I, da Costa Vieira R, Stella C, Loturco E, Carvalho AL, Veo C, Neto C, Silva SM, D'Amora P, Salzgeber M, Matos D, Silva CR, Oliveira JR, Rabelo I, Yamakawa P, Maciel R, Biscolla R, Chiamolera M, Fraietta R, Reis F, Mori M, Marchioni D, Carioca A, Maciel G, Tomioka R, Baracat E, Silva C, Granato C, Diaz R, Scarpellini B, Egle D, Fiegl H, Himmel I, Troi C, Nagourney R. Inborn-like errors of metabolism are determinants of breast cancer risk, clinical response and survival: a study of human biochemical individuality. Oncotarget 2018; 9:31664-31681. [PMID: 30167086 PMCID: PMC6114970 DOI: 10.18632/oncotarget.25839] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/12/2018] [Indexed: 01/16/2023] Open
Abstract
Breast cancer remains a leading cause of morbidity and mortality worldwide yet methods for early detection remain elusive. We describe the discovery and validation of biochemical signatures measured by mass spectrometry, performed upon blood samples from patients and controls that accurately identify (>95%) the presence of clinical breast cancer. Targeted quantitative MS/MS conducted upon 1225 individuals, including patients with breast and other cancers, normal controls as well as individuals with a variety of metabolic disorders provide a biochemical phenotype that accurately identifies the presence of breast cancer and predicts response and survival following the administration of neoadjuvant chemotherapy. The metabolic changes identified are consistent with inborn-like errors of metabolism and define a continuum from normal controls to elevated risk to invasive breast cancer. Similar results were observed in other adenocarcinomas but were not found in squamous cell cancers or hematologic neoplasms. The findings describe a new early detection platform for breast cancer and support a role for pre-existing, inborn-like errors of metabolism in the process of breast carcinogenesis that may also extend to other glandular malignancies. Statement of Significance: Findings provide a powerful tool for early detection and the assessment of prognosis in breast cancer and define a novel concept of breast carcinogenesis that characterizes malignant transformation as the clinical manifestation of underlying metabolic insufficiencies.
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Affiliation(s)
- Ismael da Silva
- Gynecology Department, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil.,Fleury Laboratories, São Paulo, Brazil.,Barretos Cancer Hospital (HCB), Barretos, Brazil
| | | | - Carolina Stella
- Gynecology Department, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Edson Loturco
- Department of Surgery, Urology Unit, Human Reproduction Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | | | - Carlos Veo
- Barretos Cancer Hospital (HCB), Barretos, Brazil
| | | | | | - Paulo D'Amora
- Gynecology Department, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Marcia Salzgeber
- Gynecology Department, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Delcio Matos
- Department of Surgery, Surgical Gastroenterology Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Celso R Silva
- Clinical and Experimental Oncology Department, Hematology and Hemotherapy Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Jose R Oliveira
- Clinical and Experimental Oncology Department, Hematology and Hemotherapy Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Iara Rabelo
- Clinical and Experimental Oncology Department, Hematology and Hemotherapy Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Patricia Yamakawa
- Clinical and Experimental Oncology Department, Hematology and Hemotherapy Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Rui Maciel
- Fleury Laboratories, São Paulo, Brazil.,Department of Medicine, Endocrinology Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Rosa Biscolla
- Department of Medicine, Endocrinology Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Maria Chiamolera
- Department of Medicine, Endocrinology Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Renato Fraietta
- Department of Surgery, Urology Unit, Human Reproduction Division, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Felipe Reis
- Biophysics Department, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Marcelo Mori
- Department of Biochemistry and Tissue Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Dirce Marchioni
- Nutrition Department, School of Public Health, University of São Paulo School of Medicine (FMUSP), São Paulo, Brazil
| | - Antonio Carioca
- Nutrition Department, School of Public Health, University of São Paulo School of Medicine (FMUSP), São Paulo, Brazil
| | - Gustavo Maciel
