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Mahal BA, Margolis M, Hubbell E, Chen C, Venstrom JM, Abran J, Kartlitz JJ, Wyatt AW, Klein EA. A Targeted Methylation-Based Multicancer Early Detection Blood Test Preferentially Detects High-Grade Prostate Cancer While Minimizing Overdiagnosis of Indolent Disease. JCO Precis Oncol 2024; 8:e2400269. [PMID: 39208374 PMCID: PMC11371104 DOI: 10.1200/po.24.00269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/12/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
PURPOSE Indolent prostate cancer (PCa) is prevalent in the intended use population (adults age 50-79 years) for blood-based multicancer early detection (MCED) tests. We examined the detectability of PCa by a clinically validated, targeted methylation-based MCED test. METHODS Detectability by Gleason grade group (GG), clinical stage, association of detection status with tumor methylated fraction (TMeF), and overall survival (OS) were assessed in substudy 3 of Circulating Cell-Free Genome Atlas (CCGA; ClinicalTrials.gov identifier: NCT02889978) and PATHFINDER (ClinicalTrials.gov identifier: NCT04241796) studies. RESULTS Test sensitivity for PCa in substudy 3 of CCGA was 11.2% (47/420). The test detected 0 (0%) of 58 low-grade (GG1), 3 (1.9%) of 157 favorable intermediate-grade (GG2), 4 (5.1%) of 78 unfavorable intermediate-grade (GG3), and 36 (31.9%) of 113 high-grade (GG4 and 5) cancers and 3 (3.2%) of 95 stage I, 11 (4.7%) of 235 stage II, 7 (14.9%) of 47 stage III, and 22 (81.5%) of 27 stage IV cases. The median TMeF was higher for detected than nondetected cases (2,106.0 parts per million [PPM]; IQR, 349.8-24,376.3 v 24.4 PPM; IQR, 17.8-38.5; P < .05). Nondetected cases had better OS (P < .05; hazard ratio [HR], 0.263 [95% CI, 0.104 to 0.533]) and detected cases had similar survival (P = .2; HR, 0.672 [95% CI, 0.323 to 1.21]) compared with SEER adjusted for age, GG, and stage. Performance was similar in PATHFINDER, with no detected GG1/2 (0/13) or stage I/II (0/16) cases. CONCLUSION This MCED test preferentially detects high-grade, clinically significant PCa. Use in population-based screening programs in addition to standard-of-care screening is unlikely to exacerbate overdiagnosis of indolent PCa.
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Affiliation(s)
- Brandon A. Mahal
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | | | | | | | | | | | | | - Alexander W. Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
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Seo SY, Youn SH, Bae JH, Lee SH, Lee SY. Detection and Characterization of Methylated Circulating Tumor DNA in Gastric Cancer. Int J Mol Sci 2024; 25:7377. [PMID: 39000483 PMCID: PMC11242052 DOI: 10.3390/ijms25137377] [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: 04/25/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Gastric cancer is the fifth most common disease in the world and the fourth most common cause of death. It is diagnosed through esophagogastroduodenoscopy with biopsy; however, there are limitations in finding lesions in the early stages. Recently, research has been actively conducted to use liquid biopsy to diagnose various cancers, including gastric cancer. Various substances derived from cancer are reflected in the blood. By analyzing these substances, it was expected that not only the presence or absence of cancer but also the type of cancer can be diagnosed. However, the amount of these substances is extremely small, and even these have various variables depending on the characteristics of the individual or the characteristics of the cancer. To overcome these, we collected methylated DNA fragments using MeDIP and compared them with normal plasma to characterize gastric cancer tissue or patients' plasma. We attempted to diagnose gastric cancer using the characteristics of cancer reflected in the blood through the cancer tissue and patients' plasma. As a result, we confirmed that the consistency of common methylated fragments between tissue and plasma was approximately 41.2% and we found the possibility of diagnosing and characterizing cancer using the characteristics of the fragments through SFR and 5'end-motif analysis.
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Affiliation(s)
- Seung Young Seo
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju-si 54907, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, 634-18 Keuman-dong, Dukjin-gu, Jeonju-si 54907, Republic of Korea
| | - Sang Hee Youn
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, 634-18 Keuman-dong, Dukjin-gu, Jeonju-si 54907, Republic of Korea
- Department of Radiation Oncology, Jeonbuk National University Medical School, Jeonju-si 54907, Republic of Korea
| | - Jin-Han Bae
- Research Center, Cancer Breaker, Yongin-si 16942, Republic of Korea
- Cancer Genomic Research Institute, Clinomics, Chungju-si 28161, Republic of Korea
| | - Sung-Hun Lee
- Cancer Genomic Research Institute, Clinomics, Chungju-si 28161, Republic of Korea
| | - Sun Young Lee
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, 634-18 Keuman-dong, Dukjin-gu, Jeonju-si 54907, Republic of Korea
- Department of Radiation Oncology, Jeonbuk National University Medical School, Jeonju-si 54907, Republic of Korea
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3
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Lopez-Valcarcel M, Lopez-Campos F, Zafra J, Cienfuegos I, Ferri M, Barrado M, Hernando S, Counago F. Liquid biopsy to personalize treatment for metastatic prostate cancer. Am J Transl Res 2024; 16:1531-1549. [PMID: 38883349 PMCID: PMC11170619 DOI: 10.62347/dicu9510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/17/2024] [Indexed: 06/18/2024]
Abstract
Liquid biopsy is an innovative approach that provides a more complete understanding of treatment response and prognosis in monitoring metastatic prostate cancer. It complements invasive tissue biopsy and involves the assessment of various biomarkers in body fluids such as blood, semen, and urine. Liquid biopsy analyzes circulating tumor cells, extracellular vesicles, circulating tumor DNA, and the secretome. This is particularly important given the heterogeneity of prostate cancer and the need for better prognostic biomarkers. Liquid biopsy can personalize the treatment of homonosensitive and castration-resistant metastatic prostate cancer by acting as a predictive and prognostic tool. This review discusses various biomarkers, assay techniques, and potential applications in daily clinical practice, highlighting the exciting possibilities that this emerging field holds for improving patient outcomes.
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Affiliation(s)
- Marta Lopez-Valcarcel
- Department of Radiation Oncology, Puerta de Hierro University Hospital Madrid, Spain
| | | | - Juan Zafra
- Department of Radiation Oncology, Virgen de la Victoria University Hospital Málaga, Spain
| | - Irene Cienfuegos
- Department of Urology, Virgen del Puerto Hospital Plasencia, Cáceres, Extremadura, Spain
| | - Maria Ferri
- Department of Radiation Oncology, Marques de Valdecilla University Hospital Santander, Cantabria, Spain
| | - Marta Barrado
- Department of Radiation Oncology, Navarra University Hospital Pamplona, Navarra, Spain
| | - Susana Hernando
- Department of Clinical Oncology, Fundación Alcorcon University Hospital Alcorcón, Madrid, Spain
| | - Felipe Counago
- Department of Radiation Oncology, GenesisCare Madrid Clinical Director, San Francisco de Asis and La Milagrosa Hospitals, National Chair of Research and Clinical Trials GenesisCare, Madrid, Spain
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4
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Das D, Avssn R, Chittela RK. A phenol-chloroform free method for cfDNA isolation from cell conditioned media: development, optimization and comparative analysis. Anal Biochem 2024; 687:115454. [PMID: 38158107 DOI: 10.1016/j.ab.2023.115454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The non-invasive invasive nature of cell-free DNA (cfDNA) as diagnostic, prognostic, and theragnostic biomarkers has gained immense popularity in recent years. The clinical utility of cfDNA biomarkers may depend on understanding their origin and biological significance. Apoptosis, necrosis, and/or active release are possible mechanisms of cellular DNA release into the cell-free milieu. In-vitro cell culture models can provide useful insights into cfDNA biology. The yields and quality of cfDNA in the cell conditioned media (CCM) are largely dependent on the extraction method used. Here, we developed a phenol-chloroform-free cfDNA extraction method from CCM and compared it with three others published cfDNA extraction methods and four commercially available kits. Real-Time PCR (qPCR) targeting two different loci and a fluorescence-based Qubit assay were performed to quantify the extracted cfDNA. The absolute concentration of the extracted cfDNA varies with the target used for the qPCR assay; however, the relative trend remains similar for both qPCR assays. The cfDNA yield from CCM provided by the developed method was found to be either higher or comparable to the other methods used. In conclusion, we developed a safe, rapid and cost-effective cfDNA extraction protocol with minimal hands-on time; with no compromise in cfDNA yields.
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Affiliation(s)
- Dhruv Das
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute (HBNI), Anushaktinagar, Trombay, Mumbai, 400094, India
| | - Rao Avssn
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Rajani Kant Chittela
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute (HBNI), Anushaktinagar, Trombay, Mumbai, 400094, India.
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5
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Kim YJ, Rho WY, Park SM, Jun BH. Optical nanomaterial-based detection of biomarkers in liquid biopsy. J Hematol Oncol 2024; 17:10. [PMID: 38486294 PMCID: PMC10938695 DOI: 10.1186/s13045-024-01531-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: 12/07/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024] Open
Abstract
Liquid biopsy, which is a minimally invasive procedure as an alternative to tissue biopsy, has been introduced as a new diagnostic/prognostic measure. By screening disease-related markers from the blood or other biofluids, it promises early diagnosis, timely prognostication, and effective treatment of the diseases. However, there will be a long way until its realization due to its conceptual and practical challenges. The biomarkers detected by liquid biopsy, such as circulating tumor cell (CTC) and circulating tumor DNA (ctDNA), are extraordinarily rare and often obscured by an abundance of normal cellular components, necessitating ultra-sensitive and accurate detection methods for the advancement of liquid biopsy techniques. Optical biosensors based on nanomaterials open an important opportunity in liquid biopsy because of their enhanced sensing performance with simple and practical properties. In this review article, we summarized recent innovations in optical nanomaterials to demonstrate the sensitive detection of protein, peptide, ctDNA, miRNA, exosome, and CTCs. Each study prepares the optical nanomaterials with a tailored design to enhance the sensing performance and to meet the requirements of each biomarker. The unique optical characteristics of metallic nanoparticles (NPs), quantum dots, upconversion NPs, silica NPs, polymeric NPs, and carbon nanomaterials are exploited for sensitive detection mechanisms. These recent advances in liquid biopsy using optical nanomaterials give us an opportunity to overcome challenging issues and provide a resource for understanding the unknown characteristics of the biomarkers as well as the mechanism of the disease.
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Affiliation(s)
- Young Jun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Won-Yeop Rho
- School of International Engineering and Science, Jeonbuk National University, Chonju, 54896, Republic of Korea
| | - Seung-Min Park
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, 637459, Singapore.
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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Varzaru B, Iacob RA, Bunduc S, Manea I, Sorop A, Spiridon A, Chelaru R, Croitoru A, Topala M, Becheanu G, Dumbrava M, Dima S, Popescu I, Gheorghe C. Prognostic Value of Circulating Cell-Free DNA Concentration and Neutrophil-to-Lymphocyte Ratio in Patients with Pancreatic Ductal Adenocarcinoma: A Prospective Cohort Study. Int J Mol Sci 2024; 25:2854. [PMID: 38474101 DOI: 10.3390/ijms25052854] [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: 12/29/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating cell-free DNA (ccfDNA) quantity correlates with the clinical characteristics and prognosis of various cancer types. We investigated whether ccfDNA levels and the neutrophil-to-lymphocyte ratio (NLR) have prognostic value in patients with pancreatic ductal adenocarcinoma (PDAC). Peripheral blood was collected from 82 patients with PDAC prior to any diagnostic procedure or the administration of chemotherapy. Plasma DNA was isolated, and ccfDNA concentration and NLR were determined. We found that ccfDNA levels were correlated with age and tumor burden. Moreover, higher values of NLR (≥3.31) were linked with worse overall survival (OS) (4 vs. 10 months; log rank p = 0.011), and an elevated ccfDNA concentration (≥25.79 ng/mL) was strongly associated with shorter OS (4 vs. 8 months; log rank p = 0.009). According to the results of the multivariable Cox regression analysis, the baseline concentration of ccfDNA was an independent prognostic factor for OS (HR 0.45, 95% CI 0.21-0.97, p = 0.041). Furthermore, the combination of ccfDNA levels with NLR greatly enhanced the prognostic accuracy of PDAC patients. Our study demonstrates that ccfDNA concentration and NLR are independent predictors of survival in PDAC. Subsequent studies should validate this combination as a prognostic indicator in PDAC patients and assess its utility for guiding therapeutic decisions.
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Affiliation(s)
- Bianca Varzaru
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Razvan Andrei Iacob
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Stefania Bunduc
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Ioana Manea
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Andrei Sorop
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Andreea Spiridon
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Raluca Chelaru
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Adina Croitoru
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Mihaela Topala
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Gabriel Becheanu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Mona Dumbrava
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Simona Dima
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Irinel Popescu
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Cristian Gheorghe
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
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7
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Kluge K, Einspieler H, Haberl D, Spielvogel C, Stoiber S, Vraka C, Papp L, Wunsch S, Egger G, Kramer G, Grubmüller B, Shariat S, Hacker M, Kenner L, Haug A. Examining the Relationship and Prognostic Significance of Cell-Free DNA Levels and the PSMA-Positive Tumor Volume in Men with Prostate Cancer: A Retrospective-Prospective [ 68Ga]Ga-PSMA-11 PET/CT Study. J Nucl Med 2024; 65:63-70. [PMID: 38050125 PMCID: PMC10755525 DOI: 10.2967/jnumed.123.266158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/27/2023] [Indexed: 12/06/2023] Open
Abstract
Functional imaging with prostate-specific membrane antigen (PSMA) ligands has emerged as the standard imaging method for prostate cancer (PCA). In parallel, the analysis of blood-derived, cell-free DNA (cfDNA) has been shown to be a promising quantitative biomarker of PCA aggressiveness and patient outcome. This study aimed to evaluate the relationship and prognostic value of cfDNA concentrations and the PSMA-positive tumor volume (PSMA-TV) in men with PCA undergoing [68Ga]Ga-PSMA-11 PET/CT imaging. Methods: We recruited 148 men with histologically proven PCA (mean age, 70.7 ± 7.7 y) who underwent [68Ga]Ga-PSMA-11 PET/CT (184.9 ± 18.9 MBq) and blood sampling between March 2019 and August 2021. Among these, 74 (50.0%) had hormone-sensitive PCA and 74 (50.0%) had castration-resistant PCA (CRPC). All patients provided written informed consent before blood sample collection and imaging. The cfDNA was extracted and quantified, and PSMA-expressing tumor lesions were delineated to extract the PSMA-TVs. The Spearman coefficient assessed correlations between PSMA-TV and cfDNA concentrations and cfDNA's relation with clinical parameters. The Kruskal-Wallis test examined the mean cfDNA concentration differences based on PSMA-TV quartiles for significantly correlated patient groups. Log-rank and multivariate Cox regression analyses evaluated the prognostic significance of high and low cfDNA and PSMA-TV levels for overall survival. Results: Weak positive correlations were found between cfDNA concentration and PSMA-TV in the overall group (r = 0.16, P = 0.049) and the CRPC group (r = 0.31, P = 0.007) but not in hormone-sensitive PCA patients (r = -0.024, P = 0.837). In the CRPC cohort, cfDNA concentrations significantly differed between PSMA-TV quartiles 4 and 1 (P = 0.002) and between quartiles 4 and 2 (P = 0.016). Survival outcomes were associated with PSMA-TV (P < 0.0001, P = 0.004) but not cfDNA (P = 0.174, P = 0.12), as per the log-rank and Cox regression analysis. Conclusion: These findings suggest that cfDNA might serve as a biomarker of advanced, aggressive CRPC but does not reliably reflect total tumor burden or prognosis. In comparison, [68Ga]Ga-PSMA-11 PET/CT provides a highly granular and prognostic assessment of tumor burden across the spectrum of PCA disease progression.
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Affiliation(s)
- Kilian Kluge
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, Vienna, Austria
| | - Holger Einspieler
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - David Haberl
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Clemens Spielvogel
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, Vienna, Austria
| | - Stefan Stoiber
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, Vienna, Austria
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Chrysoula Vraka
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Laszlo Papp
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Sabine Wunsch
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Gerda Egger
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Gero Kramer
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Bernhard Grubmüller
- Department of Urology, Medical University of Vienna, Vienna, Austria
- Department of Urology and Andrology, University Hospital Krems, Krems, Austria
- Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Shahrokh Shariat
- Department of Urology, Medical University of Vienna, Vienna, Austria
- Department of Urology and Andrology, University Hospital Krems, Krems, Austria
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
- Division of Urology, Department of Special Surgery, University of Jordan, Amman, Jordan
- Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic; and
- Department of Urology, Weill Cornell Medical College, New York, New York
| | - Marcus Hacker
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Lukas Kenner
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, Vienna, Austria
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Alexander Haug
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria;
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, Vienna, Austria
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Nguyen MTN, Rajavuori A, Huhtinen K, Hietanen S, Hynninen J, Oikkonen J, Hautaniemi S. Circulating tumor DNA-based copy-number profiles enable monitoring treatment effects during therapy in high-grade serous carcinoma. Biomed Pharmacother 2023; 168:115630. [PMID: 37806091 DOI: 10.1016/j.biopha.2023.115630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/23/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023] Open
Abstract
Circulating tumor DNA (ctDNA) analysis has emerged as a promising tool for detecting and profiling longitudinal genomics changes in cancer. While copy-number alterations (CNAs) play a major role in cancers, treatment effect monitoring using copy-number profiles has received limited attention as compared to mutations. A major reason for this is the insensitivity of CNA analysis for the real-life tumor-fraction ctDNA samples. We performed copy-number analysis on 152 plasma samples obtained from 29 patients with high-grade serous ovarian cancer (HGSC) using a sequencing panel targeting over 500 genes. Twenty-one patients had temporally matched tissue and plasma sample pairs, which enabled assessing concordance with tissues sequenced with the same panel or whole-genome sequencing and to evaluate sensitivity. Our approach could detect concordant CNA profiles in most plasma samples with as low as 5% tumor content and highly amplified regions in samples with ∼1% of tumor content. Longitudinal profiles showed changes in the CNA profiles in seven out of 11 patients with high tumor-content plasma samples at relapse. These changes included focal acquired or lost copy-numbers, even though most of the genome remained stable. Two patients displayed major copy-number profile changes during therapy. Our analysis revealed ctDNA-detectable subclonal selection resulting from both surgical operations and chemotherapy. Overall, longitudinal ctDNA data showed acquired and diminished CNAs at relapse when compared to pre-treatment samples. These results highlight the importance of genomic profiling during treatment as well as underline the usability of ctDNA.
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Affiliation(s)
- Mai T N Nguyen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00291, Finland
| | - Anna Rajavuori
- Department of Obstetrics and Gynecology, Turku University Hospital, Kiinamyllynkatu 4, Turku 20521, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00291, Finland; Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, Turku 20014, Finland
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, Turku University Hospital, Kiinamyllynkatu 4, Turku 20521, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital, Kiinamyllynkatu 4, Turku 20521, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00291, Finland.
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00291, Finland.
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9
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Alahdal M, Perera RA, Moschovas MC, Patel V, Perera RJ. Current advances of liquid biopsies in prostate cancer: Molecular biomarkers. Mol Ther Oncolytics 2023; 30:27-38. [PMID: 37575217 PMCID: PMC10415624 DOI: 10.1016/j.omto.2023.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Prostate cancer (PCa) incidence is increasing and endangers men's lives. Early detection of PCa could improve overall survival (OS) by preventing metastasis. The prostate-specific antigen (PSA) test is a popular screening method. Several advisory groups, however, warn against using the PSA test due to its high false positive rate, unsupported outcome, and limited benefit. The number of disease-related biopsies performed annually far outweighs the number of diagnoses. Thus, there is an urgent need to develop accurate diagnostic biomarkers to detect PCa and distinguish between aggressive and indolent cancers. Recently, non-coding RNA (ncRNA), circulating tumor DNA (ctDNA)/ctRNA, exosomes, and metabolomic biomarkers in the liquid biopsies (LBs) of patients with PCa showed significant differences and clinical benefits in diagnosis, prognosis, and monitoring response to therapy. The analysis of urinary exosomal ncRNA presented a substantial correlation among Exos-miR-375 downregulation, clinical T stage, and bone metastases of PCa. Furthermore, the expression of miR-532-5p in urine samples was a vital predictive biomarker of PCa progression. Thus, this review focuses on promising molecular and metabolomic biomarkers in LBs from patients with PCa. We thoroughly addressed the most recent clinical findings of LB biomarker use in diagnosing and monitoring PCa in early and advanced stages.