- Fleury Laboratories, São Paulo, Brazil.,Department of Obstetrics and Gynecology, University of São Paulo School of Medicine (HCFMUSP), São Paulo, Brazil
| | - Renato Tomioka
- Department of Obstetrics and Gynecology, University of São Paulo School of Medicine (HCFMUSP), São Paulo, Brazil
| | - Edmund Baracat
- Department of Obstetrics and Gynecology, University of São Paulo School of Medicine (HCFMUSP), São Paulo, Brazil
| | - Clovis Silva
- Department of Pediatrics, Children's Hospital, University of São Paulo School of Medicine (HCFMUSP), São Paulo, Brazil
| | - Celso Granato
- Fleury Laboratories, São Paulo, Brazil.,Retrovirology Laboratory, Infectious Diseases Unit, Medicine Department, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Ricardo Diaz
- Retrovirology Laboratory, Infectious Diseases Unit, Medicine Department, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Bruno Scarpellini
- Fleury Laboratories, São Paulo, Brazil.,Retrovirology Laboratory, Infectious Diseases Unit, Medicine Department, College of Medicine of the Federal University of São Paulo (EPM-UNIFESP), São Paulo, Brazil
| | - Daniel Egle
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Heidi Fiegl
- Department of Gynecology, Meran Hospital, Meran, Italy
| | | | - Christina Troi
- Department of Gynecology, Brixen Hospital, Brixen, Italy
| | - Robert Nagourney
- Department of Obstetrics and Gynecology, Gynecological Oncology Unit, University of California Irvine (UCI), California, USA
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Sobhani N, Generali D, Zanconati F, Bortul M, Scaggiante B. Cell-free DNA integrity for the monitoring of breast cancer: Future perspectives? World J Clin Oncol 2018; 9:26-32. [PMID: 29651384 PMCID: PMC5893994 DOI: 10.5306/wjco.v9.i2.26] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 02/02/2018] [Accepted: 03/15/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is the most common cancer and the second cause of death in women worldwide. Therapeutic options are increasing, but the response to treatments is not always efficient and the risk of recurrence covers decades. In this perspective, the need to have a proper follow-up for the therapeutic responses and for anticipating recurrence it is urgent in the clinical setting. Liquid biopsy provides the basic principle for a non-invasive method for the routinely monitoring of BC. However, due to the heterogeneity of tumors during onset and progression, the search for tumor DNA mutations of targeted genes in plasma/serum is a limiting factor. A possible approach overtaking this problem comes from the measurement of cell-free DNA integrity, which is an independent factor from the mutational status and theoretically is representative of all tumors. This review summarizes the state-of-the-art of cell-free DNA integrity researches in BC, the controversies and the future perspective.
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Affiliation(s)
- Navid Sobhani
- Department of Medical, Surgical and Health Sciences, University of Trieste, Cattinara Academic Hospital, Trieste 34149, Italy
| | - Daniele Generali
- Department of Medical, Surgical and Health Sciences, University of Trieste, Cattinara Academic Hospital, Trieste 34149, Italy
| | - Fabrizio Zanconati
- Department of Medical, Surgical and Health Sciences, University of Trieste, Cattinara Academic Hospital, Trieste 34149, Italy
| | - Marina Bortul
- Department of Medical, Surgical and Health Sciences, University of Trieste, Cattinara Academic Hospital, Trieste 34149, Italy
| | - Bruna Scaggiante
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
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46
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Bronte G, Ravaioli S, Bravaccini S. What to look for in cell-free DNA from breast cancer patients. Breast Cancer Res Treat 2018; 170:199-200. [PMID: 29480448 DOI: 10.1007/s10549-018-4728-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 10/17/2022]
Affiliation(s)
- Giuseppe Bronte
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Sara Ravaioli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Sara Bravaccini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy.
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Cheng J, Burwinkel B. Cell-free DNA in breast cancer: a long way to go. Breast Cancer Res Treat 2018; 170:201-202. [PMID: 29480447 DOI: 10.1007/s10549-018-4731-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 10/17/2022]
Affiliation(s)
- Jie Cheng
- Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.
| | - Barbara Burwinkel
- Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
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