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Affiliation(s)
- Murad Alahdal
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
- Department of Oncology, Sydney Kimmel Cancer Center, School of Medicine, Johns Hopkins University, 401 N. Broadway, Baltimore, MD 21287, USA
| | - Roshane A. Perera
- AdventHealth Celebration, 380 Celebration Place, Celebration, FL 34747, USA
| | | | - Vipul Patel
- AdventHealth Celebration, 380 Celebration Place, Celebration, FL 34747, USA
| | - Ranjan J. Perera
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
- Department of Oncology, Sydney Kimmel Cancer Center, School of Medicine, Johns Hopkins University, 401 N. Broadway, Baltimore, MD 21287, USA
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10
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Koukourakis MI, Xanthopoulou E, Koukourakis IM, Fortis SP, Kesesidis N, Karakasiliotis I, Baxevanis CN. Circulating Plasma Cell-free DNA (cfDNA) as a Predictive Biomarker for Radiotherapy: Results from a Prospective Trial in Head and Neck Cancer. CANCER DIAGNOSIS & PROGNOSIS 2023; 3:551-557. [PMID: 37671311 PMCID: PMC10475926 DOI: 10.21873/cdp.10254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/13/2023] [Indexed: 09/07/2023]
Abstract
Background/Aim The plasma levels of cell-free DNA (cfDNA) in cancer patients increase due to rapid cancer cell proliferation and death. Therefore, cfDNA can be used to study specific tumor-DNA features. In addition, the non-specific cfDNA concentration may be an important biomarker of cancer prognosis. Patients and Methods We prospectively examined the predictive role of cfDNA levels and the kinetics in the outcome of chemo-radiotherapy (CRT) in a cohort of 47 patients with locally advanced squamous cell head-neck cancer (SCHNC) treated with definitive chemo-radiotherapy. Results Increased cfDNA levels after therapy completion (after/before treatment ratio; A/B-ratio >1) were found in 26/47 patients (55.3%). Locally advanced T4-stage was significantly associated with higher cfDNA levels after CRT (3.3 ng/μl in T4-stage vs. 1.3 ng/μl in T1-3 stages, p=0.007). Patients who responded to CRT (partial/complete response) had significantly lower cfDNA levels before therapy (mean values 1.2 ng/μl vs. 2.7 ng/μl, p=0.03). A significantly worse locoregional progression-free survival in patients with an A/B-ratio >1 was documented (p=0.01; hazard ratio 3.5, 95%CI=1.2-9.7). This was also confirmed in multivariate analysis, where the A/B-ratio was an independent predictive variable of locoregional relapse (p=0.03, hazard ratio 3.9, 95%CI=1.2-13). Conclusion High post-CRT cfDNA levels could be an early biomarker for the immediate recruitment of patients with SCHNC in consolidation chemo-immunotherapy protocols.
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Affiliation(s)
- Michael I Koukourakis
- Department of Radiotherapy - Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Erasmia Xanthopoulou
- Department of Radiotherapy - Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis M Koukourakis
- Radiation Oncology Unit, 1st Department of Radiology, Aretaieion University Hospital, Athens, Greece
| | - Sotirios P Fortis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, Athens, Greece
| | - Nikolaos Kesesidis
- Laboratory of Biology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Constantin N Baxevanis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, Athens, Greece
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11
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Nishio K, Sakai K, Nishio M, Seto T, Visseren-Grul C, Carlsen M, Matsui T, Enatsu S, Nakagawa K. Impact of ramucirumab plus erlotinib on circulating cell-free DNA from patients with untreated metastatic non-small cell lung cancer with EGFR-activating mutations (RELAY phase 3 randomized study). Transl Lung Cancer Res 2023; 12:1702-1716. [PMID: 37691865 PMCID: PMC10483085 DOI: 10.21037/tlcr-22-736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 09/12/2023]
Abstract
Background An exploratory, proof-of-concept, liquid biopsy addendum to examine biomarkers within cell-free DNA (cfDNA) in the RELAY phase 3, randomized, double-blind, placebo-controlled study was conducted. RELAY showed improved progression-free survival (PFS) with ramucirumab (RAM), a human immunoglobulin G1 vascular endothelial growth factor receptor 2 antagonist, plus erlotinib (ERL), a tyrosine kinase inhibitor, compared with placebo (PL) plus ERL. Methods Treatment-naïve patients with endothelial growth factor receptor (EGFR)-mutated metastatic non-small cell lung cancer were randomized (1:1) to RAM + ERL or PL + ERL. Plasma samples were collected at baseline, on treatment, and at 30-day post-study treatment discontinuation follow-up. Baseline and treatment-emergent gene alterations and EGFR-activating mutation allele counts were investigated by next-generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR), respectively. cfDNA concentration and fragment size were evaluated by real-time polymerase chain reaction and the BioAnalyzer. Patients with a valid baseline plasma sample were included (70 RAM + ERL, 61 PL + ERL). Results TP53 mutation was the most frequently co-occurring baseline gene alteration (43%). Post-study treatment discontinuation EGFR T790M mutation rates were 54.5% (6/11) and 41.2% (7/17) by ddPCR, and 22.2% (2/9) and 29.4% (5/17) by NGS, in the RAM + ERL and PL + ERL arms, respectively. EGFR-activating mutation allele count decreased at Cycle 4 in both treatment arms and was sustained at follow-up with RAM + ERL. PFS improved for patients with no detectable EGFR-activating mutation at Cycle 4 vs. those with detectable EGFR-activating mutation. Total cfDNA concentration increased from baseline at Cycle 4 and through to follow-up with RAM + ERL. cfDNA fragment size was similar between treatment arms at baseline [mean (standard deviation) base pairs: RAM + ERL, 173.4 (2.6); PL + ERL, 172.9 (3.2)] and was shorter at Cycle 4 with RAM + ERL vs. PL + ERL [169.5 (2.8) vs. 174.1 (3.3), respectively; P<0.0001]. Baseline vs. Cycle 4 paired analysis showed a decrease in cfDNA fragment size for 84% (48/57) and 23% (11/47) of patient samples in the RAM + ERL and PL + ERL arms, respectively. Conclusions EGFR-activating mutation allele count was suppressed, total cfDNA concentration increased, and short fragment-sized cfDNA increased with RAM + ERL, suggesting the additional anti-tumor effect of RAM may contribute to the PFS benefit observed in RELAY with RAM + ERL vs. PL + ERL. Trial Registration ClinicalTrials.gov; identifier: NCT02411448.
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Affiliation(s)
- Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takashi Seto
- National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | | | | | | | | | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
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12
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Dao J, Conway PJ, Subramani B, Meyyappan D, Russell S, Mahadevan D. Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation. Int J Mol Sci 2023; 24:13219. [PMID: 37686024 PMCID: PMC10487653 DOI: 10.3390/ijms241713219] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, accuracy, and cost over solid biopsies and other oncological markers. The technology used to differentiate ctDNA and cell-free DNA (cfDNA) continues to improve with new tests and methodologies being able to detect down to mutant allele frequencies of 0.001% or 1/100,000 copies. Recognizing this development in technology, the FDA has recently given pre-market approval and breakthrough device designations to multiple companies. The purpose of this review is to look at the utility of measuring total cfDNA, techniques used to differentiate ctDNA from cfDNA, and the utility of different ctDNA-based liquid biopsy kits using relevant articles from PubMed, clinicaltrials.gov, FDA approvals, and company newsletters. Measuring total cfDNA could be a cost-effective, viable prognostic marker, but various factors do not favor it as a monitoring tool during chemotherapy. While there may be a place in the clinic for measuring total cfDNA in the future, the lack of standardization means that it is difficult to move forward with large-scale clinical validation studies currently. While the detection of ctDNA has promising standardized liquid biopsy kits from various companies with large clinical trials ongoing, their applications in screening and minimal residual disease can suffer from lower sensitivity. However, researchers are working towards solutions to these issues with innovations in technology, multi-omics, and sampling. With great promise, further research is needed before liquid biopsies can be recommended for everyday clinical management.
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Affiliation(s)
- Jonathan Dao
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick J. Conway
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Baskaran Subramani
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Devi Meyyappan
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
| | - Sammy Russell
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Daruka Mahadevan
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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13
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Oliver J, Onieva JL, Garrido-Barros M, Cobo-Dols M, Martínez-Gálvez B, García-Pelícano AI, Dubbelman J, Benítez JC, Martín JZ, Cantero A, Pérez-Ruiz E, Rueda-Domínguez A, Barragán I. Fluorometric Quantification of Total Cell-Free DNA as a Prognostic Biomarker in Non-Small-Cell Lung Cancer Patients Treated with Immune Checkpoint Blockade. Cancers (Basel) 2023; 15:3357. [PMID: 37444467 DOI: 10.3390/cancers15133357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The present study aimed to investigate the potential of basal cell-free fluorometric DNA (cfDNA) quantification as a prognostic biomarker in advanced non-small cell lung cancer (NSCLC) patients treated with an Immune Checkpoint Blockade (ICB). A discovery and validation cohort of 61 and 31 advanced lung cancer patients treated with ICB were included in this study. Quantification of cfDNA concentration was performed before the start of the treatment and patients were followed up for a median of 34 (30-40) months. The prognostic predicted value of cfDNA was evaluated based on ROC, and Cox regression was conducted via univariate and multivariate analyses to estimate the hazard ratio. We observed that a cfDNA cut-off of 0.55 ng/µL before the ICB determines the overall survival of patients with a log rank p-value of 3.3 × 10-4. That represents median survivals of 3.8 vs. 17.5 months. Similar results were obtained in the validation cohort being the log rank p-value 3.8 × 10-2 with median survivals of 5.9 vs. 24.3. The univariate and multivariate analysis revealed that the cut-off of 0.55 ng/µL before ICB treatment was an independent predictive factor and was significantly associated with a better survival outcome. High cfDNA concentrations identify patients with advanced NSCLC who do not benefit from the ICB. The determination of cfDNA is a simple test that could select a group of patients in whom new therapeutic strategies are needed.
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Affiliation(s)
- Javier Oliver
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - Juan Luis Onieva
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
- Faculty of Medicine, Campus de Teatinos s/n, Universidad de Málaga, 29071 Málaga, Spain
| | - María Garrido-Barros
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
- Faculty of Medicine, Campus de Teatinos s/n, Universidad de Málaga, 29071 Málaga, Spain
| | - Manuel Cobo-Dols
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - Beatriz Martínez-Gálvez
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - Ana Isabel García-Pelícano
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - Jaime Dubbelman
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - José Carlos Benítez
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - Juan Zafra Martín
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
- Faculty of Medicine, Campus de Teatinos s/n, Universidad de Málaga, 29071 Málaga, Spain
- Department of Radiation Oncology, Virgen de la Victoria University Hospital, 29010 Málaga, Spain
| | - Alejandra Cantero
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - Elisabeth Pérez-Ruiz
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - Antonio Rueda-Domínguez
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
| | - Isabel Barragán
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy), Regional and Virgen de la Victoria University Hospitals, Institute of Biomedical Research in Malaga and BIONAND Nanomedicine Platform (IBIMA BIONAND Platform), C/Marqués de Beccaría n°3, 29010 Málaga, Spain
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
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14
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Lichá K, Pastorek M, Repiská G, Celec P, Konečná B. Investigation of the Presence of DNA in Human Blood Plasma Small Extracellular Vesicles. Int J Mol Sci 2023; 24:ijms24065915. [PMID: 36982989 PMCID: PMC10051167 DOI: 10.3390/ijms24065915] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Extracellular DNA (ecDNA) is DNA outside of cells, which is a result of various mechanisms. EcDNA is believed to be a cause of various pathogeneses as well as their potential biomarker. EcDNA is believed to also be part of small extracellular vesicles (sEVs) from cell cultures. If ecDNA is present in sEVs in plasma, their membrane may protect it from degradation by deoxyribonucleases. Moreover, sEVs play a role in the intercellular communication, and they can therefore transfer ecDNA between cells. The aim of this study was to investigate the presence of ecDNA in sEVs isolated from fresh human plasma by the ultracentrifugation and density gradient, which serves to exclude the co-isolation of non-sEVs compartments. The novelty of the current study is the investigation of the localization and subcellular origin of the ecDNA associated with sEVs in plasma, as well as the estimation of the approximate concentration. The cup-shaped sEVs were confirmed by transmission electron microscopy. The highest concentration of particles was in the size of 123 nm. The presence of the sEVs markers CD9 and TSG101 was confirmed by western blot. It was found that 60-75% of DNA is on the surface of sEVs, but a part of the DNA is localized inside the sEVs. Moreover, both nuclear and mitochondrial DNA were present in plasma EVs. Further studies should focus on the potential harmful autoimmune effect of DNA carried by plasma EVs or specifically sEVs.
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Affiliation(s)
- Kristína Lichá
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Michal Pastorek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Gabriela Repiská
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 813 72 Bratislava, Slovakia
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
- Institute of Pathophysiology, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Barbora Konečná
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
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15
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Ren XD, Su N, Sun XG, Li WM, Li J, Li BW, Li RX, Lv J, Xu QY, Kong WL, Huang Q. Advances in liquid biopsy-based markers in NSCLC. Adv Clin Chem 2023; 114:109-150. [PMID: 37268331 DOI: 10.1016/bs.acc.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Lung cancer is the second most-frequently occurring cancer and the leading cause of cancer-associated deaths worldwide. Non-small cell lung cancer (NSCLC), the most common type of lung cancer is often diagnosed in middle or advanced stages and have poor prognosis. Diagnosis of disease at an early stage is a key factor for improving prognosis and reducing mortality, whereas, the currently used diagnostic tools are not sufficiently sensitive for early-stage NSCLC. The emergence of liquid biopsy has ushered in a new era of diagnosis and management of cancers, including NSCLC, since analysis of circulating tumor-derived components, such as cell-free DNA (cfDNA), circulating tumor cells (CTCs), cell-free RNAs (cfRNAs), exosomes, tumor-educated platelets (TEPs), proteins, and metabolites in blood or other biofluids can enable early cancer detection, treatment selection, therapy monitoring and prognosis assessment. There have been great advances in liquid biopsy of NSCLC in the past few years. Hence, this chapter introduces the latest advances on the clinical application of cfDNA, CTCs, cfRNAs and exosomes, with a particular focus on their application as early markers in the diagnosis, treatment and prognosis of NSCLC.
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Affiliation(s)
- Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Xian-Ge Sun
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Wen-Man Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Bo-Wen Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Ruo-Xu Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Jing Lv
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Qian-Ying Xu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Wei-Long Kong
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China.
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16
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Wang JJ, Sun N, Lee YT, Kim M, Vagner T, Rohena-Rivera K, Wang Z, Chen Z, Zhang RY, Lee J, Zhang C, Tang H, Widjaja J, Zhang TX, Qi D, Teng PC, Jan YJ, Hou KC, Hamann C, Sandler HM, Daskivich TJ, Luthringer DJ, Bhowmick NA, Pei R, You S, Di Vizio D, Tseng HR, Chen JF, Zhu Y, Posadas EM. Prostate cancer extracellular vesicle digital scoring assay - a rapid noninvasive approach for quantification of disease-relevant mRNAs. NANO TODAY 2023; 48:101746. [PMID: 36711067 PMCID: PMC9879227 DOI: 10.1016/j.nantod.2022.101746] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Optimizing outcomes in prostate cancer (PCa) requires precision in characterization of disease status. This effort was directed at developing a PCa extracellular vesicle (EV) Digital Scoring Assay (DSA) for detecting metastasis and monitoring progression of PCa. PCa EV DSA is comprised of an EV purification device (i.e., EV Click Chip) and reverse-transcription droplet digital PCR that quantifies 11 PCa-relevant mRNA in purified PCa-derived EVs. A Met score was computed for each plasma sample based on the expression of the 11-gene panel using the weighted Z score method. Under optimized conditions, the EV Click Chips outperformed the ultracentrifugation or precipitation method of purifying PCa-derived EVs from artificial plasma samples. Using PCa EV DSA, the Met score distinguished metastatic (n = 20) from localized PCa (n = 20) with an area under the receiver operating characteristic curve of 0.88 (95% CI:0.78-0.98). Furthermore, longitudinal analysis of three PCa patients showed the dynamics of the Met scores reflected clinical behavior even when disease was undetectable by imaging. Overall, a sensitive PCa EV DSA was developed to identify metastatic PCa and reveal dynamic disease states noninvasively. This assay may complement current imaging tools and blood-based tests for timely detection of metastatic progression that can improve care for PCa patients.
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Affiliation(s)
- Jasmine J. Wang
- Division of Medical Oncology, Department of Medicine,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Na Sun
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
- Key Laboratory for Nano-Bio Interface, Suzhou Institute of
Nano-Tech and Nano-Bionics, University of Chinese Academy of Sciences, Chinese
Academy of Sciences, Suzhou, PR China
| | - Yi-Te Lee
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Minhyung Kim
- Department of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
| | - Tatyana Vagner
- Department of Surgery, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
| | | | - Zhili Wang
- Key Laboratory for Nano-Bio Interface, Suzhou Institute of
Nano-Tech and Nano-Bionics, University of Chinese Academy of Sciences, Chinese
Academy of Sciences, Suzhou, PR China
| | - Zijing Chen
- Division of Medical Oncology, Department of Medicine,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ryan Y. Zhang
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Junseok Lee
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Ceng Zhang
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Hubert Tang
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Josephine Widjaja
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Tiffany X. Zhang
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Dongping Qi
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Pai-Chi Teng
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
| | - Yu Jen Jan
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
| | - Kuan-Chu Hou
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
| | - Candace Hamann
- Division of Medical Oncology, Department of Medicine,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Howard M. Sandler
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
- Department of Radiation Oncology, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
| | - Timothy J. Daskivich
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
- Division of Urology, Department of Surgery, Cedars-Sinai
Medical Center, Los Angeles, CA, USA
| | - Daniel J. Luthringer
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
- Department of Pathology and Laboratory Medicine,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Neil A. Bhowmick
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
| | - Renjun Pei
- Key Laboratory for Nano-Bio Interface, Suzhou Institute of
Nano-Tech and Nano-Bionics, University of Chinese Academy of Sciences, Chinese
Academy of Sciences, Suzhou, PR China
| | - Sungyong You
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
| | - Dolores Di Vizio
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
- Department of Pathology and Laboratory Medicine,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School
of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jie-Fu Chen
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Yazhen Zhu
- California NanoSystems Institute, Crump Institute for
Molecular Imaging, Department of Molecular and Medical Pharmacology, University of
California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School
of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Edwin M. Posadas
- Division of Medical Oncology, Department of Medicine,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los
Angeles, CA, USA
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17
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Škara L, Vodopić T, Pezelj I, Abramović I, Vrhovec B, Vrtarić A, Sinčić N, Tomas D, Bulimbašić S, Kuliš T, Ulamec M. Methylation pattern of caveolin-1 in prostate cancer as potential cfDNA biomarker. BIOMOLECULES AND BIOMEDICINE 2023; 23:176-186. [PMID: 36036057 PMCID: PMC9901895 DOI: 10.17305/bjbms.2022.7497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/01/2022] [Indexed: 02/03/2023]
Abstract
High prevalence and mortality of prostate cancer (PCa) are well known global health issues. Novel biomarkers for better identifying patients with PCa are the subject of extensive research. Prostate specific antigen (PSA) shows low specificity in screening and diagnostics, leading to unnecessary biopsies and health costs. Eighty patients with PCa and benign prostate hyperplasia (BPH) were included in the study. We analyzed CAV1 gene expression and methylation in tissue. CAV1 cfDNA methylation from blood and seminal plasma was accessed as a potential PCa biomarker. Although methylation in blood plasma did not differ between PCa and BPH patients, methylation in seminal plasma showed better PCa biomarker performances than tPSA (AUC 0.63 vs. AUC 0.52). Discrimination of BPH and Gleason grade group 1 PCa patients from patients with higher Gleason grade groups revealed very good performance as well (AUC 0.72). CAV1 methylation is useful biomarker with potential for further seminal plasma cfDNA research, but its diagnostic accuracy should be improved, as well as general knowledge about cfDNA in seminal plasma.
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Affiliation(s)
- Lucija Škara
- Department of Biology, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia,Correspondence to Lucija Škara:
| | - Tonći Vodopić
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Ivan Pezelj
- Department of Urology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Irena Abramović
- Department of Biology, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Borna Vrhovec
- Department of Urology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Alen Vrtarić
- Department of Clinical Chemistry, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Nino Sinčić
- Department of Biology, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Davor Tomas
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia,Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Stela Bulimbašić
- Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia,Pathology and Cytology Department, University Hospital Center Zagreb, Zagreb, Croatia
| | - Tomislav Kuliš
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia,Department of Urology, University Hospital Center Zagreb, Zagreb, Croatia
| | - Monika Ulamec
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia,Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia,Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
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18
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Webster SE, Tsuji NL, Clemente MJ, Holodick NE. Age-related changes in antigen-specific natural antibodies are influenced by sex. Front Immunol 2023; 13:1047297. [PMID: 36713434 PMCID: PMC9878317 DOI: 10.3389/fimmu.2022.1047297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction Natural antibody (NAb) derived from CD5+ B-1 cells maintains tissue homeostasis, controls inflammation, aids in establishing long-term protective responses against pathogens, and provides immediate protection from infection. CD5+ B-1 cell NAbs recognize evolutionarily fixed epitopes, such as phosphatidylcholine (PtC), found on bacteria and senescent red blood cells. Anti-PtC antibodies are essential in protection against bacterial sepsis. CD5+ B-1 cell-derived NAbs have a unique germline-like structure that lacks N-additions, a feature critical for providing protection against infection. Previously, we demonstrated the repertoire and germline status of PtC+CD5+ B-1 cell IgM obtained from male mice changes with age depending on the anatomical location of the B-1 cells. More recently, we demonstrated serum antibody from aged female mice maintains protection against pneumococcal infection, whereas serum antibody from male mice does not provide protection. Results Here, we show that aged female mice have significantly more splenic PtC+CD5+ B-1 cells and more PtC specific serum IgM than aged male mice. Furthermore, we find both age and biological sex related repertoire differences when comparing B cell receptor (BCR) sequencing results of PtC+CD5+ B-1 cells. While BCR germline status of PtC+CD5+ B-1 cells from aged male and female mice is similar in the peritoneal cavity, it differs significantly in the spleen, where aged females retain germline configuration and aged males do not. Nucleic acid sensing toll-like receptors are critical in the maintenance of PtC+ B-1 cells; therefore, to begin to understand the mechanism of differences observed between the male and female PtC+CD5+ B-1 cell repertoire, we analyzed levels of cell-free nucleic acids and found increases in aged females. Conclusion Our results suggest the antigenic milieu differs between aged males and females, leading to differential selection of antigen-specific B-1 cells over time. Further elucidation of how biological sex differences influence the maintenance of B-1 cells within the aging environment will be essential to understand sex and age-related disparities in the susceptibility to bacterial infection and will aid in the development of more effective vaccination and/or therapeutic strategies specific for males and females.
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Affiliation(s)
- Sarah E. Webster
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Naomi L. Tsuji
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Michael J. Clemente
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
- Flow Cytometry and Imaging Core, Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Nichol E. Holodick
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
- Flow Cytometry and Imaging Core, Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
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19
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Tsoneva DK, Ivanov MN, Conev NV, Manev R, Stoyanov DS, Vinciguerra M. Circulating Histones to Detect and Monitor the Progression of Cancer. Int J Mol Sci 2023; 24:ijms24020942. [PMID: 36674455 PMCID: PMC9860657 DOI: 10.3390/ijms24020942] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Liquid biopsies have emerged as a minimally invasive cancer detection and monitoring method, which could identify cancer-related alterations in nucleosome or histone levels and modifications in blood, saliva, and urine. Histones, the core component of the nucleosome, are essential for chromatin compaction and gene expression modulation. Increasing evidence suggests that circulating histones and histone complexes, originating from cell death or immune cell activation, could act as promising biomarkers for cancer detection and management. In this review, we provide an overview of circulating histones as a powerful liquid biopsy approach and methods for their detection. We highlight current knowledge on circulating histones in hematologic malignancies and solid cancer, with a focus on their role in cancer dissemination, monitoring, and tumorigenesis. Last, we describe recently developed strategies to identify cancer tissue-of-origin in blood plasma based on nucleosome positioning, inferred from nucleosomal DNA fragmentation footprint, which is independent of the genetic landscape.
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Affiliation(s)
- Desislava K. Tsoneva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Varna, 9000 Varna, Bulgaria
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
| | - Martin N. Ivanov
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
- Department of Anatomy and Cell Biology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
| | - Nikolay Vladimirov Conev
- Clinic of Medical Oncology, UMHAT “St. Marina”, 1 “Hristo Smirnenski” Blvd., 9000 Varna, Bulgaria
- Department of Propedeutics of Internal Diseases, Medical University of Varna, 9000 Varna, Bulgaria
| | - Rostislav Manev
- Clinic of Medical Oncology, UMHAT “St. Marina”, 1 “Hristo Smirnenski” Blvd., 9000 Varna, Bulgaria
- Department of Propedeutics of Internal Diseases, Medical University of Varna, 9000 Varna, Bulgaria
| | - Dragomir Svetozarov Stoyanov
- Clinic of Medical Oncology, UMHAT “St. Marina”, 1 “Hristo Smirnenski” Blvd., 9000 Varna, Bulgaria
- Department of Propedeutics of Internal Diseases, Medical University of Varna, 9000 Varna, Bulgaria
| | - Manlio Vinciguerra
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
- Correspondence:
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20
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Blood-based DNA methylation signatures in cancer: A systematic review. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166583. [PMID: 36270476 DOI: 10.1016/j.bbadis.2022.166583] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
DNA methylation profiles are in dynamic equilibrium via the initiation of methylation, maintenance of methylation and demethylation, which control gene expression and chromosome stability. Changes in DNA methylation patterns play important roles in carcinogenesis and primarily manifests as hypomethylation of the entire genome and the hypermethylation of individual loci. These changes may be reflected in blood-based DNA, which provides a non-invasive means for cancer monitoring. Previous blood-based DNA detection objects primarily included circulating tumor DNA/cell-free DNA (ctDNA/cfDNA), circulating tumor cells (CTCs) and exosomes. Researchers gradually found that methylation changes in peripheral blood mononuclear cells (PBMCs) also reflected the presence of tumors. Blood-based DNA methylation is widely used in early diagnosis, prognosis prediction, dynamic monitoring after treatment and other fields of clinical research on cancer. The reversible methylation of genes also makes them important therapeutic targets. The present paper summarizes the changes in DNA methylation in cancer based on existing research and focuses on the characteristics of the detection objects of blood-based DNA, including ctDNA/cfDNA, CTCs, exosomes and PBMCs, and their application in clinical research.
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21
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Liquid Biopsy in Diagnosis and Prognosis of Non-Metastatic Prostate Cancer. Biomedicines 2022; 10:biomedicines10123115. [PMID: 36551871 PMCID: PMC9776104 DOI: 10.3390/biomedicines10123115] [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: 11/01/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/10/2022] Open
Abstract
Currently, sensitive and specific methods for the detection and prognosis of early stage PCa are lacking. To establish the diagnosis and further identify an appropriate treatment strategy, prostate specific antigen (PSA) blood test followed by tissue biopsy have to be performed. The combination of tests is justified by the lack of a highly sensitive, specific, and safe single test. Tissue biopsy is specific but invasive and may have severe side effects, and therefore is inappropriate for screening of the disease. At the same time, the PSA blood test, which is conventionally used for PCa screening, has low specificity and may be elevated in the case of noncancerous prostate tumors and inflammatory conditions, including benign prostatic hyperplasia and prostatitis. Thus, diverse techniques of liquid biopsy have been investigated to supplement or replace the existing tests of prostate cancer early diagnosis and prognostics. Here, we provide a review on the advances in diagnosis and prognostics of non-metastatic prostate cancer by means of various biomarkers extracted via liquid biopsy, including circulating tumor cells, exosomal miRNAs, and circulating DNAs.
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22
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He W, Xiao Y, Yan S, Zhu Y, Ren S. Cell-free DNA in the management of prostate cancer: Current status and future prospective. Asian J Urol 2022. [PMID: 37538150 PMCID: PMC10394290 DOI: 10.1016/j.ajur.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objective With the escalating prevalence of prostate cancer (PCa) in China, there is an urgent demand for novel diagnostic and therapeutic approaches. Extensive investigations have been conducted on the clinical implementation of circulating free DNA (cfDNA) in PCa. This review aims to provide a comprehensive overview of the present state of cfDNA as a biomarker for PCa and to examine its merits and obstacles for future clinical utilization. Methods Relevant peer-reviewed manuscripts on cfDNA as a PCa marker were evaluated by PubMed search (2010-2022) to evaluate the roles of cfDNA in PCa diagnosis, prognosis, and prediction, respectively. Results cfDNA is primarily released from cells undergoing necrosis and apoptosis, allowing for non-invasive insight into the genomic, transcriptomic, and epigenomic alterations within various PCa disease states. Next-generation sequencing, among other detection methods, enables the assessment of cfDNA abundance, mutation status, fragment characteristics, and epigenetic modifications. Multidimensional analysis based on cfDNA can facilitate early detection of PCa, risk stratification, and treatment monitoring. However, standardization of cfDNA detection methods is still required to expedite its clinical application. Conclusion cfDNA provides a non-invasive, rapid, and repeatable means of acquiring multidimensional information from PCa patients, which can aid in guiding clinical decisions and enhancing patient management. Overcoming the application barriers of cfDNA necessitates increased data sharing and international collaboration.
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23
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Li P, Liu S, Du L, Mohseni G, Zhang Y, Wang C. Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer. Clin Epigenetics 2022; 14:118. [PMID: 36153611 PMCID: PMC9509651 DOI: 10.1186/s13148-022-01337-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/16/2022] [Indexed: 11/27/2022] Open
Abstract
Lung cancer (LC) is the main cause of cancer-related mortality. Most LC patients are diagnosed in an advanced stage when the symptoms are obvious, and the prognosis is quite poor. Although low-dose computed tomography (LDCT) is a routine clinical examination for early detection of LC, the false-positive rate is over 90%. As one of the intensely studied epigenetic modifications, DNA methylation plays a key role in various diseases, including cancer and other diseases. Hypermethylation in tumor suppressor genes or hypomethylation in oncogenes is an important event in tumorigenesis. Remarkably, DNA methylation usually occurs in the very early stage of malignant tumors. Thus, DNA methylation analysis may provide some useful information about the early detection of LC. In recent years, liquid biopsy has developed rapidly. Liquid biopsy can detect and monitor both primary and metastatic malignant tumors and can reflect tumor heterogeneity. Moreover, it is a minimally invasive procedure, and it causes less pain for patients. This review summarized various liquid biopsies based on DNA methylation for LC. At first, we briefly discussed some emerging technologies for DNA methylation analysis. Subsequently, we outlined cell-free DNA (cfDNA), sputum, bronchoalveolar lavage fluid, bronchial aspirates, and bronchial washings DNA methylation-based liquid biopsy for the early detection of LC. Finally, the prognostic value of DNA methylation in cfDNA and sputum and the diagnostic value of other DNA methylation-based liquid biopsies for LC were also analyzed.
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24
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The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors. Nat Commun 2022; 13:6467. [PMID: 36309516 PMCID: PMC9617856 DOI: 10.1038/s41467-022-34012-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Metastatic prostate cancer remains a major clinical challenge and metastatic lesions are highly heterogeneous and difficult to biopsy. Liquid biopsy provides opportunities to gain insights into the underlying biology. Here, using the highly sensitive enrichment-based sequencing technology, we provide analysis of 60 and 175 plasma DNA methylomes from patients with localized and metastatic prostate cancer, respectively. We show that the cell-free DNA methylome can capture variations beyond the tumor. A global hypermethylation in metastatic samples is observed, coupled with hypomethylation in the pericentromeric regions. Hypermethylation at the promoter of a glucocorticoid receptor gene NR3C1 is associated with a decreased immune signature. The cell-free DNA methylome is reflective of clinical outcomes and can distinguish different disease types with 0.989 prediction accuracy. Finally, we show the ability of predicting copy number alterations from the data, providing opportunities for joint genetic and epigenetic analysis on limited biological samples.
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25
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Tsering T, Li M, Chen Y, Nadeau A, Laskaris A, Abdouh M, Bustamante P, Burnier JV. EV-ADD, a database for EV-associated DNA in human liquid biopsy samples. J Extracell Vesicles 2022; 11:e12270. [PMID: 36271888 PMCID: PMC9587709 DOI: 10.1002/jev2.12270] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/20/2022] [Accepted: 09/06/2022] [Indexed: 11/06/2022] Open
Abstract
Extracellular vesicles (EVs) play a key role in cellular communication both in physiological conditions and in pathologies such as cancer. Emerging evidence has shown that EVs are active carriers of molecular cargo (e.g. protein and nucleic acids) and a powerful source of biomarkers and targets. While recent studies on EV‐associated DNA (EV‐DNA) in human biofluids have generated a large amount of data, there is currently no database that catalogues information on EV‐DNA. To fill this gap, we have manually curated a database of EV‐DNA data derived from human biofluids (liquid biopsy) and in‐vitro studies, called the Extracellular Vesicle‐Associated DNA Database (EV‐ADD). This database contains validated experimental details and data extracted from peer‐reviewed published literature. It can be easily queried to search for EV isolation methods and characterization, EV‐DNA isolation techniques, quality validation, DNA fragment size, volume of starting material, gene names and disease context. Currently, our database contains samples representing 23 diseases, with 13 different types of EV isolation techniques applied on eight different human biofluids (e.g. blood, saliva). In addition, EV‐ADD encompasses EV‐DNA data both representing the whole genome and specifically including oncogenes, such as KRAS, EGFR, BRAF, MYC, and mitochondrial DNA (mtDNA). An EV‐ADD data metric system was also integrated to assign a compliancy score to the MISEV guidelines based on experimental parameters reported in each study. While currently available databases document the presence of proteins, lipids, RNA and metabolites in EVs (e.g. Vesiclepedia, ExoCarta, ExoBCD, EVpedia, and EV‐TRACK), to the best of our knowledge, EV‐ADD is the first of its kind to compile all available EV‐DNA datasets derived from human biofluid samples. We believe that this database provides an important reference resource on EV‐DNA‐based liquid biopsy research, serving as a learning tool and to showcase the latest developments in the EV‐DNA field. EV‐ADD will be updated yearly as newly published EV‐DNA data becomes available and it is freely available at www.evdnadatabase.com.
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Affiliation(s)
- Thupten Tsering
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Mingyang Li
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Yunxi Chen
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Amélie Nadeau
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Alexander Laskaris
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Mohamed Abdouh
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Prisca Bustamante
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Julia V. Burnier
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
- Experimental Pathology UnitDepartment of PathologyMcGill UniversityMontrealQuebecCanada
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26
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The clinical value of circulating free tumor DNA in testicular germ cell tumor patients. Urol Oncol 2022; 40:412.e15-412.e24. [DOI: 10.1016/j.urolonc.2022.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/04/2022] [Accepted: 04/30/2022] [Indexed: 11/15/2022]
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27
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Circulating Cell-Free DNA Profiling Predicts the Therapeutic Outcome in Advanced Hepatocellular Carcinoma Patients Treated with Combination Immunotherapy. Cancers (Basel) 2022; 14:cancers14143367. [PMID: 35884434 PMCID: PMC9320668 DOI: 10.3390/cancers14143367] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Atezolizumab/bevacizumab (Atezo/Bev) combination immunotherapy has become a front-line therapy for unresectable hepatocellular carcinoma (u-HCC), but some patients are initially nonresponders. We investigated the potential of cell-free DNA (cfDNA)/circulating tumor DNA (ctDNA) as biomarkers for predicting the therapeutic outcome of u-HCC patients treated with anti-programmed cell death1-ligand1 (PD-L1)/vascular endothelial growth factor (VEGF) therapy. Patients with high levels of cfDNA showed a significantly lower overall response rate and shorter progression-free survival and overall survival (OS) than those with low levels of cfDNA. Ultradeep sequencing of cfDNA showed that the telomerase reverse transcriptase (TERT) promoter, tumor protein 53 (TP53) and catenin beta 1 (CTNNB1) were the most frequently mutated genes in ctDNA. Lastly, a TERT ctDNA mutation and a high alpha-fetoprotein (AFP) level were independent predictors of shorter OS in u-HCC patients treated with Atezo/Bev therapy and could stratify their prognoses. Collectively, cfDNA/ctDNA profiling may be useful to predict therapeutic outcome in u-HCC patients treated with Atezo/Bev therapy. Abstract Combination immunotherapy with anti-programmed cell death1-ligand1 (PD-L1) and anti-vascular endothelial growth factor (VEGF) antibodies has become the standard treatment for patients with unresectable HCC (u-HCC). However, limited patients obtain clinical benefits. Cell-free DNA (cfDNA) in peripheral blood contains circulating tumor DNA (ctDNA) that reflects molecular abnormalities in tumor tissue. We investigated the potential of cfDNA/ctDNA as biomarkers for predicting the therapeutic outcome in u-HCC patients treated with anti-PD-L1/VEGF therapy. We enrolled a multicenter cohort of 85 HCC patients treated with atezolizumab and bevacizumab (Atezo/Bev) between 2020 and 2021. Pretreatment plasma was collected, and cfDNA levels were quantified. Ultradeep sequencing of cfDNA was performed with a custom-made panel for detecting mutations in 25 HCC-related cancer genes. We evaluated the association of cfDNA/ctDNA profiles and clinical outcomes. Patients with high plasma cfDNA levels showed a significantly lower response rate and shorter progression-free survival and overall survival (OS) than those with low cfDNA levels. ctDNA detected in 55% of HCC patients included the telomerase reverse transcriptase (TERT) promoter in 31% of these patients, tumor protein 53 (TP53) in 21%, catenin beta 1 (CTNNB1) in 13% and phosphatase and tensin homolog (PTEN) in 7%. The presence or absence of ctDNA did not predict the efficacy of Atezo/Bev therapy. Twenty-six patients with a TERT mutation had significantly shorter OS than those without. The presence of a TERT mutation and alpha-fetoprotein (AFP) ≥ 400 ng/mL were independent predictors of poor OS according to multivariate Cox proportional hazard analysis and could be used to stratify patients treated with Atezo/Bev therapy based on prognosis. In conclusion, pretreatment cfDNA/ctDNA profiling may be useful for predicting the therapeutic outcome in u-HCC patients treated with anti-PD-L1/VEGF therapy.
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28
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Crocetto F, Russo G, Di Zazzo E, Pisapia P, Mirto BF, Palmieri A, Pepe F, Bellevicine C, Russo A, La Civita E, Terracciano D, Malapelle U, Troncone G, Barone B. Liquid Biopsy in Prostate Cancer Management—Current Challenges and Future Perspectives. Cancers (Basel) 2022; 14:cancers14133272. [PMID: 35805043 PMCID: PMC9265840 DOI: 10.3390/cancers14133272] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Prostate cancer (PCa) is a widespread malignancy, representing the second leading cause of cancer-related death in men. In the last years, liquid biopsy has emerged as an attractive and promising strategy complementary to invasive tissue biopsy to guide PCa diagnosis, follow-up and treatment response. Liquid biopsy is employed to assess several body fluids biomarkers, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating tumor DNA (ctDNA) and RNA (ctRNA). This review dissects recent advancements and future perspectives of liquid biopsy, highlighting its strength and weaknesses in PCa management. Abstract Although appreciable attempts in screening and diagnostic approaches have been achieved, prostate cancer (PCa) remains a widespread malignancy, representing the second leading cause of cancer-related death in men. Drugs currently used in PCa therapy initially show a potent anti-tumor effect, but frequently induce resistance and PCa progresses toward metastatic castration-resistant forms (mCRPC), virtually incurable. Liquid biopsy has emerged as an attractive and promising strategy complementary to invasive tissue biopsy to guide PCa diagnosis and treatment. Liquid biopsy shows the ability to represent the tumor microenvironment, allow comprehensive information and follow-up the progression of the tumor, enabling the development of different treatment strategies as well as permitting the monitoring of therapy response. Liquid biopsy, indeed, is endowed with a significant potential to modify PCa management. Several blood biomarkers could be analyzed for diagnostic, prognostic and predictive purposes, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating tumor DNA (ctDNA) and RNA (ctRNA). In addition, several other body fluids may be adopted (i.e., urine, sperm, etc.) beyond blood. This review dissects recent advancements and future perspectives of liquid biopsies, highlighting their strength and weaknesses in PCa management.
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Affiliation(s)
- Felice Crocetto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (B.F.M.); (A.P.); (B.B.)
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (G.R.); (P.P.); (F.P.); (C.B.); (U.M.); (G.T.)
| | - Erika Di Zazzo
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
- Correspondence:
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (G.R.); (P.P.); (F.P.); (C.B.); (U.M.); (G.T.)
| | - Benito Fabio Mirto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (B.F.M.); (A.P.); (B.B.)
| | - Alessandro Palmieri
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (B.F.M.); (A.P.); (B.B.)
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (G.R.); (P.P.); (F.P.); (C.B.); (U.M.); (G.T.)
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (G.R.); (P.P.); (F.P.); (C.B.); (U.M.); (G.T.)
| | | | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (D.T.)
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (D.T.)
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (G.R.); (P.P.); (F.P.); (C.B.); (U.M.); (G.T.)
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (G.R.); (P.P.); (F.P.); (C.B.); (U.M.); (G.T.)
| | - Biagio Barone
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (B.F.M.); (A.P.); (B.B.)
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29
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Tkach M, Hego C, Michel M, Darrigues L, Pierga J, Bidard F, Théry C, Proudhon C. Circulating extracellular vesicles provide valuable protein, but not DNA, biomarkers in metastatic breast cancer. JOURNAL OF EXTRACELLULAR BIOLOGY 2022; 1:e51. [PMID: 38938580 PMCID: PMC11080866 DOI: 10.1002/jex2.51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/23/2022] [Accepted: 06/27/2022] [Indexed: 06/29/2024]
Abstract
Detection of cell-free circulating tumour DNA (ctDNA) and cancer-specific extracellular vesicles (EVs) in patient blood have been widely explored as non-invasive biomarkers for cancer detection and disease follow up. However, most of the protocols used to isolate EVs co-isolate other components and the actual value of EV-associated markers remain unclear. To determine the optimal source of clinically-relevant circulating biomarkers in breast cancer, we applied a size exclusion chromatography (SEC) procedure to analyse separately the content in nucleic acids of EV-enriched and EV-depleted fractions, in comparison to total plasma. Both cellular and mitochondrial DNA (cellDNA and mtDNA) were detected in EV-rich and EV-poor fractions. Analysing specific mutations identified from tumour tissues, we detected tumour-specific cellular alleles in all SEC fractions. However, quantification of ctDNA from total plasma was more sensitive than from any SEC fractions. On the other hand, mtDNA was preferentially enriched in EV fractions from healthy donor, whereas cancer patients displayed more abundant mtDNA in total plasma, and equally distributed in all fractions. In contrast to nucleic acids, using a Multiplexed bead-based EV-analysis assay, we identified three surface proteins enriched in EVs from metastatic breast cancer plasma, suggesting that a small set of EV surface molecules could provide a disease signature. Our findings provide evidence that the detection of DNA within total circulating EVs does not add value as compared to the whole plasma, at least in the metastatic breast cancer patients used here. However, analysis of a subtype of EV-associated proteins may reliably identify cancer patients. These non-invasive biomarkers represent a promising tool for cancer diagnosis and real-time monitoring of treatment efficacy and these results will impact the development of therapeutic approaches using EVs as targets or biomarkers of cancer.
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Affiliation(s)
- Mercedes Tkach
- Institut CurieINSERM U932PSL Research UniversityParisFrance
| | - Caroline Hego
- Circulating Tumor Biomarkers laboratoryInstitut CurieINSERM CIC BT‐1428PSL Research UniversityParisFrance
| | - Marc Michel
- Institut CurieINSERM U934/CNRS UMR3215PSL Research UniversityParisFrance
| | - Lauren Darrigues
- Department of Surgical OncologyInstitut CurieParisFrance
- Université Paris‐CitéParisFrance
| | - Jean‐Yves Pierga
- Circulating Tumor Biomarkers laboratoryInstitut CurieINSERM CIC BT‐1428PSL Research UniversityParisFrance
- Université Paris‐CitéParisFrance
- Department of Medical OncologyInstitut CurieParis and Saint CloudFrance
| | - François‐Clément Bidard
- Circulating Tumor Biomarkers laboratoryInstitut CurieINSERM CIC BT‐1428PSL Research UniversityParisFrance
- Department of Medical OncologyInstitut CurieParis and Saint CloudFrance
- UVSQUniversité Paris‐SaclaySaint CloudFrance
| | - Clotilde Théry
- Institut CurieINSERM U932PSL Research UniversityParisFrance
| | - Charlotte Proudhon
- Institut CurieINSERM U934/CNRS UMR3215PSL Research UniversityParisFrance
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30
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Huang CJ, Huang WY, Chen CY, Chao YJ, Chiang NJ, Shan YS. Cancer-cell-derived cell-free DNA can predict distant metastasis earlier in pancreatic cancer: a prospective cohort study. Ther Adv Med Oncol 2022; 14:17588359221106558. [PMID: 35747164 PMCID: PMC9210094 DOI: 10.1177/17588359221106558] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Carbohydrate antigen 19-9 (CA19-9) is the only biomarker for monitoring responses during treatments of pancreatic cancer, but its accuracy for disease outcome is controversial. Fluid biopsy is a new method for diagnosis and monitoring treatment response. In this study, we investigate the usefulness of cell-free DNA (cfDNA) in predicting disease progression during the treatment of pancreatic cancer. Methods: Biopsy-proved advanced pancreatic cancer patients who received systemic chemotherapy were enrolled after signed informed consent. CA19-9 and cfDNA in blood were measured before and after every two cycles of treatments, and the disease progression was monitored by computed tomography (CT) with 3-month interval. Results: In total, 74 patients and 148 blood samples were enrolled in this study. Patients whose average blood cfDNA concentration of >9.71 ng/mL before and after first two courses of chemotherapy would subsequently show new distant metastasis (NDM) on CT scans 3 months later. The accuracy was 94.37% (AUC 0.9705, p < 0.0001) and the progression-free survival (PFS) and overall survival (OS) of patients with cfDNA concentration of >9.71 ng/mL were worse than those patients with cfDNA concentration of <9.71 ng/mL (median PFS: 95 days versus 322 days, p < 0.0001; median OS: 150 days versus 431 days, p < 0.0001). The cfDNA concentration of >9.71 ng/mL is a predictor for PFS, OS, and distant metastasis-free survival by multivariate analysis. Comparison of KRAS G12 variants detected by next-generation sequencing from tumor tissue issue and remnant DNA of cfDNA showed that increased cfDNA was primarily derived from cancer cells. Conclusion: The cancer-cell-derived cfDNA levels could be served as a powerful biomarker for prediction of NDM in patients with advanced/metastatic pancreatic cancer.
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Affiliation(s)
- Chien-Jui Huang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan
| | - Wen-Yen Huang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Yu Chen
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Jui Chao
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nai-Jung Chiang
- Department of Oncology, Taipei Veterans General Hospital, Taipei
| | - Yan-Shen Shan
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, Tainan
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31
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Mabry PL, Pronk NP, Amos CI, Witte JS, Wedlock PT, Bartsch SM, Lee BY. Cancer systems epidemiology: Overcoming misconceptions and integrating systems approaches into cancer research. PLoS Med 2022; 19:e1004027. [PMID: 35714096 PMCID: PMC9205504 DOI: 10.1371/journal.pmed.1004027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Patricia Mabry and coauthors discuss application of systems approaches in cancer research.
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Affiliation(s)
- Patricia L. Mabry
- HealthPartners Institute, Bloomington, Minnesota, United States of America
| | - Nicolaas P. Pronk
- HealthPartners Institute, Bloomington, Minnesota, United States of America
- University of Minnesota, School of Public Health, Minneapolis, Minnesota, United States of America
| | - Christopher I. Amos
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
- Baylor College of Medicine, Institute for Clinical and Translational Research, Houston, Texas, United States of America
| | - John S. Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, California, United States of America
| | - Patrick T. Wedlock
- Center for Advanced Technology and Communication in Health (CATCH), CUNY Graduate School of Public Health and Health Policy, New York City, New York, United States of America
- Public Health Informatics, Computational, and Operations Research (PHICOR), CUNY Graduate School of Public Health and Health Policy, New York City, New York, United States of America
| | - Sarah M. Bartsch
- Center for Advanced Technology and Communication in Health (CATCH), CUNY Graduate School of Public Health and Health Policy, New York City, New York, United States of America
- Public Health Informatics, Computational, and Operations Research (PHICOR), CUNY Graduate School of Public Health and Health Policy, New York City, New York, United States of America
| | - Bruce Y. Lee
- Center for Advanced Technology and Communication in Health (CATCH), CUNY Graduate School of Public Health and Health Policy, New York City, New York, United States of America
- Public Health Informatics, Computational, and Operations Research (PHICOR), CUNY Graduate School of Public Health and Health Policy, New York City, New York, United States of America
- * E-mail:
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32
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Dathathri E, Isebia KT, Abali F, Lolkema MP, Martens JWM, Terstappen LWMM, Bansal R. Liquid Biopsy Based Circulating Biomarkers in Metastatic Prostate Cancer. Front Oncol 2022; 12:863472. [PMID: 35669415 PMCID: PMC9165750 DOI: 10.3389/fonc.2022.863472] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer is the most dominant male malignancy worldwide. The clinical presentation of prostate cancer ranges from localized indolent to rapidly progressing lethal metastatic disease. Despite a decline in death rate over the past years, with the advent of early diagnosis and new treatment options, challenges remain towards the management of metastatic prostate cancer, particularly metastatic castration sensitive prostate cancer (mCSPC) and castration resistant prostate cancer (mCRPC). Current treatments involve a combination of chemotherapy with androgen deprivation therapy and/or androgen receptor signalling inhibitors. However, treatment outcomes are heterogeneous due to significant tumor heterogeneity indicating a need for better prognostic biomarkers to identify patients with poor outcomes. Liquid biopsy has opened a plethora of opportunities from early diagnosis to (personalized) therapeutic disease interventions. In this review, we first provide recent insights about (metastatic) prostate cancer and its current treatment landscape. We highlight recent studies involving various circulating biomarkers such as circulating tumor cells, genetic markers, circulating nucleic acids, extracellular vesicles, tumor-educated platelets, and the secretome from (circulating) tumor cells and tumor microenvironment in metastatic prostate cancer. The comprehensive array of biomarkers can provide a powerful approach to understanding the spectrum of prostate cancer disease and guide in developing improved and personalized treatments for patients.
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Affiliation(s)
- Eshwari Dathathri
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Khrystany T. Isebia
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - Fikri Abali
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Martijn P. Lolkema
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - John W. M. Martens
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - Leon W. M. M. Terstappen
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Ruchi Bansal
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
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33
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Chetty VK, Ghanam J, Anchan S, Reinhardt K, Brenzel A, Gelléri M, Cremer C, Grueso-Navarro E, Schneider M, von Neuhoff N, Reinhardt D, Jablonska J, Nazarenko I, Thakur BK. Efficient Small Extracellular Vesicles (EV) Isolation Method and Evaluation of EV-Associated DNA Role in Cell-Cell Communication in Cancer. Cancers (Basel) 2022; 14:cancers14092068. [PMID: 35565197 PMCID: PMC9099953 DOI: 10.3390/cancers14092068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Small extracellular vesicles (sEVs) released by all cell types function as a mediator in intercellular communication that can promote cell division and survival to remodel the tumor microenvironment to develop tumor invasion and metastasis. Even though dsDNA baggage is associated with all small EV populations, the functional role of EV-DNA in cancer remains poorly understood. This is due to a lack of methods allowing the efficient separation of small EVs (sEVs) from other non-sEV components. The main aim of our study was to develop an efficient sEV isolation method along with EV-associated DNA (EV-DNA) monitoring tool to evaluate the role of EV-DNA as a mediator of cell–cell communication in cancer. Our detailed small EV-DNA characterization confirmed that isolated sEVs using the TSU method (Tangential flow filtration + Size exclusion chromatography + Ultrafiltration) are free from contaminants such as cell-free and apoptotic bodies DNA, making TSU ideal for performing EV-DNA functional studies. Next, we revealed the exact EV-DNA distribution in the recipient cells using 3D image analysis and the association of EV-DNA with key cellular proteins, which may have an essential role in cancer. In the leukemia model, EV-DNA isolated from leukemia cell lines associated with mesenchymal stromal cells (MSCs), a crucial factor in the bone marrow (BM) microenvironment. Abstract Small extracellular vesicles (sEVs) play essential roles in intercellular signaling both in normal and pathophysiological conditions. Comprehensive studies of dsDNA associated with sEVs are hampered by a lack of methods, allowing efficient separation of sEVs from free-circulating DNA and apoptotic bodies. In this work, using controlled culture conditions, we enriched the reproducible separation of sEVs from free-circulated components by combining tangential flow filtration, size-exclusion chromatography, and ultrafiltration (TSU). EV-enriched fractions (F2 and F3) obtained using TSU also contained more dsDNA derived from the host genome and mitochondria, predominantly localized inside the vesicles. Three-dimensional reconstruction of high-resolution imaging showed that the recipient cell membrane barrier restricts a portion of EV-DNA. Simultaneously, the remaining EV-DNA overcomes it and enters the cytoplasm and nucleus. In the cytoplasm, EV-DNA associates with dsDNA-inflammatory sensors (cGAS/STING) and endosomal proteins (Rab5/Rab7). Relevant to cancer, we found that EV-DNA isolated from leukemia cell lines communicates with mesenchymal stromal cells (MSCs), a critical component in the BM microenvironment. Furthermore, we illustrated the arrangement of sEVs and EV-DNA at a single vesicle level using super-resolution microscopy. Altogether, employing TSU isolation, we demonstrated EV-DNA distribution and a tool to evaluate the exact EV-DNA role of cell–cell communication in cancer.
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Affiliation(s)
- Venkatesh Kumar Chetty
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Srishti Anchan
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Katarina Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Alexandra Brenzel
- Imaging Center Essen (IMCES), University Hospital Essen, 45147 Essen, Germany;
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; (M.G.); (C.C.)
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; (M.G.); (C.C.)
- Max Planck Institutes for Polymer Research and for Chemistry, 55128 Mainz, Germany
| | - Elena Grueso-Navarro
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany; (E.G.-N.); (I.N.)
| | - Markus Schneider
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Nils von Neuhoff
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Jadwiga Jablonska
- Department of Otorhinolaryngology, University Hospital Essen, 45147 Essen, Germany;
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany; (E.G.-N.); (I.N.)
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
- Correspondence: ; Tel.: +49-201-723-2504
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34
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Clinical Validity of Circulating Tumor DNA as Prognostic and Predictive Marker for Personalized Colorectal Cancer Patient Management. Cancers (Basel) 2022; 14:cancers14030851. [PMID: 35159118 PMCID: PMC8834623 DOI: 10.3390/cancers14030851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/21/2022] [Accepted: 02/07/2022] [Indexed: 12/30/2022] Open
Abstract
Simple Summary CtDNA analysis is a promising tool in liquid biopsy for the detection of tumor recurrence and progression, and is increasingly adopted into clinical practice. Still, guidelines for the accurate clinical interpretation of ctDNA analysis results are largely lacking, especially for tumor mutant variants detected at very low frequencies. Here, we show that cutoff determination for the detection and quantification of low-frequency mutant variants enables the accurate prediction of residual disease, tumor recurrence and progression, even before clinical evidence. CtDNA analysis using these cutoffs outperformed cfDNA and CEA level measurements. With these findings, we highlight the need to thoroughly validate each liquid biopsy assay and define the assay-specific limit of blanks (LOB) and limit of quantifications (LOQ) of BRAF p.V600E and KRAS p.G12/p.G13 assays for clinical interpretation. Our approach enables accurate clinical interpretation to support clinical decision making. Abstract Circulating tumor DNA (ctDNA) is a promising liquid biopsy (LB) marker to support clinical decisions in precision medicine. For implementation into routine clinical practice, clinicians need precise ctDNA level cutoffs for reporting residual disease and monitoring tumor burden changes during therapy. We clinically validated the limit of blank (LOB) and the limit of quantification (LOQ) of assays for the clinically most relevant somatic variants BRAF p.V600E and KRAS p.G12/p.G13 in colorectal cancer (CRC) in a study cohort encompassing a total of 212 plasma samples. We prove that residual disease detection using the LOB as a clinically verified cutoff for ctDNA positivity is in concordance with clinical evidence of metastasis or recurrence. We further show that tumor burden changes during chemotherapy and the course of disease are correctly predicted using the LOQ as a cutoff for quantitative ctDNA changes. The high potential of LB using ctDNA for accurately predicting the course of disease was proven by direct comparison to the routinely used carcinoembryonic antigen (CEA) as well as the circulating free DNA (cfDNA) concentration. Our results show that LB using validated ctDNA assays outperforms CEA and cfDNA for residual disease detection and the prediction of tumor burden changes.
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35
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Tomeva E, Switzeny OJ, Heitzinger C, Hippe B, Haslberger AG. Comprehensive Approach to Distinguish Patients with Solid Tumors from Healthy Controls by Combining Androgen Receptor Mutation p.H875Y with Cell-Free DNA Methylation and Circulating miRNAs. Cancers (Basel) 2022; 14:cancers14020462. [PMID: 35053623 PMCID: PMC8774173 DOI: 10.3390/cancers14020462] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 02/01/2023] Open
Abstract
Liquid biopsy-based tests emerge progressively as an important tool for cancer diagnostics and management. Currently, researchers focus on a single biomarker type and one tumor entity. This study aimed to create a multi-analyte liquid biopsy test for the simultaneous detection of several solid cancers. For this purpose, we analyzed cell-free DNA (cfDNA) mutations and methylation, as well as circulating miRNAs (miRNAs) in plasma samples from 97 patients with cancer (20 bladder, 9 brain, 30 breast, 28 colorectal, 29 lung, 19 ovarian, 12 pancreas, 27 prostate, 23 stomach) and 15 healthy controls via real-time qPCR. Androgen receptor p.H875Y mutation (AR) was detected for the first time in bladder, lung, stomach, ovarian, brain, and pancreas cancer, all together in 51.3% of all cancer samples and in none of the healthy controls. A discriminant function model, comprising cfDNA mutations (COSM10758, COSM18561), cfDNA methylation markers (MLH1, MDR1, GATA5, SFN) and miRNAs (miR-17-5p, miR-20a-5p, miR-21-5p, miR-26a-5p, miR-27a-3p, miR-29c-3p, miR-92a-3p, miR-101-3p, miR-133a-3p, miR-148b-3p, miR-155-5p, miR-195-5p) could further classify healthy and tumor samples with 95.4% accuracy, 97.9% sensitivity, 80% specificity. This multi-analyte liquid biopsy-based test may help improve the simultaneous detection of several cancer types and underlines the importance of combining genetic and epigenetic biomarkers.
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Affiliation(s)
- Elena Tomeva
- HealthBioCare GmbH, A-1090 Vienna, Austria; (E.T.); (O.J.S.); (B.H.)
| | | | - Clemens Heitzinger
- Center for Artificial Intelligence and Machine Learning (CAIML), TU Wien, A-1040 Vienna, Austria;
| | - Berit Hippe
- HealthBioCare GmbH, A-1090 Vienna, Austria; (E.T.); (O.J.S.); (B.H.)
- Department of Nutritional Sciences, University of Vienna, A-1090 Vienna, Austria
| | - Alexander G. Haslberger
- Department of Nutritional Sciences, University of Vienna, A-1090 Vienna, Austria
- Correspondence:
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36
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Dillinger T, Sheibani-Tezerji R, Pulverer W, Stelzer I, Hassler MR, Scheibelreiter J, Pérez Malla CU, Kuroll M, Domazet S, Redl E, Ely S, Brezina S, Tiefenbacher A, Rebhan K, Hübner N, Grubmüller B, Mitterhauser M, Hacker M, Weinhaeusel A, Simon J, Zeitlinger M, Gsur A, Kramer G, Shariat SF, Kenner L, Egger G. Identification of tumor tissue-derived DNA methylation biomarkers for the detection and therapy response evaluation of metastatic castration resistant prostate cancer in liquid biopsies. Mol Cancer 2022; 21:7. [PMID: 34980142 PMCID: PMC8722310 DOI: 10.1186/s12943-021-01445-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Affiliation(s)
- Thomas Dillinger
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Raheleh Sheibani-Tezerji
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Walter Pulverer
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Ines Stelzer
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Department of Health Economics, Center for Public Health, Medical University of Vienna, Vienna, Austria
| | - Melanie R Hassler
- Department of Pathology, Medical University of Vienna, Vienna, Austria.,Department of Urology, Medical University Vienna, Vienna, Austria
| | | | | | | | - Sandra Domazet
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria
| | - Elisa Redl
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Sarah Ely
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Andreas Tiefenbacher
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Katharina Rebhan
- Department of Urology, Medical University Vienna, Vienna, Austria
| | - Nicolai Hübner
- Department of Urology, Medical University Vienna, Vienna, Austria
| | | | - Markus Mitterhauser
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Vienna, Austria
| | - Marcus Hacker
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Vienna, Austria
| | - Andreas Weinhaeusel
- Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology GmbH, Vienna, Austria
| | - Judit Simon
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Department of Health Economics, Center for Public Health, Medical University of Vienna, Vienna, Austria
| | - Markus Zeitlinger
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Gero Kramer
- Department of Urology, Medical University Vienna, Vienna, Austria
| | - Shahrokh F Shariat
- Department of Urology, Medical University Vienna, Vienna, Austria.,Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Urology, Weill Cornell Medical College, New York, NY, USA.,Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.,Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria.,Division of Urology, Department of Special Surgery, Jordan University Hospital, The University of Jordan, Amman, Jordan.,European Association of Urology Research Foundation, Arnhem, The Netherlands
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,Unit of Laboratory Animal Pathology, University of Veterinary Medicine, Vienna, Austria.,Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, Vienna, Austria
| | - Gerda Egger
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria. .,Department of Pathology, Medical University of Vienna, Vienna, Austria. .,Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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37
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Sardarabadi P, Kojabad AA, Jafari D, Liu CH. Liquid Biopsy-Based Biosensors for MRD Detection and Treatment Monitoring in Non-Small Cell Lung Cancer (NSCLC). BIOSENSORS 2021; 11:394. [PMID: 34677350 PMCID: PMC8533977 DOI: 10.3390/bios11100394] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022]
Abstract
Globally, non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths. Despite advancements in chemotherapy and targeted therapies, the 5-year survival rate has remained at 16% for the past forty years. Minimal residual disease (MRD) is described as the existence of either isolated tumour cells or circulating tumour cells in biological liquid of patients after removal of the primary tumour without any clinical signs of cancer. Recently, liquid biopsy has been promising as a non-invasive method of disease monitoring and treatment guidelines as an MRD marker. Liquid biopsy could be used to detect and assess earlier stages of NSCLC, post-treatment MRD, resistance to targeted therapies, immune checkpoint inhibitors (ICIs) and tumour mutational burden. MRD surveillance has been proposed as a potential marker for lung cancer relapse. Principally, biosensors provide the quantitative analysis of various materials by converting biological functions into quantifiable signals. Biosensors are usually operated to detect antibodies, enzymes, DNA, RNA, extracellular vesicles (EVs) and whole cells. Here, we present a category of biosensors based on the signal transduction method for identifying biosensor-based biomarkers in liquid biopsy specimens to monitor lung cancer treatment.
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Affiliation(s)
- Parvaneh Sardarabadi
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30044, Taiwan;
| | - Amir Asri Kojabad
- Department of Hematology, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran 14535, Iran;
| | - Davod Jafari
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran 14535, Iran;
| | - Cheng-Hsien Liu
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30044, Taiwan;
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30044, Taiwan
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38
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Udomruk S, Orrapin S, Pruksakorn D, Chaiyawat P. Size distribution of cell-free DNA in oncology. Crit Rev Oncol Hematol 2021; 166:103455. [PMID: 34464717 DOI: 10.1016/j.critrevonc.2021.103455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA (cfDNA) in liquid biopsy test is a novel promising biomarker in the advancement of cancer management, including early diagnosis, screening, prognosis, identification of actionable targets, and serial tumor monitoring. The specific size pattern of DNA fragments derived from cancer cells is observed to differ from that of cfDNA fragments shed by non-cancer cells. Research into the physiological and biological properties of cfDNA reveals the molecular signature carried by each cfDNA fragments, which can reflect their tissue origins, as well as the mutational profiles with significant genetic alterations. Understanding the fragmentation and size distribution of cfDNA might be a valuable hotspot in liquid biopsy research, with the potential to drive innovation in oncology.
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Affiliation(s)
- Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Santhasiri Orrapin
- Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Orthopedics, Faculty of Medicine, Chiang Mai University, 110 Intawaroros, Sriphoom, Muang, Chiang Mai 50200, Thailand.
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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